bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 5818: Differentiation of human papillomavirus-positive head and neck squamous cell carcinoma cells
Authors: Gendreizig Sarah , Martinez-Ruiz Laura , Florido Javier , López-Rodríguez Alba , Pabla Harkiren , Brasch Frank , Escames Germaine , Busche Tobias , Sudhoff Holger , Scholtz Lars U. , Todt Ingo , Oppel Felix
Published: March 2024

Head and neck squamous cell carcinoma (HNSCC) represents a highly malignant disease and death rates remain at approximately 50% for decades. Thus, new tumor-targeting treatment strategies are desperately needed. In a previous study, we dissected human papillomavirus (HPV)-negative HNSCC cell differentiation via cornification and detected an epigenetically determined loss of cell malignancy. Analyzing the mechanisms underlying the differentiation of HNSCC cells may identify targets for anti-tumor therapy. Using patient-derived tumor cells, we created an HNSCC differentiation model in HPV+ tumor cells. Similar to HPV- cells, we observed a loss of malignant characteristics in HPV+ cell cultures in differentiating cell culture conditions including irregular enlarged cell morphology, cell cycle arrest with downregulation of Ki67, and reduced cell viability. Even though cornification was detected in HPV+ tumor cell cultures and HPV+ FFPE tumor tissue sections, cornification was not induced during HPV+ cell differentiation. Instead, RNA-seq and subsequent Gene Ontology analysis showed myocyte-like differentiation with upregulation of markers of myofibril assembly including TPM1, TAGLN, and ACTA1. Immunofluorescence staining of differentiated and undifferentiated primary HPV+ HNSCC cells confirmed an upregulation of these markers and the formation of parallel actin fibers, reminiscent of myoblast-lineage cells. Moreover, multi-marker immunofluorescence analysis of HPV+ tumor tissue sections revealed areas of cells co-expressing the identified markers of myofibril assembly, HPV surrogate marker p16, and stress-associated basal keratinocyte marker KRT17, indicating that the observed myocyte-like differentiation observed in vitro also occurred in human tissue. Normal tissue displayed a co-expression of TPM1, TAGLN, and ACTA1 in differentiating keratinocytes between the basal cell layer and the fully differentiated corneocytes. This shows that the expression of myocyte-lineage markers is reflected in differentiating non-malignant mucosal tissue. Our study suggests that the targeted differentiation of tumor cells might be therapeutically valuable in HPV+ HNSCCs as well.

Citation Format: Sarah Gendreizig, Laura Martinez-Ruiz, Javier Florido, Alba López-Rodríguez, Harkiren Pabla, Frank Brasch, Germaine Escames, Tobias Busche, Holger Sudhoff, Lars U. Scholtz, Ingo Todt, Felix Oppel. Differentiation of human papillomavirus-positive head and neck squamous cell carcinoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5818.
Abstract 5837: Aryl hydrocarbon receptor is critical for enzalutamide-resistant prostate cancer growth
Authors: Chen Chia-Hui , Wu Boyang Jason
Published: March 2024

Therapy resistance is a ubiquitous and major challenge for curing cancer including prostate cancer. As the most prevalent non-skin cancer for men, prostate cancer is responsible for more than 30,000 deaths annually in the U.S. Despite a favorable prognosis at early stages, prostate cancer progressively develop into an incurable castration-resistant stage (CRPC) where prostate cancer grows in a low-androgen environment. Enzalutamide (ENZ) is the first drug approved by FDA for treating CRPC by inhibiting the residual androgen signaling. While ENZ significantly improves overall survival and quality of life, resistance inevitably develops and greatly limits its benefit. To understand ENZ resistance and identify novel therapeutic targets with the hope of overcoming resistance, we performed RNA-seq to analyze mRNA expression profiles from three ENZ-resistant human CRPC cell lines (C4-2BENZR, CWR-R1ENZR and VCaPENZR) and identified the aryl hydrocarbon receptor (AHR) among the 114 commonly upregulated genes. AHR is a ligand-dependent transcription factor that has been shown to drive disease progression in multiple types of cancer. Stable shRNA-mediated knockdown of AHR substantially decreased growth of ENZ-resistant CRPC cells. Our pilot study also showed that AHR knockdown resulted in fewer and smaller CWR-R1ENZR tumors in a xenograft mouse model. To elucidate the underlying mechanism of AHR-mediated cancer growth, gene set enrichment analysis (GSEA) revealed a declining trend of enrichment of the 114 commonly ENZ-upregulated genes among differentially altered genes upon AHR knockdown in ENZ-resistant cells, suggesting that AHR may act as a master regulator of ENZ resistance. Moreover, we found that the Hallmark androgen response gene set is downregulated in AHR-silenced ENZ-resistant cells, implying a role of AHR in sustaining androgen response for ENZ-resistance. Consistently, we performed AHR ChIP-seq and confirmed that AHR bound to promoter regions of several androgen-regulated genes in CWR-R1ENZR cells. In addition, three peroxisome-related Hallmark gene sets are also negatively enriched in AHR-knockdown cells, which provides a rationale for further exploring a potential AHR-dependent connection of peroxisomal function to ferroptosis as a newly emerging mechanism of action for ENZ. In summary, our study suggests that AHR plays a critical role in maintaining ENZ-resistant CRPC growth with the likely involvement of modulating androgen signaling and ferroptosis susceptibility.

Citation Format: Chia-Hui Chen, Boyang Jason Wu. Aryl hydrocarbon receptor is critical for enzalutamide-resistant prostate cancer growth [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 5837.
Abstract 5838: Un-methylation of NUDT21 promotes the development of enzalutamide resistance in prostate cancer by regulation of 3’UTR usage switch
Authors: Lin Shin-Chih (Kenny) , Lin Shih-Chieh
Published: March 2024

Enzalutamide, a second-generation anti-androgen drug, is a new treatment option for castration resistant prostate cancer (CRPC) patient. However, almost all CRPC patients develop drug resistance for enzalutamide after six to twelve months of treatment. According to our current findings, 3'UTR usage switches of RNA transcripts were observed in the prostate cancer specimen after acquiring enzalutamide resistance and nudix hydrolase 21 (NUDT21), an alternative polyadenylation (APA) regulator, was overexpressed in the enzalutamide resistant (EnzaR) cells, suggesting its potential role involved in regulation of 3'UTR usage switch. However, the underlying mechanism of how NUDT21 regulates 3'UTR usage switch during the development of enzalutamide resistance is still unclear. Interestingly, a potential mono-methylation (MME) is identified in NUDT21 protein by us, and it has never been examined before. Thus, we hypothesize that MME of NUDT21 may regulate the specificity of 3'UTR usage switch and involve in the development of EnzaR. To test the idea, a monoclonal antibody recognized NUDT21 MME was generated by us. Moreover, protein arginine methyltransferase 7 (PRMT7) was identified to be responsible for adding MME to NUDT21. In addition, androgen treatment increased both expression levels of NUDT21 MME and PRMT7 while decreased the expression level of NUDT21 total form in LNCaP cells via androgen receptor (AR) dependent manner. Next, co-treatment of enzalutamide and PRMT7 inhibitor leaded to increase of un-MME form of NUDT21 and it greatly enhanced the enzalutamide resistance in LNCaP cells. Importantly, binding profile of NUDT21 total form indeed had 3'UTR usage switch from distal to proximal APA site in COUP-TFII transcript after acquiring enzalutamide resistance, while its MME form attenuated this phenomenon. In addition, expression levels of NUDT21 MME and its total form were shown to conversely express in prostate cancer specimens. Finally, un-MME form of NUDT21 promoted the cancer growth in vitro and in vivo while its MME form did not. Taken together, our results suggest that down-regulation of PRMT7 by enzalutamide may lead to decrease of NUDT21 MME level and contribute to develop enzalutamide resistance by causing the 3'UTR usage switch of NUDT21 downstream transcript.

Citation Format: Shin-Chih (Kenny) Lin, Shih-Chieh Lin. Un-methylation of NUDT21 promotes the development of enzalutamide resistance in prostate cancer by regulation of 3’UTR usage switch [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 5838.
Abstract 5868: Upregulation of HER3 and MET in non-small cell lung cancer cells resistant to EGFR tyrosine kinase inhibitor
Authors: Larsen Margaret , Lyu Hui , Tan CongCong , Wu Yakun , Liu Bolin
Published: March 2024

Introduction: Prior research demonstrates the importance of studying epidermal growth factor receptor (EGFR) activating mutations for better understanding the biology of non-small cell lung cancer (NSCLC), which comprises the majority (~80%) of lung cancers. EGFR-targeted tyrosine kinase inhibitors (TKIs) have been used in the clinic to treat NSCLC with EGFR activating mutations. First and second-generation EGFR-TKIs are effective in NSCLC patients with the most common EGFR mutations (exon 19 deletion (Del19) and exon 21-point mutation (L858R)). A third generation EGFR-TKI, osimertinib (AZD9291), has been developed to target the T790M resistance mutation, but patients are starting to show resistance to this line of therapy as well. Our study aims to elucidate the underlying mechanism(s) of EGFR-TKI resistance in NSCLC cells.

Methods: NSCLC cell lines, including PC-9 and HCC827, which have the Del19 EGFR activating mutation, were utilized for experiments. From the parental cell lines, several cell lines resistant to the EGFR-TKIs were previously established. Cell proliferation (MTS) assays were used to confirm the resistance phenotype of the established cell lines. Western blot assays and RT-qPCR were utilized to determine changes in the expression level of several membrane receptors and their downstream effectors.

Results: Our preliminary analysis showed that both human epidermal growth factor 3 (HER3) and mesenchymal-epithelial transition factor (MET) were upregulated in the EGFR-TKI-resistant cell lines as compared to their parental counterparts. Further studies revealed an increased level of phosphorylated STAT3 (p-STAT3) and ERK1/2 (p-ERK1/2) in the resistant cell lines when compared to the parental cell lines, suggesting the possible involvement of HER3 and/or MET in the activation of downstream signaling pathways. Upregulation of HER3 and MET was found at both the protein and mRNA level.

Conclusion: Based on our initial findings, membrane receptors, including HER3 and MET, could be working together to continue activating downstream signaling pathways to evade the effects of osimertinib, resulting in resistance. Additional work is underway to define the role of HER3 and MET in the NSCLC cells resistant to EGFR-TKIs.

Citation Format: Margaret Larsen, Hui Lyu, CongCong Tan, Yakun Wu, Bolin Liu. Upregulation of HER3 and MET in non-small cell lung cancer cells resistant to EGFR tyrosine kinase inhibitor [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 5868.
Abstract 5878: ZNF397 loss triggers TET2-driven epigenetic rewiring, lineage plasticity, and AR-targeted therapy resistance
Authors: Mu Ping , Xu Yaru , Deng Su
Published: March 2024

Cancer cells exhibit phenotypical plasticity and epigenetic reprogramming, which allows them to evade lineage-dependent targeted treatments by adopting lineage plasticity. The underlying mechanisms by which cancer cells exploit the epigenetic regulatory machinery to acquire lineage plasticity and therapy resistance remain poorly understood. We identified Zinc Finger Protein 397 (ZNF397) as a bona fide co-activator of the androgen receptor (AR), essential for the transcriptional program governing AR-driven luminal lineage. ZNF397 deficiency facilitates the transition of cancer cell from an AR-driven luminal lineage to a Ten-Eleven Translocation 2 (TET2)-driven lineage plastic state, ultimately promoting resistance to therapies inhibiting AR signaling. Intriguingly, our findings indicate that TET2 inhibitor can eliminate the AR targeted therapies resistance in ZNF397-deficient tumors. These insights uncover a novel mechanism through which prostate and breast cancers acquire lineage plasticity via epigenetic rewiring and offer promising implications for clinical interventions designed to overcome therapy resistance dictated by lineage plasticity.

Citation Format: Ping Mu, Yaru Xu, Su Deng. ZNF397 loss triggers TET2-driven epigenetic rewiring, lineage plasticity, and AR-targeted therapy resistance [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 5878.
Abstract 5899: Evaluation of Up284 as a selective proteasome inhibitor for prostate cancer therapy
Authors: Karanam Balasubramanyam , Anchoori Ravi , Chang Yung
Published: March 2024

Recent research into prostate cancer treatment has unveiled a promising contender known as Up284. In laboratory experiments, this compound has exhibited a remarkable preference for targeting prostate cancer cells as opposed to normal cells. Specifically, in vitro cell viability assays using MTT have shown that prostate cancer cells display high sensitivity to Up284 at low nanomolar IC50 values, while primary human prostate epithelial cells and mouse keratinocytes exhibit minimal sensitivity. This establishes a notable therapeutic window between cancerous and non-cancerous cells, with Up284 significantly inhibiting colony formation in PC3 cells. Additional functional assays have confirmed Up284's potential, including the 4UbFL Reporter Gene assay, which has revealed robust, dose-dependent proteasome inhibition. This effect is supported by the accumulation of polyubiquitinated proteins in various prostate cancer cell lines following Up284 treatment, suggesting a distinct mechanism of toxicity compared to bortezomib. Furthermore, Up284 has been found to induce apoptosis in PC3 cells, surpassing the efficacy of bortezomib. Competitive binding assays have shown that Up284 exhibits a stronger binding affinity to the proteasomal receptor RPN13 than the prototype inhibitor RA190B. This is further supported by a Cellular Thermo Stabilization Assay (CETSA), which indicates that Up284 stabilizes RPN13 in cells.

A preliminary in vivo study utilizing the bone metastatic prostate cancer genetically engineered mouse model(BMPC GEMM) model for metastatic prostate adenocarcinoma has demonstrated that Up284 leads to significant tumor regression and increased levels of poly-ubiquitinated proteins in residual tumor tissues. Moreover, when Up284 is conjugated with an E3 ligase ligand, it successfully degrades RPN13, resulting in the death of PC3 cells. Up284 has also shown favorable pharmacokinetics/pharmacodynamics (PK/PD) profiles and safety in animal models. It is well-tolerated in mice and holds promise for oral administration, demonstrating a proteasome-dependent reporter protein stabilization effect superior to ixazomib. Importantly, Up284 has induced tumor regression and improved survival rates in various cancer models, including ovarian and breast cancers.

In conclusion, Up284 emerges as a lead candidate for targeted prostate cancer therapy due to its high specificity, substantial therapeutic index, and potent anti-cancer activity both in vitro and in vivo. Further development and clinical investigation of Up284 are warranted to fully explore its therapeutic potential.

Citation Format: Balasubramanyam Karanam, Ravi Anchoori, Yung Chang. Evaluation of Up284 as a selective proteasome inhibitor for prostate cancer therapy [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 5899.
Abstract 5927: ACBP/DBI inhibition suppresses NASH-induced hepatocarcinogenesis
Authors: Li Sijing , Motiño Omar , Lambertucci Flavia , Maiuri Maria Chiara , Martins Isabelle , Kroemer Guido
Published: March 2024

Background: Non-alcoholic fatty liver disease (NAFLD) or its severe form non-alcoholic steatohepatitis (NASH) is becoming an ever more prevalent risk factor of hepatocellular carcinoma (HCC). Currently, there are no approved drugs for the treatment of NASH. Extracellular ACBP/DBI (Acyl coenzyme A binding protein, also called diazepam-binding inhibitor) acts as an autophagy checkpoint and neutralization of ACBP/DBI prevents NASH. Therefore, we investigated the functional roles, mechanisms, and clinical relevance of ACBP/DBI in HCC.

Methods: ACBP/DBI was blocked by four strategies: an inducible Acbp/Dbi knockout (Acbp-/-, control: Acbp+/+), a constitutive Gabrg2F77I mutation that prevents binding of ACBP/DBI to the receptor (control: WT), induction of ACBP/DBI-specific autoantibodies (induced by KLH-DBI, control: KLH), and monoclonal anti-DBI antibody (control: isotype). Three different types of HCC mouse models, including toxins/diet-based NASH-induced models (western diet plus CCl4), hydrodynamic transfection of oncogenes (Myc+Ctnnb1), and orthotopic transplantation (Hep55.1C) were used in combination with the aforementioned ACBP/DBI inhibition strategies to determine the association of ACBP/DBI and HCC.

Results: ACBP/DBI inhibition attenuates tumorigenesis in mice with NASH, blunts oncogene induced HCC, and reduces the growth of orthotopically transplanted cancers. Mechanistically, ACBP/DBI inhibition retards cell cycle, suppresses cell proliferation, and favors ferroptosis, as determined by RNA-seq data and mass spectrometric metabolomics. CCK-8 proliferation, colony formation, and cell cycle assays performed on Huh-7, HepG2 and Hep55.1C cells demonstrated that ACBP/DBI knockdown reduced cell proliferation and induced G0/G1 arrest. IHC detection of Ki67 and PCNA in liver sections revealed antiproliferative effects of ACBP/DBI inhibition. qRT-PCR demonstrated the ACBP/DBI inhibition-induced upregulation of cell cycle inhibitor genes and downregulation of genes invoded in G0/G1 phase in liver tissues. qRT-PCR and immunoblot confirmed the upregulation of pro-ferroptotic and the downregulation of anti-ferroptotic genes and proteins in liver tissues upon ACBP/DBI inhibition. Primary HCC cell lines from Acbp+/+ and Acbp-/- mice further confirmed the pro-ferroptotic effects of ACBP/DBI inhibition obtained in liver tissues. Acbp-/- cell lines were more sensitivity to RSL3-induced ferroptosis.

Conclusion: ACBP/DBI inhibition constitutes a potential strategy for treating NASH and NASH-induced HCC.

Citation Format: Sijing Li, Omar Motiño, Flavia Lambertucci, Maria Chiara Maiuri, Isabelle Martins, Guido Kroemer. ACBP/DBI inhibition suppresses NASH-induced hepatocarcinogenesis [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 5927.
Abstract 5954: Big data-driven discovery of novel oncogenic fusion genes for anticancer therapy
Authors: Kim Dooho , Park Jong Woo , Kim Jung-Ae , Kim Jeong-Hoon , Park Tae Sub , Park Joonghoon
Published: March 2024

The integration of big data analytics with cancer research is catalyzing a transformative approach in cancer treatment, primarily focusing on the discovery of novel and efficacious anticancer targets. Our study presents an advanced algorithm, specifically crafted to exploit the extensive data available in the field of oncology. We started with the genomic and clinical information of 8,864 patients with 33 different cancers (TCGA). Then we implemented the following algorithm to discover anti-cancer targets by analyzing the clinical significance (cBioPortal), drug development status (Cortellis), and oncogenicity (DepMap) of candidate genes: Candidate genes = {gene | gene ∈ Genes, [Frequency(gene) > 50, Drug(gene) ∈ {'biological testing', 'preclinical stage'}, Association(gene) ≥ 0.4, Publication(gene) ≤ 200] ∨ [Publication(gene) ≥ 200 ∧ Boolean(gene)]}. We employed this algorithm to analyze fusion genes, which represent promising anti-cancer targets known for their potential to elicit substantial clinical responses, but there is a high demand for new ones. We identified four druggable therapeutic targets out of a total of 15,291 fusion genes through the algorithm: frame-shifted FGFR3-TACC3, in-framed DLK1-RPS11, frame-shifted CHP1-RAD51B, and in-framed TBC1D22A-SMYD3. We conducted in vitro validation studies of these fusion genes in NIH3T3 cell lines, and it confirmed that all of the fusion genes not only produce mRNA and protein levels but also induce oncogenic effects on cellular behavior. In the case of FGFR3-TACC3, the introduced fusion gene induced mRNA (p < 0.05) and protein expression (p < 0.05) even when frame-shifted. In addition, the proliferation rate of transformed cells increased more than 4-fold on day 10 (p < 0.0001) and colony formation increased more than 5-fold on day 21 (p < 0.01) compared to wild-type cells. These results demonstrate the tumorigenicity of the fusion genes. Taken together, this study emphasizes the crucial role of big data in propelling oncology research forward. The algorithm we developed can offer a new pathway for creating innovative cancer treatment, marking a significant advancement in the realm of personalized cancer therapy.

Citation Format: Dooho Kim, Jong Woo Park, Jung-Ae Kim, Jeong-Hoon Kim, Tae Sub Park, Joonghoon Park. Big data-driven discovery of novel oncogenic fusion genes for anticancer therapy [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 5954.
Abstract 5995: How FDA-approved drug, Aprepitant, induces immunogenic death of cancer cells
Authors: Dai Xinyi , Zhu Junyao , Perry Sofia , Jiang Qianjin , Shapiro David J.
Published: March 2024

Aprepitant is a long-standing FDA approved anti-nausea drug, recently re-purposed as an early-stage anticancer agent; how aprepitant kills cancer cells was not well studied. We find that aprepitant kills human and mouse cancer cells by hyperactivating the stress response pathway, the anticipatory unfolded protein response (a-UPR), thereby inducing immune cell activating necrotic cell death. Aprepitant is a small molecule neurokinin-1 receptor (NK-1R) antagonist widely used to prevent nausea and vomiting in cancer patients undergoing chemotherapy. Recently aprepitant has shown promise in mouse xenograft studies of colon, lung and pancreatic cancer and melanoma. Since aprepitant was thought to trigger release of calcium stored in the lumen of the endoplasmic reticulum, the step that we showed triggers hyperactivation of the a-UPR by ErSO family anticancer agents, we explored the role of the a-UPR in aprepitant action. Aprepitatnt robustly activates the PERK arm of the UPR increasing p-PERK and peIF2α, inhibiting protein synthesis. Notably, aprepitant treatment results in ATP depletion and activation of AMPK. Aprepitant induced rapid cell death was not blocked by apoptosis inhibitors or necroptosis inhibitors. In both standard 2-dimensional cell culture and 3-dimensional organoid culture aprepitant-treated breast cancer cells displayed typical features of necrotic cell death, including cell swelling, membrane rupture, and cytoplasmic vacuolization. Cell death by necrosis and membrane rupture leads to release of immune cell activating cell contents termed damage-associated molecular patterns (DAMPs). Aprepitant treatment induces release of the classic DAMPs, HMGB1 and ATP and medium from aprepitant-treated breast cancer cells enhances migration of differentiated human THP-1 macrophage. Thus aprepitant and other necrosis inducing therapies elicit immunogenic cell death (ICD) and may have the potential to enhance adjuvant immunotherapy. Genome-wide CRISPR screens with negative selection against aprepitant and other studies are being used to explore the pathways of aprepitant induced cell death and evaluate its therapeutic efficacy. Since FDA-approved aprepitant has been widely used for many years, identifying its pathway of action will both accelerate its clinical transition as an anticancer agent and help identify patients whose genetic profiles make them most likely to benefit from aprepitant therapy.

Citation Format: Xinyi Dai, Junyao Zhu, Sofia Perry, Qianjin Jiang, David J. Shapiro. How FDA-approved drug, Aprepitant, induces immunogenic death of cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5995.
Abstract 6028: Preferential tumor-to-normal tissue biodistribution and single-dose efficacy with ABD147, a DLL3-targeted engineered antibody-based radiotherapeutic, in preclinical small cell lung cancer models
Authors: Kulic Iva , Melese Etienne S. , Cummins Emma , Mandel Alex , Viswas Raja , Abrams Michael , Judge Adam
Published: March 2024

Targeted radiotherapies represent an emerging treatment modality for aggressive cancers with limited treatment options, such as small cell lung cancer (SCLC). ABD147 is a Delta Ligand 3 (DLL3)-targeted antibody conjugate designed to carry and deliver cytotoxic radioactive isotopes to DLL3-expressing tumor cells. DLL3 is commonly expressed on the cell surface of neuroendocrine cancer cells, including SCLC, but has limited and predominantly intracellular expression in non-malignant tissues. The ABD147 antibody specifically binds human DLL3 with high affinity and is internalized by DLL3-expressing cancer cells. To minimize radiation exposure to normal tissue, ABD147 has been engineered to clear quickly from the blood compartment. Using indium-111 to determine ABD147 pharmacokinetics and biodistribution in mice, we demonstrate rapid blood and normal tissue clearance of 111In-ABD147, as designed, following a single intravenous dose administration. However, 111In-ABD147 retains high tumor accumulation (activity concentration of up to 30% ID/g) in xenograft mouse models of SCLC despite low DLL3 surface antigen expression on tumor cells (≤ 3000 copies). 111In-ABD147 shows a favorable tumor-to-normal tissue distribution with predominant liver clearance. Following ABD147 therapeutic radioisotope delivery of actinium-225 or lutetium-177 (225Ac-ABD147, 177Lu-ABD147), we demonstrate single-dose tumor regression and dose-dependent sustained anti-tumor efficacy, corresponding to an extension of survival out to 84 days in multiple SCLC xenograft models. In summary, ABD147 can preferentially deliver radionuclides to DLL3-expressing tumor tissue while substantially reducing the systemic radioactive exposure typical of conventional IgG radioconjugates. Following promising results in preclinical models, including potent anti-tumor activity, 225Ac-ABD147 is now progressing into clinical development.

Citation Format: Iva Kulic, Etienne S. Melese, Emma Cummins, Alex Mandel, Raja Viswas, Michael Abrams, Adam Judge. Preferential tumor-to-normal tissue biodistribution and single-dose efficacy with ABD147, a DLL3-targeted engineered antibody-based radiotherapeutic, in preclinical small cell lung cancer models [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 6028.
Abstract 6059: Discovery of ETS-007, a first-in-class degrader targeting N-terminal domain of androgen receptor derived from AR liquid-liquid phase separation inhibitor
Authors: Li Yingjie , Fei Mingyue , Miao Yingke , Feng Lijian , Fan Xiaofei , Li Jinping , Chen Yaozhong , Xu Ming , Cui Wenqi , Zheng Qiangang , Zhu Jidong
Published: March 2024

Patients with advanced prostate cancer inevitably acquire resistance to anti-androgen therapies, and progress to lethal castration-resistant prostate cancer (CRPC). The resistance mechanisms involve AR gene amplification and overexpression, constitutively active ligand-independent splice variants such as AR-V7, and the mutations in the AR ligand-binding domain (LBD). Our previous study has shown that the AR N-terminal domain (NTD) is responsible for AR liquid-liquid phase separation (LLPS) capability, which is essential for AR/AR-V7 transcriptional activity. We conducted a compound library screening using an AR LLPS phenotypic assay and identified ET0516 as a hit to specifically inhibit AR LLPS and its downstream gene expression, indicating that inhibition of AR. LLPS through targeting its NTD is a feasible approach to overcome the resistance to current anti-androgens therapy. Here we report the identification of a novel AR degrader, ETS-007 which is originated and evolved from internal LLPS phenotypic screening, that effectively degrades both AR and AR-V7 proteins with DC50 of single-digit nM by inducing a protein-protein interaction between AR NTD and an E3 ligase complex. ETS-007 induced AR and AR-V7 polyubiquitination, followed by degradation which could be blocked by the protease inhibitor MG132. ETS-007 significantly inhibited cell proliferation in AR and/or AR-V7 positive cell lines, e.g. LNCaP and 22RV1, and downregulated the androgen responsive genes such as PSA and TMPRSS2. Compared with enzalutamide and ARV-110, ETS-007 could block transcriptional activities of AR-V7, and AR mutants in luciferase report assay. Oral administration of ETS-007 in an enzalutamide-resistant 22RV1 xenograft model led to intratumoral AR-V7 degradation and concomitant decrease in PSA protein levels, resulting in a remarkable tumor regression. Taken together, our findings provide preclinical evidence that ETS-007 as a potent AR-NTD degrader derived from our LLPS platform can effectively block the transcriptional activities of both AR and AR-V7 for the treatment of metastatic CRPC.

Citation Format: Yingjie Li, Mingyue Fei, Yingke Miao, Lijian Feng, Xiaofei Fan, Jinping Li, Yaozhong Chen, Ming Xu, Wenqi Cui, Qiangang Zheng, Jidong Zhu. Discovery of ETS-007, a first-in-class degrader targeting N-terminal domain of androgen receptor derived from AR liquid-liquid phase separation inhibitor [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 6059.
Abstract 6150: MMP14 and MKLN1 as colorectal cancer susceptibility genes and a drug repurposing candidate from genome-wide association study in South Korea
Authors: Yun Dabin , Yang Jung-Ho , Kweon Sun-Seong , Sim Jin-ah , Kim Minjung , Park Ji Won , Jeong Seung Yong , Shin Aesun , Song Nan
Published: March 2024

Background: One of the major topics about colorectal cancer (CRC) is to find susceptible genes. Furthermore, functional interpretation of post-GWAS analysis gains attention and various approaches to find drug-repurposing candidates are used in cancer research. Our study aims to identify susceptible genes for CRC and provide drug-repurposing candidates.

Methods: CRC patients in Seoul National University Hospital with prospective follow-up were recruited. From blood-derived DNA, genome-wide SNPs were genotyped using the Korea Biobank Array and 409,063 SNPs were extracted. SNP-based logistic regression model was fit for the event of CRC estimating beta values. Furthermore, post-GWAS analysis was conducted using regulatory function, multiple annotation and gene expression database. Drug-repurposing candidate was identified through the pre-trained deep neural network with susceptible genes.

Results: We used 500 participants of CRC cases and 1,500 participants of healthy controls. For GWAS, statistically significant associations were mapped to MKLN1, MMP14, PTPN14 and MKL2 genes. For post-GWAS analysis, strong associations were found for MKLN1 (rs75170436, 7q32.3, Beta=-0.90, P-value=5.90×10-13) and MMP14 (rs3751489, 14q11.2, Beta=-1.91, P-value=2.31×10-12). From the drug-repurposing analysis, PPARδ/β agonist (GW0742; Binding score=3.79(MKLN1), 12.06(MMP14)) was identified for both genes with the highest score.

Conclusions: We revealed MKLN1 and MMP14 genes as susceptible genes associated with CRC development. Additionally, we identified PPARδ/β agonist (GW0742) as a drug-repurposing candidate for the treatment of CRC. These findings can promote the understanding of CRC development and provide a novel therapeutic candidate for CRC patients in the future.

Citation Format: Dabin Yun, Jung-Ho Yang, Sun-Seong Kweon, Jin-ah Sim, Minjung Kim, Ji Won Park, Seung Yong Jeong, Aesun Shin, Nan Song. MMP14 and MKLN1 as colorectal cancer susceptibility genes and a drug repurposing candidate from genome-wide association study in South Korea [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 6150.
Abstract 6205: Identify drugs for metastatic castration-resistance prostate cancer (mCRPC) patients with high glycolytic activity through in silico approach
Authors: Su Mei-Chi , Lee Adam M. , Huang R. Stephanie
Published: March 2024

Prostate cancer (PC) remains a prominent cause of cancer-related mortality among men in the United States. A significant factor contributing to the mortality of PC patients is the development of resistance to second-generation antiandrogen therapies, particularly androgen receptor-signaling inhibitors (ARSI), which is pronounced in patients with late-stage PC, metastatic castration-resistance prostate cancer (mCRPC). Therefore, there is an urgent need for novel therapeutics beyond AR signaling inhibition for patients with mCRPC. One of the key drivers of resistance to ARSI and a critical feature of CRPC is cancer metabolism reprogramming to elevated glycolysis. However, the current research on finding drugs to impede high-glycolytic tumor growth is hurdled by a resistance raised from metabolic plasticity. The aim of this research is to quickly repurpose existing drugs for inhibiting high-glycolytic mCRPC growth while proactively circumstancing resistance from metabolic plasticity through computational approaches. To do this, we imputed a large number of drug responses in patients with mCRPC using a computational algorithm (OncoPredict), identified drugs that were projected to show higher sensitivity in high-glycolytic tumors, and performed in vitro validation. Furthermore, to maximize drug efficacy, we identified biomarkers for drug candidates. By implementing this computational pipeline, we identified a number of drugs with various mechanisms of action that show higher efficacy in mCRPC with high glycolysis. Furthermore, we successfully validated the efficacy of these nominated drug candidates including an anti-parasitic agent, an HSP90 inhibitor, and a CDK inhibitor. These drug candidates exhibited superior tumor growth inhibition in in vitro models of high glycolysis-induced advanced PC. In conclusion, this study introduces an innovative in silico approach to unveil the existing drugs’ unknown potential for the treatment of patients with mCRPC. Our findings hold promise for development of effective therapeutics for combating this challenging disease.

Citation Format: Mei-Chi Su, Adam M. Lee, R. Stephanie Huang. Identify drugs for metastatic castration-resistance prostate cancer (mCRPC) patients with high glycolytic activity through in silico approach [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 6205.
Abstract 6226: Identifying nested spatial units as a conserved organizing principle of the spatial tumor microenvironment
Authors: Behera Vivek , Giba Hannah , Doran Benjamin A. , Kline Justin P. , Raman Arjun S.
Published: March 2024

Heterogeneity of therapeutic response amongst cancer patients has a profound impact on cancer-related mortality. It has been widely hypothesized that diversity in clinical outcomes is driven by variability in tumor biology at scales ranging from inter-patient to inter-cellular. Indeed, the advent of technologies describing the tumor microenvironment (TME) at cellular resolution has demonstrated that TME organization is heterogeneous with respect to intra-tumor spatial location, body tumor location (primary vs metastatic), patient, and tumor type. However, the organizing principles that govern TME heterogeneity remain unclear. Without such organizing principles, it remains an arduous task to link descriptions of tumor biology heterogeneity to clinical outcomes in a mechanistically explainable manner. Through the application of network statistical inference models to spatial transcriptomic data, we have identified that nested spatial units (NSUs) are a core organizing principle of the TME. We find that NSUs are widely conserved across 96 patient biopsies of 14 distinct tumor types and 3 body locations (primary, abdominal metastases, brain metastases). Moreover, NSUs represent a transferrable organizing blueprint that allows for the spatial location of individual spots (5-50 cells) in a tumor biopsy to be predicted by the NSUs of a secondary, unrelated biopsy (Pearson correlation of spot-spot distance: 0.04 - 0.71, median 0.25). By using NSUs as the organizing unit of comparison, we identify variation in gene expression, biological pathways, and multicellular structures occurring across tumors in a distance-dependent manner. In summary, NSUs provide a foundation for the comparative analysis of tumor spatial biology and a path by which spatial biology can be mechanistically linked to patient outcomes.

Citation Format: Vivek Behera, Hannah Giba, Benjamin A. Doran, Justin P. Kline, Arjun S. Raman. Identifying nested spatial units as a conserved organizing principle of the spatial tumor microenvironment [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 6226.
Abstract 6237: Large-scale imputation models for multi-ancestry proteome-wide association analysis
Authors: Wu Chong , Zhang Zichen , Yang Xiaochen , Zhao Bingxin
Published: March 2024

Proteome-wide association studies (PWAS) decode the intricate proteomic landscape of biological mechanisms for complex diseases. Traditional PWAS model training relies heavily on individual-level reference proteomes, thereby restricting its capacity to harness the emerging summary-level protein quantitative trait loci (pQTL) data in the public domain. Here we introduced a novel framework to train PWAS models directly from pQTL summary statistics. By leveraging extensive pQTL data from the UK Biobank, deCODE, and ARIC studies, we applied our approach to train large-scale European PWAS models (total n = 88,838 subjects). Furthermore, we developed PWAS models tailored for Asian and African ancestries by integrating multi-ancestry summary and individual-level data resources (total n = 914 for Asian and 3,042 for African ancestries). We validated the performance of our PWAS models through a systematic multi-ancestry analysis of over 700 phenotypes across five major genetic data resources. Specifically, we identified several novel and well-known genes for various cancers; we highlighted eight genes associated with six cancer traits across all three PWAS model cohorts, including CTSF, RSPO3, CRTAM, LAYN, CHRDL2, DPEP1, NFASC, and NAAA. Our results bridge the gap between genomics and proteomics for drug discovery, highlighting novel protein-phenotype links and their transferability across diverse ancestries. The developed PWAS models and data resources are freely available at www.gcbhub.org.

Citation Format: Chong Wu, Zichen Zhang, Xiaochen Yang, Bingxin Zhao. Large-scale imputation models for multi-ancestry proteome-wide association 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 6237.
Abstract 6246: De novo mutation discovery in a mouse model and a human patient sample of non-Hodgkin's lymphoma
Authors: Sullivan Delaney K. , Albinali Eissa , Boffelli Mayuko , Pachter Lior
Published: March 2024

Cancer encompasses many different diseases, all typically involving an accumulation of genetic alterations. However, despite the genomic complexity of this group of diseases, cancer genomic studies typically rely on sequence alignment to a "reference genome" prior to analysis. Such approaches can provide gene expression quantification of known, annotated genes. However, they miss the detection of fusion genes, novel transcripts, virus insertions, and other genetic insults that may be present in cancer beyond an altered gene expression profile. Here, we develop a workflow for de novo identification and quantification of "outside of reference genome" genetic aberrations. This workflow leverages klue, a method we developed that is based on the compact de Bruijn graph, which can extract sequences uniquely found in a "tumor" sample but not in a "normal" control sample from genomic sequencing data. We first applied this method to an RNA-seq experiment from the EμSRα-tTA/TetO-MYC mouse model, which is a MYC-driven autochthonous transgenic mouse model of T-cell acute lymphoblastic lymphoma (T-ALL). We extracted k-mer contigs present in the mouse tumor samples but are present neither in the spleens of wild-type mice of the same genetic background nor in the standard mouse reference genome assembly. We then mapped RNA-seq reads from the T-ALL mouse tumor samples to these contigs. The contigs with the highest number of mapped reads (i.e. the highest counts) were run through BLAST to determine their identities. The mapped contigs with the highest counts were the tTA transgenic element sequence and the human MYC transgene. This result showcases this workflow's success in isolating and quantifying "reference-absent” tumor-unique sequences. Next, we applied klue to whole genome sequencing (WGS), whole exome sequencing (WES), and RNA-seq data from a patient with B-cell follicular lymphoma (with matched normal specimen) from the Texas Cancer Research Biobank, as this data is unrestricted open access. Tumor-unique contigs in sequencing reads were extracted and analyzed with BLAST and BLAT. In one case, a nonsynonymous point mutation in the SPI1 (also known as PU.1) oncogene was found. The sequencing reads from the tumor sample showed both the "normal variant" of SPI1 as well as the mutant SPI1:H268P, suggesting a heterozygous mutation. Altogether, these results suggest that the idea of first identifying tumor-unique sequences then doing post hoc analysis of those sequences is a viable approach for de novo mutation discovery in cancer genomics.

Citation Format: Delaney K. Sullivan, Eissa Albinali, Mayuko Boffelli, Lior Pachter. De novo mutation discovery in a mouse model and a human patient sample of non-Hodgkin's lymphoma [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 6246.
Abstract 6256: Prevalence of BRCA1 and BRCA2 proteins in breast cancer in a nigerian population and their relationship with different breast cancer morphological variants
Authors: Raphael Solomon , Oluwasesan Abdul
Published: March 2024

Background: Breast cancer is the commonest site specific cancer in women and a leading cause of cancer death among women in Nigeria and globally. The trend in Nigeria and Africa is that breast cancers are seen in younger age groups, are of higher grades and follow an aggressive course. It has been suggested that this may largely be due to mutation in BRCA genes with the attendant alteration in function of its proteins. This study aimed at determining the prevalence of BRCA1 and BRCA2 proteins in breast cancers seen in our environment as well as to see any association between these proteins and different morphological variants.

Materials and Methods: A descriptive study using tissue blocks of all histologically diagnosed breast cancer in our department between 2013 and 2017. Fresh sections were recut for histological grading and immunohistochemistry. Proteintech BRCA1 and BRCA2 polyclonal antibodies and detection kit were used.

Results: One hundred and thirty (130) cases met the inclusion criteria for this study. The mean (SD) age of the patients was 44.8 (10.3) years with ages ranging from 26 to 79 years. There were more cases of breast cancer (73.1%) seen before 50 years. Two (2) Male Breast Cancer (MBC) cases were seen, giving the female to male ratio of 64:1. The commonest morphological variant encountered was Invasive Carcinoma, No Special Type at 84.6% of cases. This was followed by invasive medullary (7.8%). The least common variant was papillary cancer at 0.8%. The tumors seen were mostly grade 3 (71.2%), followed by grade 2 at 22.7% and the least was grade 1 at 6.1%. Positivity for BRCA1 and BRCA2 proteins was seen in 27.7% and 30.0% of cases respectively. One of the MBC showed reactivity for BRCA1 protein. No significant relationship was seen between BRCA 1/2 proteins expression and age or breast cancer histotypes.

Conclusion: BRCA 1 and 2 proteins are an important risk factor for breast cancers seen in this environment. However, there is no association with age distribution and morphological variants of the breast cancer in our population.

Citation Format: Solomon Raphael, Abdul Oluwasesan. Prevalence of BRCA1 and BRCA2 proteins in breast cancer in a nigerian population and their relationship with different breast cancer morphological variants [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 6256.