bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 7074: Perturbed RNA N6-methyladenosine methylome in SETD2 mutant clear cell renal carcinoma
Authors: Shaikh Shafiq , Wagner Ryan , Hlady Ryan , Robertson Keith D. 
Published: March 2024

Abstract
Clear cell renal carcinoma (ccRCC), which arises from the epithelial cells of the proximal tubule represents 70% of all renal cell carcinoma. Mutations that drive ccRCC in conjunction with near ubiquitous and early VHL loss include, PBRM1 (33 - 45%), BAP1 (15%) and SETD2 (13%). Loss of SETD2 leads to diminished occupancy of H3K36me3 in active gene bodies, which is progressively deregulated in primary RCC and metastasis, linking loss of H3K36me to tumor progression and metastasis. N6-Methyladenosine (m6A) is an important post-transcriptional regulator of RNA transcript stability and half-life. Preliminary findings have shown H3K36me3 (deposited by SETD2), targeting the core m6A methyltransferase machinery (METTL3, METTL14 and WTAP) to the mRNA by virtue of its interaction to METTL14 subunit. The goal of this study is to investigate if H3K36me3 depletion as observed in SETD2 mutant ccRCC, leads to a deregulated m6A methylome. We further investigate how deregulated methylome in key pathways leads to cancer initiation and progression in ccRCC. To accomplish our goals, we generated isogenic ccRCC cell lines with H3K36me3 depletion by knocking out SETD2. RNA-immunoprecipitation and sequencing for m6A (MeRIP) showed global deregulation of m6A methylome in SETD2KO isogenic ccRCC cell lines. We also show a number of pro-tumorigenic genes and pathways including cell invasion, inflammation and stemness being differentially methylated and expressed in SETD2KO ccRCC cell lines. Furthermore, we show SETD2KO cells being more sensitive to METTL3 inhibition suggesting the relevance of m6A hypermethylated transcripts in promoting pro-tumorigenic and growth promoting processes in SETD2KO ccRCC cell lines.
Citation Format: Shafiq Shaikh, Ryan Wagner, Ryan Hlady, Keith D. Robertson. Perturbed RNA N6-methyladenosine methylome in SETD2 mutant clear cell renal carcinoma [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 7074.
Abstract 7100: Quantitative proteomics reveal the mechanism of TTFields therapy for glioblastoma
Authors: Mei Qi , Gao Yanmei , Li Rong , Wang Chenxu , Hu Guangyuan , Huang He 
Published: March 2024

Abstract
Glioblastoma (GBM) is a highly malignant brain tumor, and conventional treatments such as surgical resection and chemotherapy have limited effectiveness, with a high rate of recurrence and poor prognosis for patients. In 2011, the FDA approved a novel therapy for recurrent GBM known as Tumor Treating Fields (TTFields). TTFields use alternating intermediate-frequency (200 kHz) and low-intensity (1-3 V/cm) electric fields to interfere with tumor cells, inducing apoptosis and inhibiting tumor growth. This study aimed to explore the molecular mechanisms of TTFields therapy at the systems biology level using quantitative proteomics technology. We analyzed U87 cells before and after TTFields treatment using quantitative proteomics and identified a total of 7679 proteins. Among them, 804 proteins were significantly upregulated after TTFields treatment, and 1141 proteins were significantly downregulated. Pathway enrichment analysis of differentially expressed proteins showed that upregulated proteins were mainly associated with cell proliferation, cell cycle, and transcription, possibly representing compensatory responses to the TTFields treatment. Further analysis revealed a significant upregulation of the tumor proliferation key protein PARP1, which was validated by protein immunoblotting experiments. Based on this analysis, we hypothesized that combining TTFields with Olaparib (a PARP1 inhibitor) might enhance the sensitivity of TTFields. Subsequently, we performed cell proliferation experiments to evaluate the concomitant application strategy, and the results demonstrated that Olaparib in combination with TTFields treatment significantly reduced the survival rate of U87 cells compared to single-drug treatment. In conclusion, using quantitative proteomics, this study revealed the biological processes underlying the inhibitory effects of TTFields on GBM proliferation. Under TTFields intervention, the expression of PARP1 was upregulated, and the use of a PARP1 inhibitor in combination significantly increased the sensitivity of TTFields. Therefore, this study not only elucidated the molecular mechanisms of TTFields therapy for GBM treatment at the systems biology level, but also provided support for further enhancing the efficacy of TTFields.
Citation Format: Qi Mei, Yanmei Gao, Rong Li, Chenxu Wang, Guangyuan Hu, He Huang. Quantitative proteomics reveal the mechanism of TTFields therapy for glioblastoma [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 7100.
Abstract 7106: Distinct functions of EHMT1 and EHMT2 in cancer chemotherapy and immunotherapy
Authors: Kang Zhihua , Fu Pan , Ma Hui , Li Tao , Lu Kevin , Liu Juan , Ginjala Vasudeva , Romanienko Peter , Feng Zhaohui , Guan Ming , Ganesan Shridar , Xia Bing 
Published: March 2024

Abstract
EHTM1 (GLP) and EHMT2 (G9a) are closely related protein lysine methyltransferases often thought to function together as a heterodimer to methylate histone H3 and non-histone substrates in diverse cellular processes including transcriptional regulation, genome methylation, and DNA repair. Here we show that EHMT1/2 inhibitors cause DNA replication stress, accumulation of single-stranded replication gaps, increased expression of STING, emergence of cytosolic DNA, and activation of the cGAS-STING pathway. Remarkably, EHMT1/2 inhibition strongly potentiates the efficacy of alkylating chemotherapy and anti-PD-1 immunotherapy in mouse models of tripe negative breast cancer. Mechanistically, the effects of EHMT inhibition on DNA replication and alkylating agent sensitivity are largely caused by the loss of EHMT1-mediated methylation of DNA ligase I (LIG1), whereas the elevated STING expression is, at least part, caused by its promoter demethylation. Moreover, depletion of EHMT2, and not EHMT1, leads to STING induction, which is correlated with more complete demethylation of the STING1 promoter. On the other hand, depletion of EHMT1, and not EHMT2, results in cytosolic DNA accumulation, which presumably activates the cGAS-STING pathway. These results reveal distinct functions of the two EHMT paralogs and provide enlightening paradigms and corresponding molecular basis for combination therapies involving alkylating agents and immune checkpoint inhibitors.
Citation Format: Zhihua Kang, Pan Fu, Hui Ma, Tao Li, Kevin Lu, Juan Liu, Vasudeva Ginjala, Peter Romanienko, Zhaohui Feng, Ming Guan, Shridar Ganesan, Bing Xia. Distinct functions of EHMT1 and EHMT2 in cancer chemotherapy and immunotherapy [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 7106.
Abstract 7109: Fasn inhibition enhances the efficacy of chemotherapy by inhibiting DNA damage response in colorectal cancer
Authors: Banerjee Moumita , Zaytseva Yekaterina , Hasani Sumati , Ryachahou Piotr , Izumi Tadahide , Evers B. Mark , Gao Tianyan 
Published: March 2024

Abstract
Altered lipid metabolism plays a significant role in progression of colorectal cancer, however, its role in chemotherapy resistance remains poorly understood. We previously identified FASN, the rate limiting enzyme in de novo lipogenesis, as an important regulator of colorectal cancer progression. However, TVB-3664, a potent and specific small molecule inhibitor of FASN, showed limited effect in reducing tumor burden in pre-clinical studies as a stand-alone therapy. Therefore, the goal of this study is to evaluate the combinatorial efficacy of TVB-3664 in improving the therapeutic indices of standard chemotherapy in colorectal cancer. Using a combination of colon cancer cell lines and patient derived organoids we showed that TVB-3664 potentiates chemotherapy drug-induced double-strand DNA breaks (DSBs) and apoptotic cell death by altering histone acetylation levels. In addition, TVB-3664 treatment blocked DNA damage response (DDR) by decreasing ATM expression and Chk1/2 phosphorylation. Mechanistically, inhibition of FASN prevents the activation of both DSB repair pathways, namely homologous recombination (HR) and classical non-homologous end joining (NHEJ), by blocking BRCA1 and 53BP1 recruitment to γH2AX foci, respectively. Moreover, we found that the inhibitory effect of TVB-3664 on DNA repair requires ACLY-dependent acetylation as genetic or pharmacological inhibition of ACLY attenuates TVB-3664-inducded DNA damage. Functionally, combining TVB-3664 with irinotecan synergistically decreased xenograft tumor growth and significantly delayed tumor relapse after withdrawal of therapy. Taken together, we identified a novel mechanism by which FASN inhibitors improve the efficacy of conventional chemotherapy by blocking DNA damage response to delay tumor recurrence and overcome a major challenge in treating colorectal cancer patients.
Citation Format: Moumita Banerjee, Yekaterina Zaytseva, Sumati Hasani, Piotr Ryachahou, Tadahide Izumi, B. Mark Evers, Tianyan Gao. Fasn inhibition enhances the efficacy of chemotherapy by inhibiting DNA damage response in colorectal 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 7109.
Abstract 7120: Investigating PARP1 selective inhibitor DSB1559 efficacy in BRCA1-associated triple negative breast cancer
Authors: Nelson Adam , Zheng Kelly F. , Wanderley Carlos , Michaud Daniel E. , Cowley Phillip M. , Campbell Gillian M. , McGuinness Barry E. , Wise Alan , Guerriero Jennifer 
Published: March 2024

Abstract
Background: Poly (ADP-ribose) polymerase inhibitors (PARPi) have improved outcomes of BRCA-associated breast cancer. However, toxicity can limit patient response as well as the ability to be combined with other therapeutics. Current PARPi broadly inhibit members of the PARP protein family, however only inhibition of PARP1 is needed for PARPi-mediated cell death. As inhibition of PARP2 is associated with hematological toxicity seen in PARPi patients, selectively inhibiting PARP1 may reduce PARPi toxicity and lead to better outcomes for patients. Here we characterize and test the efficacy of the PARP1 selective inhibitor (PARP1i) DSB1559 compared to Olaparib in BRCA1-associated triple negative breast cancer (TNBC).
Methods: NanoBRET, PARylation, and pharmacokinetic/pharmacodynamic assays were performed to examine DSB1559 potency, PARP family selectivity, and in vivo behavior. Immunocompetent FVB/n mice bearing BRCA1-deficient TNBC (CMV-Cre;Brca1f/f;Trp53f/f) tumors were treated daily with PARPi (Olaparib) or PARP1i (DSB1559) for 60 days and followed for survival. CellTiter-Glo and qPCR assays were used to examine DSB1559 effect on cell viability and STING activation, respectively.
Results: DSB1559 is a novel and potent PARP1 inhibitor which has superior selectivity for PARP1 compared to Olaparib and PARP1i AZD5305. DSB1559 has highly desirable physico-chemical and in vitro ADME properties, which translate to high oral bioavailability and moderate clearance in rodent PK studies. Additionally, DSB1559 demonstrated superior tumor residence time and tumor/plasma ratio compared to AZD5305. Compared to Olaparib, DSB1559 significantly increased STING activation and reduced cell viability in BRCA1-associated murine TNBC cells. BRCA1-associated TNBC-bearing immune-competent mice treated with DSB1559 had significantly reduced tumor growth and increased overall survival (median survival 74 days) compared to Olaparib (median survival 18 days). Analysis of changes in the tumor microenvironment are ongoing.
Conclusions: Taken together, DSB1559 is a highly selective PARP1 inhibitor that demonstrates superior efficacy compared to Olaparib in a BRCA1-associated immune-competent TNBC model.
Citation Format: Adam Nelson, Kelly F. Zheng, Carlos Wanderley, Daniel E. Michaud, Phillip M. Cowley, Gillian M. Campbell, Barry E. McGuinness, Alan Wise, Jennifer Guerriero. Investigating PARP1 selective inhibitor DSB1559 efficacy in BRCA1-associated triple negative breast 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 7120.
Abstract 7133: Phenomics-enabled discovery and optimization of small-molecule RBM39 degraders as an alternative to CDK12 targeting in high-grade serous ovarian cancer (HGSOC)
Authors: Neumann Chase , Shankaran Harish , Nadella Kiran , Biette Kelly , Rowley Shane , Gardner Ethan , Swaidani Shadi , Manda Vamshi , Chen Lu , Beshnova Daria , Saeed Ashraf , Bailey Christopher , Paulsen Janet , Rearden Paul , Brooks Carl , Bhandari Ashish , Gibson Chris , Schaevitz Laura , Haque Imran , Donnella Hayley , Cuccarese Michael , Evangelista Marie 
Published: March 2024

Abstract
Phenomics-enabled drug discovery is a powerful approach to identify novel targets and relationships previously unappreciated in biology. We built a phenomics platform leveraging high content microscopy and generated unique phenoprints for &gt;7,000 genes using CRISPR/Cas9 technology and a diverse chemical library of &gt;1 million compounds. This phenomics dataset contains an unprecedented quantity of gene-gene, gene-compound, and compound-compound relationships. We applied our phenomics platform and an inference based target-agnostic drug discovery approach to discover novel genes and small molecules that mimic CDK12 inhibition, an important transcriptional regulator of DNA damage response, while avoiding inhibition of the paralog CDK13. We discovered a novel and unappreciated association between CDK12 and RBM39 as well as small molecule degraders of RBM39. We established structure activity relationships (SAR) solely leveraging our phenomics platform, to generate REC-1170204, an RBM39 degrader. Unlike inhibitors of CDK12, we show that REC-1170204 does not directly inhibit CDK12, CDK13 or other kinases. However, REC-1170204 demonstrates candidate quality properties with improved potency, selectivity, and drug-like characteristics. Finally we show that REC-1170204 shows efficacy in High Grade Serous Ovarian cancer (HGSOC) pre-clinical models and synergizes with PARP inhibition in a PARP-resistant patient-derived xenograft (PDX) model. Together, our data suggests that targeting RBM39 may provide an attractive and safer approach to targeting CDK12 in the clinic.
Citation Format: Chase Neumann, Harish Shankaran, Kiran Nadella, Kelly Biette, Shane Rowley, Ethan Gardner, Shadi Swaidani, Vamshi Manda, Lu Chen, Daria Beshnova, Ashraf Saeed, Christopher Bailey, Janet Paulsen, Paul Rearden, Carl Brooks, Ashish Bhandari, Chris Gibson, Laura Schaevitz, Imran Haque, Hayley Donnella, Michael Cuccarese, Marie Evangelista. Phenomics-enabled discovery and optimization of small-molecule RBM39 degraders as an alternative to CDK12 targeting in high-grade serous ovarian cancer (HGSOC) [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 7133.
Abstract 7142: Optimizing estradiol dimers through linker design: Enhancing anticancer efficacy by targeting microtubule dynamics
Authors: Dzubak Petr , Jurášek Michal , Řehulka Jiří , Gurská Soňa , Polishchuk Pavel , Dráber Pavel , Huml Lukáš , Drašar Pavel B. , Ivanova Alexandra , Mokshyna Olena , Hrubá Lenka , Hajdúch Marián 
Published: March 2024

Abstract
We investigated the development and anticancer efficacy of novel estradiol dimers (ED), targeting the dynamics of microtubules—an essential factor in effective cancer therapy. Employing copper-catalyzed azide-alkyne cycloaddition (CuAAC), two distinct series of ED variants were synthesized. The initial series included thirteen dimers, derived from 17α-ethinyl estradiol, incorporating varied five-atom linkers with central carbon, nitrogen, or oxygen atoms, and, in some instances, modified with benzyl groups containing hydroxy or methoxy substituents. These dimers were evaluated for their cytotoxic properties and impact on the cell cycle, revealing certain structures with substantial efficacy, compared with the original ED. The subsequent series, encompassing twelve variants, concentrated on structural alterations within the aromatic bridges linking the estradiol units. In this series, linkers of simpler composition and fewer substituents demonstrated increased selectivity and potency against cancer cell lines, particularly ED3 and ED5, which exhibited cytotoxicity levels comparable to established tubulin inhibitors. Both dimers series showed the ability to disrupt microtubule assembly and mitotic processes, confirmed through cell-based evaluations and in vitro tubulin assembly assays. Complementing these results, in silico modelling and binding free energy calculations exhibited a strong correlation with the demonstrated biological activities, especially in terms of binding affinity to the colchicine site. Collectively, these findings highlight the promise of estradiol dimers as potential anticancer agents and emphasize the critical role of linker structures in enhancing their biological effectiveness. Work was supported by the Ministry of Education, Youth and Sports of the Czech Republic through infrastructural projects (CZ-OPENSCREEN - LM2018130; EATRIS-CZ - LM2018133) and National Institute for Cancer Research (Programme EXCELES, ID Project No. LX22NPO5102) - Funded by the European Union - Next Generation EU.
Citation Format: Petr Dzubak, Michal Jurášek, Jiří Řehulka, Soňa Gurská, Pavel Polishchuk, Pavel Dráber, Lukáš Huml, Pavel B. Drašar, Alexandra Ivanova, Olena Mokshyna, Lenka Hrubá, Marián Hajdúch. Optimizing estradiol dimers through linker design: Enhancing anticancer efficacy by targeting microtubule dynamics [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 7142.
Abstract 7144: BR0L075 (SCB01A), a microtubule inhibitor targeting the colchicine binding site, induces immunogenic cell death
Authors: Bano Ayesha , Liu Xinli 
Published: March 2024

Abstract
BPR0L075 (also known as SCB01A in phase II clinical trial) is a novel anti-microtubule drug with potent anti-tumor and anti-angiogenic activity in vitro and in vivo. BPR0L075 inhibits tubulin polymerization (microtubule de-stabilizer) by binding to the colchicine-binding site of tubulin. We previously reported that BPR0L075 overcomes paclitaxel (microtubule stabilizer) resistance and induces vascular-disruption in vitro and in vivo. We observed that breast and ovarian cancer cells treated with BPR0L075 in vitro induced key hallmarks of immunogenic cell death (ICD). In both human and murine, ovarian (OVCAR3, ID8) and breast cancer (MDA-MB-231, 4T1) cell lines, treatment with low nanomolar concentration of BPR0L075 significantly decreased the viability of cells evidenced by SRB assay. Using a known ICD inducer mitoxantrone as a positive control, both flow cytometric analysis and immunofluorescence staining assays demonstrated that BPR0L075 treatment led to a time- and dose-dependent translocation of calreticulin, an endoplasmic reticulum chaperone protein, on the plasma membrane of dying cells which sends an “eat me” signal. The BPR0L75 treatment also led to secretion of High Mobility Group Box 1 (HMGB1), a non-histone chromatin-binding nuclear protein, as well as adenosine triphosphate (ATP) from the cell into the extracellular space using ELISA assay. These damage-associated molecular patterns (DAMPs) are known to lead to antigen-presenting cell recruitment, phagocytosis, maturation of dendritic cells, and chemotaxis. The appearance of the ICD biomarkers (calreticulin exposure, HMGB1 and ATP release) supports BPR0L075 as an ICD-inducing antimitotic agent. Further in vivo studies are warranted to delineate the effect of BPR0L075 on immune activation and recruitment of immune cells to the tumor microenvironment.
Citation Format: Ayesha Bano, Xinli Liu. BR0L075 (SCB01A), a microtubule inhibitor targeting the colchicine binding site, induces immunogenic cell death [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 7144.