bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3135: BSI-730, a bispecific antibody targeting HER2 and PD-L1 for the development of a first-in-class bispecific ADC
Authors: Hao Xiaoyao , Li Hongyan , Liu Xiaodong F. , Liu Jinyu , Dai Wenwen , Pan Ying , Hu Hui-Han , Li Jun , Xia Shukai , Lyu Qun , Davis Hugh M. , Chen Mingjiu , Peng Zeyu
Published: March 2024

Background: Antibody-drug conjugates (ADCs) have become a promising therapeutic option for patients with cancer. Bispecific ADCs targeting two tumor-associated antigens have potential differential anti-tumor advantages. HER2 and PD-L1 are co-expressed in some tumor cell types, such as breast cancer, gastric cancer, lung adenocarcinoma and urothelial carcinoma. A bispecific ADC targeting HER2 and PD-L1 should provide therapeutic benefit, particularly for patients with HER2 low cancer. Dual-target mediated cytotoxicity combined with PD-L1 mediated immunotherapy provides an innovative approach for cancer patients.

Experimental procedures: An anti-PD-L1 monoclonal antibody was identified from A/J mice immunized with PD-L1-ECD-Fc and screened by the Biosion proprietary SynTracer® High Throughput Endocytosis Platform. A “knob-in-hole” bispecific antibody, BSI-730, targeting HER2 and PD-L1 was created with trastuzumab and the humanized anti-PD-L1 scFv. Target binding specificity, binding activity, and affinity of BSI-730 were evaluated by protein-based ELISA, cell-based FACS and Biacore-based SPR, and the ligand blocking activity of PD-L1 portion was measured by competitive ELISA and cell-based FACS. The internalization activities on various cancer cell lines with different expression levels of HER2 and PD-L1 were evaluated by using the SynTracer® Platform.

Summary: BSI-730, a HER2/PD-L1 bispecific antibody, showed comparable binding affinity to HER2 as compared to trastuzumab, as well as comparable bioactivity to the parental anti-PD-L1 antibody regarding PD-L1 binding and PD-1/PD-L1 blocking. Based on a cell-based reporter assay, BSI-730 was able to reverse PD-L1 mediated T-cell suppression and exhibited comparable potency to the parental anti-PD-L1 antibody. The internalization of BSI-730 on HER2 low cancer cell lines was stronger than that of trastuzumab whereas the internalization of BSI-730 on HER2 high cancer cell lines was comparable to that of trastuzumab.

Conclusion: BSI-730 is a novel bispecific antibody for the development of a first-in-class bispecific ADC with the potential advantage of increased potency that can be further investigated to treat HER2 and PD-L1 co-expression tumors, particularly HER2 low tumors.

Citation Format: Xiaoyao Hao, Hongyan Li, Xiaodong F. Liu, Jinyu Liu, Wenwen Dai, Ying Pan, Hui-Han Hu, Jun Li, Shukai Xia, Qun Lyu, Hugh M. Davis, Mingjiu Chen, Zeyu Peng. BSI-730, a bispecific antibody targeting HER2 and PD-L1 for the development of a first-in-class bispecific ADC [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 3135.
Abstract 3153: Regulation of ATF4-mediated stress responses by NUAK2 in ovarian cancer
Authors: Chen Li , Wong Oscar GW , Cheung Claire LY , Wong Esther SY , Chan Karen KL , Ngan Hextan YS , Chan Yusanne YS , Cheung Annie NY
Published: March 2024

NUAK family kinase 2 (NUAK2) a member of the AMPK-related serine/threonine kinase family with crucial roles in various cancer cellular processes. The aim of this study was to elucidate the expression and functions of NUAK2 in ovarian cancer while investigating the underlying molecular mechanisms. Analysis of several publicly available databases suggested a significant increase in NUAK2 mRNA levels in ovarian cancer compared to normal tissue. The overexpression of NUAK2 in ovarian cancer was confirmed by immunohistochemistry of NUAK2 in our local collection of ovarian tumor tissues comprised of carcinomas of various histological types (N=88) as well as benign and borderline tumors (N=19). Intense nuclear NUAK2 immunoreactivity was observed in serous and clear-cell carcinomas. Furthermore, nuclear expression of NUAK2 was significantly correlated with higher tumor grade and poorer overall and disease-free survival. Knocking out NUAK2 in SKOV3 cells by CRISPR-Cas9 resulted in suppressed cell growth and migration. Transcriptome by RNA sequencing and pathway enrichment analysis of SKOV3 cells overexpressing NUAK2 revealed activation of activating transcription factor 4 (ATF4) -dependent unfolded protein response (UPR) in the cell. NUAK2 knockout exaggerated the reactive oxygen species level induced by the endoplasmic reticulum (ER) stress inducer tunicamycin treatment. NUAK2 upregulated ATF4 protein expression during ER stress, facilitating its translocation into the nucleus upon exposure to tunicamycin. SKOV3 with NUAK2 knockout grew significantly slower than its parental line in mice as demonstrated by in vivo imaging. Collectively, our study highlights NUAK2 as an oncogene in ovarian cancer and underscores its involvement in the UPR pathway.

Citation Format: Li Chen, Oscar GW Wong, Claire LY Cheung, Esther SY Wong, Karen KL Chan, Hextan YS Ngan, Yusanne YS Chan, Annie NY Cheung. Regulation of ATF4-mediated stress responses by NUAK2 in ovarian 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 3153.
Abstract 317: Using the Biomek NGeniuS Next Generation Library Prep System to automate the Illumina TruSight Oncology 500 assay
Authors: Smith Zach
Published: March 2024

Cancer researchers using next generation sequencing (NGS) need reliable sample preparation methodologies that generate high-quality, sequence-ready libraries from often-challenging samples. This process can be aided using automated liquid handling systems.

The Biomek NGeniuS Next Generation Library Prep System from Beckman Coulter Life Sciences is a reliable, easy-to-use, purpose-built liquid handler for NGS library preparation ideal for laboratories requiring more flexibility and less hands-on time. The user-friendly software requires no programming skills, making it easy to set up and run. Biomek NGeniuS Next Generation Library Prep System’s hardware features include an on-deck thermal cycler, gripper, temperature-controlled reagent storage, and high-density tip storage which reduces user interventions and enables more walkaway time. An extensive and growing library of complimentary demonstrated NGS sample prep protocols allows the user to select from a variety of applications for NGS workflows. One such workflow is Illumina TruSight Oncology 500 assay, which represents a comprehensive NGS assay targeting the full coding regions of 523 genes implicated in the pathogenesis of solid tumors. Using enrichment-based library preparation techniques for use with formalin-fixed, paraffin-embedded (FFPE) samples, the Illumina TruSight Oncology 500 assay, when running the DNA Only workflow, can detect single nucleotide variants (SNVs), indels, amplifications, and multinucleotide variants (MNVs) in a single sequencing run. The Illumina TruSight Oncology 500 assay also detects immunotherapy biomarkers for tumor mutational burden (TMB) and microsatellite instability (MSI) in DNA samples. The Illumina TruSight Oncology 500 assay also offers a combined RNA/DNA workflow that also allows for the assessment of fusion events.

In this poster, we show the utility of the Biomek NGeniuS Next Generation Library Prep System to perform the Illumina TruSight Oncology 500 assay, which saves researchers valuable hands-on time and offers a highly streamlined setup process for users new to liquid handling automation.

Confidential - Company Proprietary

Citation Format: Zach Smith. Using the Biomek NGeniuS Next Generation Library Prep System to automate the Illumina TruSight Oncology 500 assay [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 317.
Abstract 3180: Suppression of the CPEB3 ribozyme modulates the progression of glioblastoma
Authors: Chen Claire , Wang Eric , Tong Lily , Nikan Mehran , Bota Daniela A. , Benavente Claudia , Luptak Andrej
Published: March 2024

Glioblastoma multiforme (GBM) is the most aggressive primary malignant brain tumor in adults, with a poor prognosis that highlights a dire clinical need for innovative therapeutic interventions. Despite significant advances in diagnoses and multimodality therapies, the overall prognosis for patients with GBM remains poor, with a median survival time of 15-18 months. Therefore, there is an unmet medical need to develop alternative treatment strategies to improve clinical outcomes. Dysregulation of post-transcriptional control and translational machinery have been implicated in malignant tumor development. Cytoplasmic polyadenylation element binding proteins (CPEB1-CPEB4) are RNA-binding proteins that regulate poly(A) tail elongation of target mRNAs and subsequently contribute to phenotypic changes in cancer cells. Notably, a self-cleaving ribozyme was identified in the CPEB3 gene, but its role in cancer is wholly unexplored. Considering the role of CPEB3 as a tumor suppressor gene and the promotion of cancer progression through the downregulation of CPEB3, our hypothesis is that the CPEB3 ribozyme regulates CPEB3 expression, and its activity contributes to the progression of tumors. Using antisense oligonucleotides (ASOs) as an approach, we demonstrated that inhibition of CPEB3 ribozyme resulted in an increase of CPEB3 mRNA and protein expression. Blocking the CPEB3 ribozyme led to a significant reduction in cell proliferation, migration, and invasion in GBM cell lines. Gene set enrichment analysis (GSEA) revealed the downregulation of epithelial-mesenchymal transition (EMT), angiogenesis, and hypoxia gene sets in GBM cells treated with ASO compared to Ctrl-ASO. We further measured VEGFA mRNA and protein expression and found that ASO-treated GBM cells secreted significantly less VEGF in conditioned media. Inhibition of the CPEB3 ribozyme also mitigated the EMT process in GBM cells. Subsequently, ASO strategies were applied to patient-derived glioma stem cells (GSCs), representing a clinically relevant model for pre-clinical therapeutic intervention. We found that treatment of CPEB3 ribozyme ASO up-regulated CPEB3 mRNA and inhibited cell proliferation in GSCs. Furthermore, the combination of ASO and temozolomide chemotherapy exhibited a more pronounced decrease in GSCs proliferation compared to individual treatment alone. Collectively, this study highlights the significance of the CPEB3 ribozyme in GBM and explores therapeutic approaches focused on targeting CPEB3 in cancer.

Citation Format: Claire Chen, Eric Wang, Lily Tong, Mehran Nikan, Daniela A. Bota, Claudia Benavente, Andrej Luptak. Suppression of the CPEB3 ribozyme modulates the progression of 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 3180.
Abstract 3213: A novel CDH17/PD-1 bispecific antibody for treatment of advanced gastrointestinal cancers
Authors: Wong Kwan Wa , Wong Po Yee , Chow Kronos , O Chui Yee , Wong Dennis , Luk John Moon , Wong Kwong Fai
Published: March 2024

Targeting immune checkpoints like programmed death receptor 1 (PD-1) with monoclonal antibodies has achieved durable responses in a range of cancers, however, immune-related adverse events may occur in a subset of patients. As such, we developed a bispecific antibody targeting cadherin-17 (CDH17) and PD-1 with a hope to rejuvenate specifically the exhausted T cells within tumor microenvironment. In healthy individuals, CDH17 is expressed at a restricted level in intestinal epithelial junction that is not accessible to biologics, however, in gastrointestinal cancers, CDH17 is overexpressed and can be targeted by antibodies. Our new CDH17/PD-1 bispecific antibody would reactivate anti-tumor immunity with reduced risk of on-target off-tumor toxicity. Different bispecific antibody formats were designed, cloned, and expressed. Strong binders were first identified using CDH17 and PD-1 ELISA. The binding affinities to CDH17 and PD-1 of the selected candidate were examined using biolayer interferometry. The effect of these bispecific antibodies on blocking PD-1/PD-L1 axis in T cells was demonstrated in a cell-based reporter assay. T-cell mediated killing on CDH17-positive GI cancer cells and induction of T cell activation markers upon antibody treatment were also studied. A total of 7 CDH17/PD-1 bispecific antibodies of different formats were screened. Of these candidates, one, named ARB204, was selected because of its potent binding to both antigens in ELISA (i.e., EC50 values: CDH17, 1.6nM; PD-1, 0.4nM) and biolayer interferometry (i.e., KD values: CDH17, 2.4E-09M; PD-1, 6.02E-11M). ARB204 blocked PD-1/PD-L1 axis in the reporter assay with EC50 value 4.4nM. Notably, ARB204 redirected T cells to eradicate CDH17-positive pancreatic AsPC1 cells with an EC50 value of 3.5nM. No cytotoxicity against CDH17-negative cancer cells were seen. ARB204 effectively bound CDH17 on GI cancer cells and PD-1 on T cells. This bispecific design allowed selective T-cell mediated killing on cancer cells expressing CDH17, mitigating the risk of off-tumor toxicity. ARB204 warrants further studies on its immune checkpoint inhibition in animal models.

Citation Format: Kwan Wa Wong, Po Yee Wong, Kronos Chow, Chui Yee O, Dennis Wong, John Moon Luk, Kwong Fai Wong. A novel CDH17/PD-1 bispecific antibody for treatment of advanced gastrointestinal 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 3213.
Abstract 3233: EP102: Pharmacological Inhibition of METTL3 causes tumor growth inhibition and prolongs survival in preclinical models of NSCLC, ovarian and squamous cell carcinoma
Authors: Fraser Graeme , Sorlet Catherine , Parmentier Nicolas , Brunel Elodie , Coremans Christian , Rorive Sarah , Hartiel Anne-France , Oukoloff Killian , Dutheuil Guillaume
Published: March 2024

METTL3 is the RNA methyltransferase predominantly responsible for the addition of N-6-methyladenosine (m6A), the most abundant epigenetic modification to mRNA. The prevalence of m6A and the activity and expression of METTL3 have been linked to the appearance and progression of numerous hematological and solid tumor cancers. EPICS has discovered and optimized small molecule inhibitors of METTL3 (“M3i”). The aim of the current study is to evaluate the efficacy of M3i in various CDX mouse tumor models. M3i compound potency was evaluated in vitro by measuring enzymatic inhibition of METTL3/14 by scintillation proximity assay (IC50 = 2 nM). The anti-proliferative effects of M3i were measured in cell viability assays following a 72h treatment of A549 (NSCLC, IC50 = 190 nM), SKOV3 (ovarian, IC50 = 9 nM) and FaDu (hypopharyngeal squamous cell carcinoma, IC50 = 24 nM) cells. Complementary data in all three cell lines demonstrates a clear concentration-response for a target engagement biomarker (m6A; IC50 = 2-8 nM, across cell lines) as well as M3i-induced changes in biomarkers of oncogenic drivers. M3i (30 mg/kg, IP, QD) was tested in vivo in mouse models using FaDu (subcutaneous implant) in addition to A549 and SKOV3 (both orthotopic implants); all animal models were performed by LabCorp (MI, USA). Daily M3i treatment significantly prolonged survival in all three disease models consistent with efficacy on tumor growth inhibition as measured by imaging (A549, SKOV3) or direct measurement of tumor volume in the case of subcutaneous implant (FaDu). M3i has previously been shown to be effective in mouse CDX and PDX models of AML. The current results extend the application of METTL3 inhibitors to include the treatment of various types of solid tumors. The efficacy of M3i as a single-agent on tumor growth inhibition and survival advances the validation of METTL3 as a cancer target and provides additional evidence for the applicability of mRNA epigenetic mechanisms to the treatment of solid tumors.

Citation Format: Graeme Fraser, Catherine Sorlet, Nicolas Parmentier, Elodie Brunel, Christian Coremans, Sarah Rorive, Anne-France Hartiel, Killian Oukoloff, Guillaume Dutheuil. EP102: Pharmacological Inhibition of METTL3 causes tumor growth inhibition and prolongs survival in preclinical models of NSCLC, ovarian and squamous cell 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 3233.
Abstract 3236: Discovery of hydrazide-based HDAC8 selective PROTACs
Authors: Xiao Yufeng , Liu Yi , Awasthee Nikee , Meng Chengcheng , He Michael , Hale Seth , Karki Rashmi , Lin Zongtao , Kridel Robert , Liao Daiqing , Zheng Guangrong
Published: March 2024

HDAC8 plays crucial roles in biological processes and is a highly desirable target for therapeutic interventions. However, due to the conserved catalytic domain among HDACs, developing specific inhibitors for these isozymes has proven challenging. HDAC8 also has deacetylase-independent activity which cannot be blocked by an inhibitor. Previously we reported the discoveries of a potent HDAC3 degrader XZ9002 and an HDAC3/8 dual degrader YX968. In this study, we carried out further optimizations based on the warhead of YX968 through rational design, which led to the discovery of YX862 and YL246, novel hydrazide-based HDAC8 selective PROTAC degraders with single-digit nanomolar DC50 and excellent selectivity. We demonstrated that the degradation of HDAC8 affects its non-histone substrates; however, it does not trigger profound histone hyper-acetylation and gene expression alteration, highlighting the unique role of HDAC8. The PROTACs developed in this study are well-characterized HDAC8 degraders without triggering pan-HDAC inhibition which represent valuable tool compounds for exploring the biological and therapeutic potential of HDAC8 in cancers and beyond.

Citation Format: Yufeng Xiao, Yi Liu, Nikee Awasthee, Chengcheng Meng, Michael He, Seth Hale, Rashmi Karki, Zongtao Lin, Robert Kridel, Daiqing Liao, Guangrong Zheng. Discovery of hydrazide-based HDAC8 selective PROTACs [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 3236.
Abstract 3272: PJA1 inhibits docetaxel-induced pyroptosis and results in chemoresistance in nasopharyngeal carcinoma
Authors: Liu Na , Li Ying-Qing , Huang Sheng-Yan
Published: March 2024

Background: Nasopharyngeal carcinoma (NPC) is highly prevalent in South China. More than 70% of patients are diagnosed with locoregionally advanced NPC (LA-NPC) at initial presentation, and the addition of induction chemotherapy (IC) to concurrent chemoradiotherapy is recommended for these patients. However, chemoresistance is a main reason for treatment failure in NPC patients, and the exact regulatory mechanism underlying chemoresistance in NPC remains to be elucidated.

Methods: A gene expression dataset and STRING database were used to identify core module and gene that are related to the efficacy of docetaxel-cisplatin-5-fluorouracil (TPF) IC in NPC patients. In vitro and in vivo functional experiments were used to test the effects of PJA1 on docetaxel chemoresistance of NPC cells. The flow cytometric analysis, western blot, and lactate dehydrogenase (LDH) release assays were performed to determine the effects of PJA1 on GSDME-mediated cell pyroptosis. Co-immunoprecipitation, mass spectrometry, immunofluorescence staining, and ubiquitination assays were performed to explore the regulatory manners between PJA1 and PGAM5-DRP1 axis. Finally, multiplex immunofluorescence and immunohistochemical staining were used to evaluate the clinical significance of PJA1 -PGAM5-DRP1 axis in patients with NPC.

Results: PJA1 was identified as a key E3 ligase of the top-ranked module ubiquitin-proteasome system dysregulation that involved in NPC chemoresistance, which was highly expressed in NPC patients with nonresponse to the TPF IC. PJA1 facilitated the docetaxel resistance of NPC cells through inhibiting the GSDME-mediated pyroptosis. Mechanistically, PJA1 promoted the degradation of the mitochondrial protein PGAM5 by increasing its K48-linked ubiquitination at K88, further increasing the phosphorylation of DRP1 at S637 and reducing the mitochondrial reactive oxygen species (ROS) production, in turn resulting in a suppressive of GSDME-mediated pyroptosis. PGAM5 knockdown fully restored the docetaxel sensitization effect of PJA1 knockdown. Moreover, RTA402, a pharmacological inhibitor of PJA1, enhanced the docetaxel sensitivity of NPC cells. Clinically, high PJA1 expression indicated resistance to TPF IC an inferior survival in NPC patients.

Conclusions: Our study emphasizes the essential role of E3 ligase PJA1 in regulating chemoresistance in NPC and provides new therapeutic strategies for NPC patients based on targeting the ubiquitin-proteasome system.

Citation Format: Na Liu, Ying-Qing Li, Sheng-Yan Huang. PJA1 inhibits docetaxel-induced pyroptosis and results in chemoresistance in nasopharyngeal 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 3272.
Abstract 3320: In vivo and in vitro experience with novel direct Pan-RAS inhibitors
Authors: Arshad Tariq , Donninger Howard , Clarke Goeff , Burlison Joe , Monsen Rob , Sabo Mike
Published: March 2024

RAS oncogenes are frequently activated by mutations in human cancer, where they act as driving elements of the disease. Mutation rates can range from ~25% of Non Small Cell Lung cancers to over 90% of pancreatic cancers. RAS proteins can also be hyper-activated to drive cancer at a significant frequency in the absence of RAS gene mutations when their protein regulatory systems are damaged. Thus, RAS may be the most frequently activated oncoprotein in cancer. We have developed a series of novel, direct, RAS inhibitors with a unique binding site on RAS. The binding of the agents alters the structure of the RAS effector loop and blocks the association with RAS downstream effectors. We used in silico library screening followed by Medicinal Chemistry optimization to develop the compounds. We have validated the agents using Microscale Thermophoresis and NMR to quantify binding to recombinant RAS protein. We have used mutant and wild type RAS driven tumor cell lines in 3D growth and protein-based RAS signaling assays to quantify and characterize the action of the family of inhibitors. We have used xenograft assays to demonstrate compound anti-tumor activity in RAS driven cell lines and pdx systems. We have identified compounds that can bind mutant and wild type K, H, N and M-RAS. We can suppress the association of mutant and wild type RAS protein with its effector RAF-1 in treated cells. The compounds can suppress 3D growth of mutant or wild type RAS driven tumor cell lines and repress tumor development in vivo. The compound family bind to a different site than either clinical agent AMG-510 (K-RAS G12C specific) or MRTX-1133 (K-RAS G12D specific). They exhibit distinct RAS signal inhibition patterns compared to these agents. They can also co-operate with the clinical agents and reduce drug resistance effects.

Citation Format: Tariq Arshad, Howard Donninger, Goeff Clarke, Joe Burlison, Rob Monsen, Mike Sabo. In vivo and in vitro experience with novel direct Pan-RAS 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 3320.
Abstract 3328: Oridonin derivative compounds target STATs to inhibit triple-negative breast cancer
Authors: Vontz Gabrielle , Li Jun , Liang Zhipin , Ma Ruixia , Wang Pingyuan , Chen Haiying , Zhou Jia , Shen Qiang
Published: March 2024

Breast cancer remains the second leading cause of cancer related deaths in women. Despite the development of targeted treatments and immunotherapies, triple-negative breast cancer (TNBC) continues to evade effective treatment. TNBC lacks sufficient expression of druggable markers, ER, PR, and Her2, and exhibits especially aggressive characteristics including later diagnosis, lower survival rate, and higher rates of metastasis and reoccurrence. Currently, cytotoxic chemotherapy and radiation remain the standard of care for TNBC. Our work utilizes compounds from nature to develop therapies for TNBC with improved efficacy and safety. Oridonin, a natural kaurene-type diterpenoid enriched in the medicinal herb Rabdosia rubescens, is a promising anticancer agent, but exhibits limited bioavailability and potency. Our team successfully developed oridonin derivative CYD0618 compound that exhibits significantly improved solubility and anticancer activity. This study aims to characterize the mechanism of action of CYD0618 on TNBC cells. We found that CYD0618 reduces the proliferation of TNBC cells in vitro with IC50s at the nanomolar level. We also found CYD0618 has high potency against TNBC in vivo. Within a xenograft mouse model, CYD0618 suppresses the growth of TNBC tumors and extends animal survival. Using Western blot to probe for putative targets, we found CYD0618 reduces activation of STAT3, a transcription factor critically involved in proliferation, survival, and transformation of epithelial cells. Because STAT3 is constitutively active in ~70% of human cancers, there has been a tremendous effort to develop STAT3 targeting therapies; however, none has achieved FDA approval. In addition to STAT3, we show CYD0618 also suppresses other STAT transcription factors. Compared to selective STAT3 degradation by PROTAC treatment, poly-STAT targeting by CYD0618 exhibits superior activity against TNBC cells. Our study identifies CYD0618 as a novel poly-STAT inhibitor with promising activity against TNBC.

Citation Format: Gabrielle Vontz, Jun Li, Zhipin Liang, Ruixia Ma, Pingyuan Wang, Haiying Chen, Jia Zhou, Qiang Shen. Oridonin derivative compounds target STATs to inhibit 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 3328.
Abstract 3371: PRMT blockade induces defective DNA replication stress response via ATR suppression and synergizes with PARP inhibition
Authors: Bisht Deepa , Li Yang , Dobrolecki Lacey E. , Sallas Christina , Zhang Xudong , Kerr Travis D. , Wang Yalong , Awasthi Sharad , Kaundal Babita , Wu Siqi , Peng Weiyi , Mendillo Marc L. , Lu Yiling , Jeter Collene R. , Peng Guang , Liu Jinsong , Westin Shannon N. , Sood Anil K. , Lewis Michael T. , Das Jishnu , Yi S. Stephen , Bedford Mark T. , McGrail Daniel J. , Sahni Nidhi
Published: March 2024

Aberrant protein arginine methylation has been observed in multiple cancer types, making it an attractive drug target. Proteins can undergo asymmetric arginine methylation by type I protein arginine methyltransferases (PRMTs), predominately by PRMT1 and to a lesser extent PRMT4, or symmetric arginine methylation by type II PRMTs, predominately PRMT5. Here, we performed targeted proteomics following inhibition of PRMT1, PRMT4, and PRMT5 across cancer cell lines. We found that inhibition of both type I and type II PRMTs suppressed levels of total and phosphorylated ATR protein in cancer cell lines, and down-regulated expression of the ATR gene. Loss of ATR from PRMT inhibition resulted in defective DNA replication stress response activation in following exogenous replication stress. Since PARP inhibitors are known to induce replication stress, we next combined PRMT inhibition with PARP inhibition and found inhibition of PRMT1 or PRMT5 greatly exacerbated PARP inhibitor induced DNA damage. Based on this observation, we assessed the combination of PARP and PRMT inhibition in a panel of cell lines. While inhibition of both type I and type II PRMTs were synergistic with PARP inhibition in both cells with intact and deficient homologous recombination, type I PRMT inhibition resulted in higher toxicity in non-malignant cells. Therefore, we validated the synergy of combined PARP/PRMT5 inhibition in primary patient-derived organoids. Finally, we demonstrate that the combination of PARP and PRMT5 inhibition improves overall survival in both BRCA-mutant and wild-type patient-derived xenograft models without any detectable hematological toxicities typically associated with PARPi combination therapies. Taken together, these results demonstrate that PRMT5 inhibition may be a well-tolerated approach to improve tumor sensitivity to PARP inhibition.

Citation Format: Deepa Bisht, Yang Li, Lacey E. Dobrolecki, Christina Sallas, Xudong Zhang, Travis D. Kerr, Yalong Wang, Sharad Awasthi, Babita Kaundal, Siqi Wu, Weiyi Peng, Marc L. Mendillo, Yiling Lu, Collene R. Jeter, Guang Peng, Jinsong Liu, Shannon N. Westin, Anil K. Sood, Michael T. Lewis, Jishnu Das, S. Stephen Yi, Mark T. Bedford, Daniel J. McGrail, Nidhi Sahni. PRMT blockade induces defective DNA replication stress response via ATR suppression and synergizes with PARP inhibition [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 3371.
Abstract 3401: Uncovering virus induced dysregulated processes in cancer and their impact on outcomes
Authors: moghadam Mohadeseh Soleimanpour , Khosh Azad , Ebrahimi Diako
Published: March 2024

The National Cancer Institute has designated several viruses such as EBV, HBV, HCV, HIV, HPV, and HTLV as agents that either cause cancer or increase the risk of developing cancer. However, extensive analyses of tumor genome and transcriptome datasets have identified numerous additional virus types, the functional implications of which remain largely unknown. Viral infection often dysregulates unique molecular processes within tumor cells and alters the composition of immune cells in the tumor microenvironment. For instance, HPV-positive tumors have been shown to exhibit a significantly elevated expression of the DNA editing enzyme APOBEC3B compared to HPV-negative tumors. Furthermore, HPV positive tumors display and increased number of C-to-T mutations induced by this protein. The genome and transcriptome of tumor tissue biopsies contain a wealth of information about these virus-associated signatures. However, advanced signal processing approaches are needed to extract these viral signatures from complex tumor datasets, and elucidate their specific roles in cancer. Here, we developed a quantitative approach to investigate the link between viral infection and dysregulation of a seven-membered A3 enzyme family (A3A/B/C/D/F/G/H). The primary role of these enzymes is to restrict viral infections by inducing C-to-U mutations in viral genomes. However, at least three members of this enzyme family (A3A/B/H) can also induce mutations in cellular DNA, and drive tumor formation and evolution. We used NMF (Nonnegative Matrix Factorization) to deconvolute the expression profiles of A3 enzymes in >10,000 bulk RNAseq datasets from diverse TCGA tumors. This analysis revealed the expression profiles of A3 enzymes within tumor and tumor microenvironment cells including various immune cells. Next, we conducted an association analysis to identify the link between the presence of viral infection and the proportion of each of these tumor and tumor microenvironment expression profiles. As expected, our analyses revealed strong associations between tumor-specific A3 expression profiles and infections by oncolytic viruses such as HPV. Notably, and somewhat unexpectedly, our analyses also revealed associations with viruses about which little is known in the field of cancer. For example, in certain tumors, we identified a robust association between bacteriophages and a tumor-specific A3 expression profile characterized by A3B upregulation. Taken together, our analyses provide evidence for the link between A3 dysregulation and infection by viruses including bacteriophages.

Citation Format: Mohadeseh Soleimanpour moghadam, Azad Khosh, Diako Ebrahimi. Uncovering virus induced dysregulated processes in cancer and their impact on outcomes [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 3401.
Abstract 3431: Genetically determined circulating lactase/phlorizin hydrolase concentrations and risk of colorectal cancer: A two-sample mendelian randomization study
Authors: Han Sihao , Yao Jiemin , Yamazaki Hajime , Streicher Samantha , Rao Jianyu , Nianogo Roch , Zhang Zuo-Feng , Huang Brian
Published: March 2024

Background: Colorectal cancer (CRC) ranks as the third most common cancer worldwide. Despite its established connection with genetic, dietary, and lifestyle factors, gaps remain in the understanding of its etiology. Lactase-phlorizin hydrolase (LPH) plays a critical role in milk digestion and influences crucial nutrient absorption and gut microbiota composition. A direct relationship of CRC risk with LPH level remains unexplored. Our study aims to elucidate the potential causal link between genetically determined LPH levels and CRC risk.

Methods: We applied a two-sample Mendelian Randomization (MR) strategy to investigate the causal link between elevated LPH levels and CRC risks. Genetic instruments for LPH (one cis-variant and three trans-variants) were derived from the Fenland Study, and CRC-associated summary statistics for these instruments were extracted from the FinnGen Study, PLCO Atlas Project, and Pan-UK Biobank. Primary MR analyses focused on a cis-variant (rs4988235) for LPH levels, with results integrated via meta-analysis. MR analyses using all variants were also undertaken. This analytical approach was further extended to assess CRC subtypes, specifically colon and rectal cancer.

Results: Meta-analysis across the three datasets illustrated an inverse association between genetically predicted LPH level and CRC risk (OR: 0.92 [95% CI, 0.89-0.95]). Subtype analyses revealed associations of genetically predicted elevated LPH levels with reduced risks for both colon cancer (OR: 0.92 [95% CI, 0.89-0.96]) and rectal cancer (OR: 0.92 [95% CI, 0.87, 0.98]). Consistency was observed across varied analytical methods and different datasets.

Conclusions: Our study suggests an inverse relationship between genetically determined LPH level and CRC risk. Further exploration is warranted to unveil the underlying mechanisms and validate LPH’s potential role in CRC prevention.

Citation Format: Sihao Han, Jiemin Yao, Hajime Yamazaki, Samantha Streicher, Jianyu Rao, Roch Nianogo, Zuo-Feng Zhang, Brian Huang. Genetically determined circulating lactase/phlorizin hydrolase concentrations and risk of colorectal cancer: A two-sample mendelian randomization study [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 3431.
Abstract 3466: Prognostic implications of lymph node micrometastasis in patients with gastric cancer
Authors: Yamamoto Atsushi , Okamoto Hirotaka
Published: March 2024

Purpose: The clinical significance of lymph node micrometastasis (LNMM) remains controversial in gastric cancer (GC). In this study, we investigated the prognostic impact of patients with LNMM GC.Methods: A total of 624 patients with pathologically lymph node metastasis negative (pN0) and N1 status (pN1) who underwent gastrectomy between 2004 and 2018 were enrolled in this retrospective study. The diameter of tumor cell clusters in metastatic lymph nodes was measured in 120 patients with pN1 GC. Results: Patients with lymph node tumors of diameter < 1500 μm (LNMM) had significantly better prognosis than those with tumors of diameter ≥ 1500 μm (p = 0.012; log-rank test). Cox’s proportional hazards model revealed that LNMM (p = 0.016), several dissected lymph nodes (p = 0.049), and the provision of adjuvant chemotherapy (p = 0.002) were independent prognostic factors for overall survival of patients with pN1 GC. There was no significant difference in overall survival between patients with LNMM who received chemotherapy and those who did not (p = 0.332). Conclusions: LNMM is associated with favorable prognosis and could be an independent prognostic marker in patients with pN1 GC. LNMM in GC may be considered as one of the factors preventing adjuvant chemotherapy.

Citation Format: Atsushi Yamamoto, Hirotaka Okamoto. Prognostic implications of lymph node micrometastasis in patients with gastric 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 3466.
Abstract 3490: Unveiling sex differences in lung adenocarcinoma through multi-omics integrative protein signaling networks
Authors: Chen Chen , Saha Enakshi , DeMeo Dawn L. , Quackenbush John , Lopes-Ramos Camila M.
Published: March 2024

Sex differences in lung adenocarcinoma (LUAD) are evident in incidence rates, prognostic outcomes, and therapy responses, yet the underlying molecular mechanisms driving these disparities remain underexplored. In this study, we conducted a comprehensive proteogenomic analysis encompassing 38 females and 73 males with LUAD from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) dataset. Employing Transcription Inference using Gene Expression and Regulatory data (TIGER), we inferred sex-differentially activated transcription factors (TFs) from The Cancer Genome Atlas (TCGA) LUAD gene expression data and identified sex-differentially activated kinases using CPTAC protein phosphorylation data. We further constructed a comprehensive kinase-TF signaling network by integrating these sex-differentially activated kinases with TFs, identifying all paths shorter than 3 in the protein interaction networks to highlight druggable pathways. Our analyses revealed that many proteins exhibit not only sex-biased abundance but also sex-biased phosphorylation and acetylation. Furthermore, these sex-biased proteins were associated with critical biological pathways including cell proliferation, immune response, and metabolism. Using kinase-TF signaling networks, we found substantial sex bias in the activities of clinically actionable TFs and kinases, including the glucocorticoid receptor (NR3C1), AR, AURKA, CDK6, and MAPK14. Leveraging the PRISM cancer cell line screening database, we identified several small-molecule drugs, such as glucocorticoid receptor agonists and aurora kinase inhibitors, potentially exhibiting sex-specific efficacy as LUAD therapeutics. Our findings showed that the activity of some clinically relevant TFs and kinases differ by sex in LUAD, underscoring the need to consider sex as a biological variable and the utility of multi-omics integrative protein signaling networks in advancing our understanding of cancer biology and the development of sex-aware therapeutics.

Citation Format: Chen Chen, Enakshi Saha, Dawn L. DeMeo, John Quackenbush, Camila M. Lopes-Ramos. Unveiling sex differences in lung adenocarcinoma through multi-omics integrative protein signaling networks [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 3490.
Abstract 3497: Glioma Immune Microenvironment Composition Calculator (GIMiCC): A method of estimating the proportions of eighteen key cell types from human brain tissue assayed using Illumina DNA methylation microarray technology
Authors: Pike Steven C. , Wiencke John K. , Zhang Ze , Molinaro Annette M. , Koestler Devin C. , Christensen Brock C. , Kelsey Karl T. , Salas Lucas A.
Published: March 2024

Precise detection of both tumor subclass and immune composition is critical in the pursuit of personalized immunotherapeutic treatment strategies for glioma. DNA methylation (DNAm) biomarkers are promising on both fronts. DNAm-based biomarkers for molecular classification have been developed and integrated into World Health Organization (WHO) diagnostic criteria. However, prediction of the tumor microenvironment is not as well defined. To fill this gap, we present GIMiCC, an approach for cellular deconvolution of DNAm microarray data for four WHO 2021 tumor subclasses: glioblastoma, oligodendroglioma, grade 2/3 astrocytoma and grade 4 astrocytoma. Using data from 17 isolated cell types, we describe the derivation of the deconvolution libraries and test the method on independent datasets from the Cancer Genome Atlas (TCGA) and the DKFZ molecular neuropathology classifier (PMID: 29539639). We utilize GIMiCC to illustrate that DNAm-based glioma classification is unlikely to be biased by compositional variation. In addition, we utilize GIMiCC to identify composition independent DNAm alterations that are associated with high immune infiltration. Our future work aims to optimize GIMiCC and advance the clinical evaluation of glioma with this new tool.

Citation Format: Steven C. Pike, John K. Wiencke, Ze Zhang, Annette M. Molinaro, Devin C. Koestler, Brock C. Christensen, Karl T. Kelsey, Lucas A. Salas. Glioma Immune Microenvironment Composition Calculator (GIMiCC): A method of estimating the proportions of eighteen key cell types from human brain tissue assayed using Illumina DNA methylation microarray technology [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 3497.
Abstract 350: Targeting prohibitins by fluorizoline leads to the activation of ISR and apoptosis through DELE1 and HRI by an impairment of the mitochondrial protein import machinery
Authors: Sánchez-Vera Ismael , Maritorena-Hualde Nekane , Schuler Max-Hinderk , Cosialls Ana M- , Lavilla Rodolfo , Pons Gabriel , Jae Lucas T , Iglesias-Serret Daniel , Gil Joan
Published: March 2024

Prohibitins are ubiquitously expressed within the cell, but they are mainly located at the inner mitochondrial membrane. These proteins are closely associated with tumour progression, invasion, and apoptotic resistance, being overexpressed in various primary tumours such as lymphoma and endometrial cancer. Notably, we have developed a novel synthetic molecule, fluorizoline, which induces apoptosis by selectively targeting PHBs in different cancer cell lines and primary samples from various haematological neoplasias. We have previously described that fluorizoline-induced apoptosis is mediated through the activation of the pro-apoptotic branch of the integrated stress response (ISR) pathway in HeLa and HAP1 cells, concretely, by the ATF4-CHOP-NOXA axis. In a recent study, we identified compensatory mechanisms for four ISR-related kinases. Importantly, HRI emerged as the primary kinase responsible for activating this pathway and promoting apoptosis, suggesting that mitochondrial stress could lead to this activation of the ISR.Here, we investigate the OMA1-DELE1-HRI molecular pathway responsible for sensing mitochondrial stress and activating the ISR cancer cell lines. Firstly, we demonstrate that fluorizoline treatment triggers the cleavage of large DELE1 (L-DELE1) to its cleaved form (S-DELE1) through western blot analysis, and its subsequent sorting to the cytosol as confirmed by confocal analysis. Using DELE1 KO lines generated by CRISPR/Cas9 technology, we demonstrate that DELE1 is involved in the activation of the ISR and apoptosis induced by fluorizoline. However, although we cannot rule out OMA1 involvement, fluorizoline-induced ISR activation does not strongly depend on OMA1. Interestingly, our data suggests that targeting PHBs, either by fluorizoline or by their downregulation, could result in mitochondrial protein import machinery impairment. This impairment may potentially be the cause of DELE1 accumulation in the cytosol, leading to the subsequent activation of the ISR by HRI upon fluorizoline treatment.

Citation Format: Ismael Sánchez-Vera, Nekane Maritorena-Hualde, Max-Hinderk Schuler, Ana M- Cosialls, Rodolfo Lavilla, Gabriel Pons, Lucas T Jae, Daniel Iglesias-Serret, Joan Gil. Targeting prohibitins by fluorizoline leads to the activation of ISR and apoptosis through DELE1 and HRI by an impairment of the mitochondrial protein import machinery [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 350.
Abstract 3502: Multi-omics approach to cholangiocarcinoma-related biology and development of precision medicine
Authors: Kwon Woo Young , Kang Incheon , Lee Sung Hwan
Published: March 2024

Introduction: Cholangiocarcinoma is a diverse tumor entity characterized by distinct tumor biology and clinical phenotypes, which are influenced by the unique tumor microenvironment (TME) and anatomical location—whether intrahepatic, peri-hilar, or distal extrahepatic. Consequently, there is a clear need for a precision strategy that relies on cancer-specific, multi-omic features, moving away from traditional molecular subtypes derived from bulk RNA sequencing.

Methods: We conducted thorough multi-omic analyses utilizing data from the Cancer Dependency Map (DepMap) project. This encompassed cancer-specific molecular characterization through various omics data, genome-wide loss-of-function screening employing the CRISPR-Cas9 system, and drug sensitivity assessments via compound screening. These efforts aimed to reveal cancer-specific molecular subtypes with clinical relevance. The identified cancer-specific molecular signatures were subsequently validated in independent translational cohorts.

Results: Through integrative profiling of the transcriptome in bile duct cancer cell lines (n=39) obtained from the Cancer Cell Line Encyclopedia (CCLE), we unveiled cancer-specific molecular subtypes exhibiting distinct tumor biology across all omics layers, coupled with clinical relevance and prognostic significance. The major molecular features of each subtype demonstrated reproducibility in validation cohorts. Additionally, subtype-specific molecular biomarkers, encompassing mutational signatures and metabolites, were identified. Finally, we analyzed target drugs with subtype-specific genetic dependencies to formulate a precision strategy tailored to the distinct molecular characterizations of each subtype.

Conclusions: A thorough analysis utilizing a multi-omics dataset uncovered precision strategies founded on cancer-specific molecular subtypes of cholangiocarcinoma, both in terms of tumor classification and discriminative therapeutic opportunities. It is imperative to conduct prospective translational studies in conjunction with clinical trials, all centered around the cancer-specific molecular subtypes, to establish a precision strategy for effectively managing cholangiocarcinoma.

Citation Format: Woo Young Kwon, Incheon Kang, Sung Hwan Lee. Multi-omics approach to cholangiocarcinoma-related biology and development of precision medicine [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 3502.