bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4356: An isoform-resolution transcriptomic atlas of colorectal cancer from long-read single-cell sequencing
Authors: Li Zhongxiao , Zhang Bin , Chan Jia Jia , Tabatabaeian Hossein , Tong Qing Yun , Chew Xiao Hong , Fan Xiaonan , Chan Charlene , Driguez Patrick , Cheong Faith , Wang Shi , Siew Bei En , Tan Ian Jse-Wei , Lee Kai-Yin , Lieske Bettina , Cheong Wai-Kit , Kappei Dennis , Tan Ker-Kan , Gao Xin , Tay Yvonne
Published: March 2024

Colorectal cancer (CRC), a complex and molecularly heterogenous disease that lacks robust predictive markers and targeted therapies, is the second leading cause of cancer death worldwide. In recent years, technological advances in short-read single-cell RNA sequencing (scRNA-seq) have been instrumental in deciphering tumor cell heterogeneities. However, most studies have focused on gene-level expression quantification without considering alterations in transcript structures arising from widespread alternative end processing and/or splicing which are frequently dysregulated in cancer. Here, we combined short- and long-read scRNA-seq of CRC patient samples to build the first isoform-resolution CRC transcriptomic atlas. We identified 394 dysregulated transcript structures in tumor epithelial cells, including 299 derived from the coupling of multiple alternative splicing events. Additionally, we characterized genes and isoforms associated with different colon epithelial lineages and tumor cell subpopulations exhibiting varying levels of stemness and differentiation, as well as their distinct prognostic implications. Finally, we built an algorithm by integrating mass spectrometry data and novel peptides derived from predicted open reading frames of recurrent tumor-specific transcripts to curate a panel of recurring neoepitopes. Overall, this study unveils the transcriptomic landscape of CRC and may drive the identification of neoantigens based on full-length transcriptomic atlases to aid future development of more universal neoantigen-based cancer vaccines.

Citation Format: Zhongxiao Li, Bin Zhang, Jia Jia Chan, Hossein Tabatabaeian, Qing Yun Tong, Xiao Hong Chew, Xiaonan Fan, Charlene Chan, Patrick Driguez, Faith Cheong, Shi Wang, Bei En Siew, Ian Jse-Wei Tan, Kai-Yin Lee, Bettina Lieske, Wai-Kit Cheong, Dennis Kappei, Ker-Kan Tan, Xin Gao, Yvonne Tay. An isoform-resolution transcriptomic atlas of colorectal cancer from long-read single-cell sequencing [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 4356.
Abstract 4429: Plasma metabolic profiles in association with subsequent risk of colorectal cancer in the UK Biobank cohort
Authors: Yuan Fangcheng , Jia Guochong , Wen Wanqing , Zheng Wei
Published: March 2024

Background: Dysregulation of metabolic processes contributes to colorectal cancer (CRC) etiology. We aimed to comprehensively evaluate the prospective associations between pre-diagnostic metabolic biomarkers and CRC risk in 230,420 UK Biobank participants.

Methods: A total of 249 metabolic biomarkers were measured by nuclear magnetic resonance spectroscopy from baseline plasma samples. Cox proportional hazard models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for the associations of metabolic biomarkers with CRC risk after adjusting for potential confounders. Subgroup analyses were performed by sex and CRC subsites (i.e., proximal colon, distal colon, rectum). We also conducted factor analyses to identify latent factors and examined their associations with CRC risk.

Results: During a median follow-up time of 9.7 years, 2,410 incident primary CRC cases were identified after excluding participants diagnosed with CRC within two years after blood collection. After correcting for multiple testing, 50 metabolic biomarkers, including lipids and lipoproteins, fatty acids, ketone bodies, and inflammation, were significantly associated with incident CRC risk. No statistically significant differences were observed for the biomarker-CRC associations by sex and CRC subsite. In the sensitivity analysis, excluding cholesterol-lowering medication users did not alter the main findings. In factor analyses, we identified a significant association of CRC risk (HR = 1.08; 95% CI = 1.04-1.13; P-value = 6.89×10-5) with a metabolite pattern which was positively correlated with triglycerides and inversely correlated with relative concentrations of omega-6 fatty acids and polyunsaturated fatty acids.

Conclusion: We identified multiple metabolic biomarkers and a metabolite pattern associated with CRC risk in a large prospective cohort. These findings suggest lipid metabolism may contribute to carcinogenesis of the colorectum.

Citation Format: Fangcheng Yuan, Guochong Jia, Wanqing Wen, Wei Zheng. Plasma metabolic profiles in association with subsequent risk of colorectal cancer in the UK Biobank cohort [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 4429.
Abstract 4487: Simple modifications of 3-HPT for improved in-vivo activtiy
Authors: Kern Ryan E. , Huang Susanna , Arunsi Uche , Oyelere Adegboyega
Published: March 2024

One of the key targets in the treatment of castration resistant prostate cancer is HDAC6. HDAC6 removes acetyl groups from Heat shock protein 90 (HSP90), which is a protein chaperone that folds the androgen receptor. By inhibiting HDAC6 it is possible to prevent the expression of mutated androgen receptors, that are no longer responsive to androgen deprivation therapy, treating castration resistant prostate cancer. The Oyelere lab has previously demonstrated that 3-Hydroxypyridin-2-thione (3-HPT) can serve as a scaffold for HDAC6 inhibitors. While the unaltered 3-HPT has been shown on its own to inhibit HDAC6 in enzyme specific assays. The unaltered 3-HPT had no effect in whole cell assays. This work investigated simple modification of the 3-HPT scaffold to improve the in-vivo activity of 3-HPT. This work is an extension of work previously done in the Oyelere lab. The aim of this work is to apply simple modifications to the 3-HPT scaffold to improve the in-vitro activity. Previously 3-HPT was shown on its own to inhibit HDAC6 with an IC50 of 681nM but have no effect on cell assays. The hypothesis was that by converting the secondary amine into a tertiary amine the pharmacokinetic-properties of 3-HPT allowing can be improved focusing on cellular entry. The specific modification was the addition of alkanes and fluorinated alkanes at the secondary amine. This addition should improve the charge of the compounds improving the invitro activity. Based on molecular docking studies using Autodock vina, the introduction of fluorines improves the binding to HDAC6 by interacting with a hydrophilic pocket near the zinc ion. The preliminary in-vivo results in LnCAP and DU145 cells demonstrate that the addition of fluorinated alkanes has substantially improved the IC50 compared to the base 3-HPT compound. The base 3-HPT compound has an IC50 of greater than 100µM while the compounds with fluorinated alkanes have IC50 values in the range of 2-15µM. this data indicates improved drug likeness.

Preliminary IC50 values of compounds in prostate cancer cell lines Compound Name LNCaPIC50 (µM) DU145IC50 (µM) Vero IC50 (µM) SH-1-78 >100 >100 >100 SH-1-94 2.50 19.29 22.53 RK-1-187 96.95 95.45 88.57 SH-1-110 1.27 21.47 17.41 RK-2-16 2.09 62.86 18.76 RK-2-17 >100 >100 >100 RK-2-64 78.36 >100 76.45 RK-2-67 14.19 26.95 11.38

Citation Format: Ryan E. Kern, Susanna Huang, Uche Arunsi, Adegboyega Oyelere. Simple modifications of 3-HPT for improved in-vivo activtiy [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 4487.
Abstract 4506: Discovery of potent, highly selective and orally efficacious SMARCA2 degraders
Authors: Leng Lingying , Yang Lin , Tu Wenbin , Rej Rohan , Allu Srinivasa Rao , Huang Liyue , Jiang Wei , Wang Yu , Stuckey Jeanne , Sarkari Farzad R , Wang Meilin , Wang Lu , Wen Bo , Sun Duxin , Wang Shaomeng
Published: March 2024

In human non-small cell lung cancer, melanoma and other types of human cancers, the mammalian SWItch/Sucrose Non-Fermentable (SWI/SNF) helicase SMARCA4 is frequently mutated, which leads to inactivation of its functions. SMARCA2, a close homologous protein of SMARCA4, is an attractive synthetic lethality target for human cancers with SMARCA4 deficiency. Herein, we report the discovery and biological evaluation of potent, highly selective, orally efficacious SMARCA2 PROTAC degraders exemplified by UM-SMD-8801. UM-SMD-8801 has DC50 <10 nM and Dmax >90% against SMARCA2 and >1,000-fold degradation selectivity over SMARCA4. Consistently, UM-SMD-8801 potently inhibits cell growth in SMARCA4 mutated cancer cell lines with low nanomolar IC50 values and shows >100-fold weaker activity in SMARCA4 wild-type cancer cell lines. UM-SMD-8801 has a good overall pharmacokinetic profile and an excellent oral bioavailability in mice. Oral administration of UM-SMD-8801 is highly effective in reducing SMARCA2 protein by >90% in tumor tissues in mice, while having minimal effect on SMARCA4 protein. UM-SMD-8801 represents a very promising SMARCA2 degrader for extensive evaluation as a potential new therapy for the treatment of SMARCA4-deficient human cancers.

Citation Format: Lingying Leng, Lin Yang, Wenbin Tu, Rohan Rej, Srinivasa Rao Allu, Liyue Huang, Wei Jiang, Yu Wang, Jeanne Stuckey, Farzad R Sarkari, Meilin Wang, Lu Wang, Bo Wen, Duxin Sun, Shaomeng Wang. Discovery of potent, highly selective and orally efficacious SMARCA2 degraders [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 4506.
Abstract 4517: Novel chemical degraders targeting NSD2 in head and neck squamous cell carcinoma (HNSCC)
Authors: Ismail Amr , Roshchina Ekaterina , Topchu Iuliia , Schiltz Gary , Boumber Yanis
Published: March 2024

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. Despite advances in treatments and significant efficacy of immunotherapy drugs in HNSCC, no effective targeted therapies have been approved in this disease yet. NSD2 is a histone lysine methyltransferase, which is overexpressed in HNSCC and is implicated in tumor growth, cell cycle regulation, epithelial-mesenchymal transition (EMT) and metastasis not only in HNSCC, but also in many other solid tumors. Development of inhibitors to the catalytic activity of NSD2 has been rather limited to date, which necessitates an alternative approach. To target NSD2, we have recently developed a series of novel proteolysis targeting chimeras (PROTACs), which chemically degrade NSD2 utilizing native cellular machinery - ubiquitin-proteasome system - with VHL as an E3 ligase. A series of >40 compounds were tested in HNSCC cell lines (JHU-011 and FaDu) and NSD2-dependent multiple myeloma cell line (KMS11) for degradation activity against NSD2 protein, and H3K36me2 chromatin mark reduction, using Western blot. We also tested their anti-proliferative activity in cell viability assay (CTB) and clonogenic assay. Compounds NUCC-0227381, NUCC-0227384, NUCC-0227414 and NUCC-0227383 show promising results by reducing NSD2 and H3K36me2 levels. NUCC-0227383 compound was highly promising, as it was the most potent in reducing NSD2/K36me2 levels without affecting NSD1/NSD3 levels and had profound effects on HNSCC cell growth. Lead compound NUCC-0227383 was chosen for further testing and in preliminary testing, showed a dose-dependent, VHL-mediated, and proteasome dependent function. Proteomics analysis, testing for specificity of NUCC-0227383 against a panel of histone methyltransferases, and in vivo testing of this promising compound against HNSCC is planned.

Citation Format: Amr Ismail, Ekaterina Roshchina, Iuliia Topchu, Gary Schiltz, Yanis Boumber. Novel chemical degraders targeting NSD2 in head and neck squamous cell carcinoma (HNSCC) [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 4517.
Abstract 4550: Synergistic combinations of lurbinectedin with ONC212 in pancreatic cancer
Authors: Tummala Tej , Uruchurtu Ashley S. Sevilla , Liguori Nicholas R. , Abbas E. , Azzoli Christopher G. , El-Deiry Wafik S.
Published: March 2024

Pancreatic cancer is a devastating disease with a poor five-year survival rate of approximately 12%. Given the poor prognosis of the disease, there is urgent need for novel therapeutic regimens. Lurbinectedin is chemotherapeutic compound that stalls and degrades RNA Polymerase II after binding to guanine-rich sequences in the minor groove of DNA. This stalls transcription machinery and leads to single- and double- stranded breaks in DNA and subsequent apoptosis. Our group recently described lurbinectedin’s potency as both a single agent and combinatorial agent with irinotecan and 5-fluorouracil in pancreatic cancer cell lines. We also recently discovered a synergistic interaction between lurbinectedin and ONC201/TIC10, a novel compound that induces the TRAIL apoptotic pathway, in small cell lung cancer cell lines. Synergy was accompanied by an activation of p-Chk1 and the integrated stress response. We now demonstrate a synergistic combination of lurbinectedin and ONC212, an imipridone and chemical derivative of ONC201, results in highly efficient killing of pancreatic tumor cells at sub-nanomolar concentrations of lurbinectedin and sub-micromolar concentrations of ONC212. We hypothesize that the integrated stress response underlies lurbinectedin and ONC212 synergy. We further hypothesize a combination of lurbinectedin and ONC212 will sensitize the tumor cells to CD8+ T-cell killing, which will be examined via co-culture assays. Our results are developing insights into a novel combinatorial therapeutic regimen while investigating the molecular mechanisms underlying synergism.

Citation Format: Tej Tummala, Ashley S. Sevilla Uruchurtu, Nicholas R. Liguori, E. Abbas, Christopher G. Azzoli, Wafik S. El-Deiry. Synergistic combinations of lurbinectedin with ONC212 in pancreatic 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 4550.
Abstract 4559: SMAD3 mediates oxaliplatin resistance in esophageal adenocarcinoma
Authors: Ballout Farah , Lu Heng , Bhat Nadeem , Chen Lei , Peng Dunfa , Chen Zheng , Zaika Alexander , McDonald Oliver , El-Rifai Wael
Published: March 2024

Background: Resistance to conventional treatments is a significant barrier to esophageal adenocarcinoma (EAC) therapy. TGF-β signaling appears to be important for EAC tumorigenesis; however, its role in EAC chemoresistance remains understudied. This study investigates the role of SMAD3 in EAC resistance to the frontline chemotherapeutic drug oxaliplatin.

Methods: Publicly available datasets were analyzed to determine SMAD3 expression in EAC versus normal samples. Western blot, quantitative real-time polymerase chain reaction, immunofluorescence staining, and flow cytometric analyses were utilized to validate bioinformatic results. Human EAC cell lines (OE33 and OE19) were treated with pharmacologic inhibitors or transfected with small interfering RNA and assessed for DNA damage and apoptotic cell death. Patient-derived organoids and patient-derived xenograft models of EAC were used to confirm our findings in vivo.

Results: SMAD3 was significantly upregulated in EAC versus normal tissue samples. Total and phosphorylated SMAD3 protein levels were upregulated in EAC tissues accompanied by increased expression of several genes regulated by SMAD3. Notably, oxaliplatin-resistant EAC cells exhibited overexpression of SMAD3. Chemotherapy non-responding patients showed enrichment of SMAD3 gene expression when compared to responders in the clinical dataset GSE165252. Knockdown or inhibition of SMAD3 hindered DNA repair and sensitized EAC cells to oxaliplatin treatment in vitro and in vivo. Mechanistically, SMAD3 promoted ATM phosphorylation by interacting with protein phosphatase 2A (PP2A) and sequentially inhibiting the binding of PP2A to ATM.

Conclusion: Our results reveal a pivotal role for SMAD3 in mediating oxaliplatin resistance in EAC and thus hold a significant potential in guiding future drug development and combination strategies.

Citation Format: Farah Ballout, Heng Lu, Nadeem Bhat, Lei Chen, Dunfa Peng, Zheng Chen, Alexander Zaika, Oliver McDonald, Wael El-Rifai. SMAD3 mediates oxaliplatin resistance in esophageal adenocarcinoma [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 4559.
Abstract 4589: Synergistic effects of EZH1/2 dual inhibition and cisplatin on lung cancer cell lines with loss of SMARCA4 and SMARCA2
Authors: Lee Jeongjae , Keam Bhumsuk , Kim Soyeon , Youk Jeonghwan , Kim Miso , Kim Tae Min , Kim Dong-Wan , Seog Heo Dae
Published: March 2024

Purpose: SMARCA4 mutations are observed in approximately 10% of non-small cell lung cancer (NSCLC) cases and are implicated in various biological functions. Lung cancers harboring these mutations are associated with poor prognosis and often exhibit resistance to conventional chemotherapies, highlighting the urgent need for innovative therapeutic strategies. We evaluated the efficacy of a novel EZH1/2 dual inhibitor, HM97662, and its synergistic potential with cisplatin in SMARCA4-deficient lung cancer cell lines.

Experimental Design: CCLE datasets were employed to identify cell lines harboring truncated mutations in the SMARCA4 gene. Immunoblotting was conducted to verify the inactivation of SMARCA4 and to check for the expression of SMARCA2. We assessed cellular viability and colony-forming capabilities of lung cancer cell lines

(NCI-H1975, PC9, A549, HCC15, NCI-H522, NCI-H1581, NCI-H1048, NCI-H841) to determine the cytotoxic effects of an EZH1/2 dual inhibitor as well as cisplatin, both as single agents and in combination.

Results: Immunoblotting showed distinct lung cancer cell lines characterized by three profiles: proficient SMARCA4 expression, absent SMARCA4 but present SMARCA2 expression, and concurrent loss of both SMARCA4 and SMARCA2. After 14 days of treatment with the EZH1/2 dual inhibitor HM97662, there was a significant reduction in cell proliferation, particularly in the both SMARCA4- and SMARCA2-loss cell lines. Furthermore, colony-forming assays demonstrated a significant decrease in colony-forming ability upon HM97662 treatment, an effect exclusive to the both SMARCA4 and SMARCA2 loss cell lines. Pre-treatment with 1 µM of HM97662 for 7 days potentiated the cytotoxicity of cisplatin compared to untreated controls in the SMARCA4/2 loss cell lines, as indicated by a lower IC50 value.

Conclusion: The novel EZH1/2 dual inhibitor, HM97662, exhibits antitumor activity and a synergistic effect with cisplatin in lung cancer cell lines with concomitant loss of SMARCA4 and SMARCA2. These findings suggest the potential utility of EZH1/2 dual inhibition as a targeted therapeutic approach in lung cancers characterized by the dual loss of SMARCA4/2.

Citation Format: Jeongjae Lee, Bhumsuk Keam, Soyeon Kim, Jeonghwan Youk, Miso Kim, Tae Min Kim, Dong-Wan Kim, Heo Dae Seog. Synergistic effects of EZH1/2 dual inhibition and cisplatin on lung cancer cell lines with loss of SMARCA4 and SMARCA2 [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 4589.
Abstract 4610: Dual inhibition of CDK4/6 and IL-6 pathways as a novel therapeutic approach for triple-negative breast cancer cells
Authors: Caroland Kailey , Shi Changyou , Lo Hui-Wen , Lin Jiayuh
Published: March 2024

Triplenegative breast cancer (TNBC) is highly aggressive and associated with poor clinical outcomes. TNBC stands as a major cause of death among breast cancer patients and offers only a few therapeutic options. Abemaciclib, a cyclin dependent kinase 4/6 (CDK4/6) inhibitor, has received FDA approval for use in hormone receptor-positive, HER2-negative, and metastatic breast cancers. However, acquired resistance to CDK4/6 inhibitors in treating TNBC is becoming an increasing concern. Our recent results indicated that CDK4/6 inhibitors can induce IL-6 levels in TNBC cells as a potential resistance mechanism by augment IL-6 signaling axis, and that targeting IL-6 signaling can sensitize TNBC cells to CDK4/6 inhibitor therapy. In this study, combination of Abemaciclib with an IL-6/GP130 inhibitor (bazedoxifene) was tested in TNBC cells. We examined the effect of the combination on cell viability, cell migration, and invasion of human and mouse TNBC cell lines. Our data demonstrated that the bazedoxifene and abemaciclib combination treatment synergistically inhibited TNBC cell viability, cell migration, and invasion in vitro. These results support dual inhibition of CDK4/6 and IL-6 as a novel therapeutic approach for TNBC.

Citation Format: Kailey Caroland, Changyou Shi, Hui-Wen Lo, Jiayuh Lin. Dual inhibition of CDK4/6 and IL-6 pathways as a novel therapeutic approach for triple-negative breast 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 4610.
Abstract 4648: Metabolic vulnerabilities of drug-resistant melanoma with therapeutic potential
Authors: Yu Yanlin , Huang Lei , Chen Weiping , Merlino Glenn
Published: March 2024

Melanoma has been at the center of revolutions in both targeted BRAF therapy and immune therapy. However, the resistance to current therapeutic drugs has been a formidable obstacle to continuing benefit to patients. Overcoming resistance and new therapeutic agents and strategies are the primary goals of current cancer research. We currently found that metabolic pathways altered significantly in BRAFi-resistant melanoma. We hypothesized that BRAFi-resistant melanoma rewires its metabolic routes to reach its needs in energy and biosynthetic precursors, both essential for escaping the BRAFi attack. We found that five amino acids transporters and metabolic enzymes (ASNS, slc7a11, slc7a5, slc3a2, slc4a7) were the significant increase in resistant melanoma. Knockdown by shRNA or knockout by crispr/cas9 of these amino acids transporters or/and metabolic enzymes enhanced the sensitivity of BRAFi resistant melanoma to BRAFi. In contrast, overexpression of these amino acid transporters or/and metabolic enzymes promoted the ability of resistance of BRAFi in parent melanoma cells. Moreover, the inhibition of these amino acid transporters and metabolic enzymes by small molecular inhibitors significantly attenuated the resistance of the BRAFi-resistant melanoma whereas less affected the parent melanoma. Notably, we confirmed that blocking these amino acid transporters and metabolic enzymes by shRNA and/or small molecular inhibitors could rescue the sensitivity of resistant melanoma cells and inhibit resistant-melanoma cell growth in the preclinical mouse model in vivo. Importantly, we found that overexpression of slc7a11, slc7a5 and slc3a2 correlated with worse survival in melanoma in SK-TCGA data. Our findings uncovered the mechanism of how metabolic reprogramming fueled melanoma cell growth and proliferation for escaping drug attacks and offered a rational strategy to guide clinical treatment. The identified novel molecular proteins represented a promising therapeutic target for BRAF mutant melanoma patients with resistance to current therapy.

Citation Format: Yanlin Yu, Lei Huang, Weiping Chen, Glenn Merlino. Metabolic vulnerabilities of drug-resistant melanoma with therapeutic potential [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 4648.
Abstract 4655: Targeting FAK improves the tumor penetration of antibody-drug conjugates to strengthen the anti-cancer responses
Authors: Zhang Baoyuan , Zhang Zhixiang , Gao Jiaming , Lu Shiqiang , Pang Ran , Li Dongfang , Huang Xun , Qin Natasha , Liu Leo , Wang Zaiqi
Published: March 2024

Antibody-drug conjugates (ADCs) such as HER2 ADC Enhertu and TROP2 ADC Trodelvy have been proved to be the promising therapeutic agents in portion of cancer diseases. However, there are still numerous patients refractory to the therapy, indicating that the efficacy of ADCs may need to be further optimized. Here, we report that the excessive cancer-associated fibroblasts (CAFs) can serve as a fibrotic barrier, to the detriment of anti-tumor effects from ADCs by alleviating their tissue penetration. Mechanistically, the cancer cells can transform the normal fibrotic cells into CAFs which are featured by the hyperactivated focal adhesion kinase (FAK) signaling. The fast-growing CAFs would decrease the tumor uptake of the big molecules, conferring drug resistance of ADCs to the cancer cells. Targeting FAK with a small molecule inhibitor IN10018 is capable to reduce CAFs associated tumor barrier, elevating the tissue penetration of different types of ADCs regardless their respective targets. The combination regimen comprising IN10018 and the ADCs targeting either HER2 or TROP2 outperformed each monotherapy with respect to antitumor outcomes in different animal experiments. The preclinical evidence for the dual regimen of IN10018 and ADCs warrants a further validation in clinical settings.

Citation Format: Baoyuan Zhang, Zhixiang Zhang, Jiaming Gao, Shiqiang Lu, Ran Pang, Dongfang Li, Xun Huang, Natasha Qin, Leo Liu, Zaiqi Wang. Targeting FAK improves the tumor penetration of antibody-drug conjugates to strengthen the anti-cancer responses [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 4655.
Abstract 4673: Genome-scale metabolic models identify gene targets that enhance drug response of drug-resistant breast cancer cells
Authors: Jung Hae Deok , Lim JinA , Ryu Han Suk , Kim Yoosik , Kim Hyun Uk
Published: March 2024

Adaptive drug resistance poses a significant therapeutic challenge in treatment of breast cancer patients. Metabolic reprogramming in cancer cells is one of the major mechanisms associated with drug resistance. In this study, we aim to identify gene targets that enhance the drug response of drug-resistant breast cancer cells through downregulation. We hypothesized that metabolic perturbation in drug-resistant breast cancer cells could revert their metabolic features to those of drug-sensitive cells. To predict such gene targets, we used a computational model known as a genome-scale metabolic model (GEM). A GEM simulates the entire metabolic reaction fluxes of a cell under varying genetic and/or environmental conditions. We specifically targeted two engineered MCF7 breast cancer cell lines: one resistant to doxorubicin and the other to paclitaxel. First, we generated proteome data from drug-sensitive and drug-resistant MCF7 cell lines, and used them to construct the cell-specific GEMs. Subsequently, single-gene knockout simulation was conducted using these cell-specific GEMs. The initial list of the gene knockout targets was subjected to pathway analysis involving proteome and metabolome data to finalize the gene targets. The final gene targets were expected to lead to metabolic features similar to those of drug-sensitive MCF7 upon the downregulation. In vitro experiments using inhibitors were conducted to validate these predicted gene targets. This study provides a computational approach that can also be applied to other types of drug-resistant cancer cells.

Citation Format: Hae Deok Jung, JinA Lim, Han Suk Ryu, Yoosik Kim, Hyun Uk Kim. Genome-scale metabolic models identify gene targets that enhance drug response of drug-resistant breast 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 4673.
Abstract 4686: Identification of ART3 as a novel synthetic lethal partner of the BRCA1 mutation in breast cancer
Authors: Neiger Hannah , Pei Xinyu , Nguyen Anh , Wang Wenjia , Siegler Emily L. , Zhou James , Lau Kristie , Tan Alexandra , Shi Yihui
Published: March 2024

Breast cancer (BC), the most prevalent malignancy in women, ranks fourth in cancer mortality as of 2022. Mutations in the BRCA genes significantly elevate BC risk and are associated with markedly reduced survival compared to non-carriers. These genes are crucial in homologous recombination, a mechanism essential for error-free DNA repair. Despite advancements, treatment options for BRCA mutation-driven cancers remain limited. Synthetic lethality (SL) has emerged as a promising strategy, with poly(ADP-ribose) polymerase inhibitors (PARPi) being the first developed drugs based on this principle. However, PARPi's effectiveness is limited, as nearly 40% of BRCA-mutated BCs are unresponsive, and resistance often develops in initial responders. Therefore, novel mutation-specific targeted therapies are urgently needed. In this study, we employed the novel computational method 'Mining Synthetic Lethals (MiSL)' to analyze TCGA pan-cancer primary tumor data, identifying ART3 as a potential SL partner of the BRCA1 germline mutation. Our approach focused on the intersection of genetic interactions and cancer vulnerabilities, providing a unique insight into SL relationships. siRNA-mediated silencing of ART3 in BRCA1-mutated cells consistently led to decreased cell viability, apoptosis induction, and G2/M cell cycle arrest. Following stable transfection with an inducible ART3 shRNA construct, we confirmed significant reduction in cell viability in BRCA1-deficient cells through colony formation assays. RNA sequencing of ART3 knockdown cells revealed transcriptional changes in genes involved in cell cycle progression, apoptosis, and growth and proliferation pathways compared with control cells. Immunofluorescent staining revealed increased DNA damage foci with decreased DNA repair in ART3 knockdown BRCA1-deficient cells. In conclusion, our study identifies ART3 as a novel SL partner of the BRCA1 mutation in BC. This discovery paves the way for developing new therapeutic strategies for BRCA1-mutated breast cancers and novel chemoprevention approaches for individuals carrying germline BRCA1 mutations. Future research will focus on further elucidating the molecular mechanisms underlying this SL interaction and exploring its therapeutic potential in clinical settings.

Citation Format: Hannah Neiger, Xinyu Pei, Anh Nguyen, Wenjia Wang, Emily L. Siegler, James Zhou, Kristie Lau, Alexandra Tan, Yihui Shi. Identification of ART3 as a novel synthetic lethal partner of the BRCA1 mutation in 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 4686.
Abstract 4692: A novel ceramide synthase 2 agonist and its implication in triple-negative breast cancer therapy
Authors: Alatawi Hissah , Koo Nayeong , Mahmud Iqbal , Nair Haritha , Singh Amandeep , Garrett Timothy J. , Sharma Arun K. , Hong Sukwon , Narayan Satya
Published: March 2024

Based on the biological/molecular markers, breast cancer can be classified into five subgroups: Luminal A (ER+/PR+/HER2-), Luminal B (ER+/PR-/HER2- or ER+/PR+/HER2+, triple-positive), ER-/PR-/HER2+, and ER-/PR-/HER2- (triple-negative). Significant progress has been made in treating hormone-responsive and HER2-expressing breast cancer. However, the targeted therapies are limited for triple-negative breast cancer (TNBC) due to lack of well-defined druggable targets. Additionally, all breast cancer subtypes can quickly develop resistance to current treatments. Thus, there is an urgent need for therapeutic strategies targeting pathways common to all subtypes, irrespective of receptor status. In this effort, we have synthesized a novel biisoquinoline-derivative, DH20931 (US Patent ID: US9914733B2) that induces cytotoxicity in breast cancer cells, including TNBC cells. The spatial molecular modeling and enzymatic assays show that DH20931 interacts with and stimulates ceramide synthase 2 (CerS2) activity, reduces the growth of hormone-responsive, HER2-expressing, and TNBC cells in monolayer and 3D spheroid culture models. DH20931 treatment increases the level of very long chain fatty acid (VLCFA) containing ceramides, induces lipotoxic endoplasmic reticulum (ER) stress, and ATF4/CHOP/PUMA pathway of apoptosis. Based on Swiss-ADME analysis, DH20931 possess all the properties of a druggable molecule and obeys the Lipinski-rule-of-five. Thus, DH20931 can be developed as a novel targeted therapeutic agent independent of ER, PR and HER2 status that potentially may reduce the morbidity and mortality for women with breast cancer.

Citation Format: Hissah Alatawi, Nayeong Koo, Iqbal Mahmud, Haritha Nair, Amandeep Singh, Timothy J. Garrett, Arun K. Sharma, Sukwon Hong, Satya Narayan. A novel ceramide synthase 2 agonist and its implication in triple-negative breast 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 4692.
Abstract 4697: Surface localization of enolase-1 (ENO-1) as an attractive theranostic target in docetaxel-resistant neuroendocrine-like prostate cancer cells
Authors: Torres Krystal Rubi Santiago , Casiano Carlos A. , Almaguel Frankis , Duran Alfonso , Whitley Kristen
Published: March 2024

Prostate cancer (PCa) is American men's second most common cancer. Although taxane-based chemotherapy is the last line of defense for Metastatic Castration Resistant Prostate Cancer (mCRPC), it invariably fails due to chemoresistance. The protein-specific membrane antigen (PSMA) has been an effective target for the imaging and therapy of mCRPC. Although PSMA radioligand therapy (PSMA-RLT) is a theranostics option for men with advanced PCa, about 30% have a limited response due to neuroendocrine-like PCa (NEPC), which lacks PSMA expression. Enolase (ENO) is a promising theranostic alternative due to its cell surface localization in many human tumors. We observed that chemosensitive PCa cell lines expressing NEPC markers express both ENO-1 and ENO-2; however, docetaxel-resistant NEPC-like cells only express ENO-1 and have a metabolic vulnerability due to the loss of ENO-2. We hypothesize that ENO-1 is expressed on the surface of NEPC-like cell lines and can be targeted with small molecule inhibitors (SMIs) that could potentially be used as theranostics agents. Additionally, we have observed changes in the expression and localization of ENO-1 in NEPC-like cell lines under different glucose concentrations. Our data show that under high glucose conditions, found on metabolically active metastatic tumors, ENO-1 is highly expressed on the cell surface, making it a promising candidate target for theranostics. However, low glucose conditions inhibit the activity of the c-MYC oncogene resulting in ENO-1 downregulation and upregulation of MBP1, the small splice variant of ENO1 that blocks the transcriptional activity of c-MYC. Our efforts to confirm ENO-1 surface expression on NEPC-like cell lines entailed using confocal microscopy, cell fractionation analysis followed by Western blotting, and Flow cytometric cell surface staining. We also evaluated the cytotoxicity of SMIs designed to target ENO-1 in chemoresistant NEPC-like cell lines using MTT viability assays, clonogenic assays, and Hoffman Modulation microscopy imaging. Our long-term goal is to identify an alternative treatment for patients with NEPC by establishing ENO-1 as a novel theranostics target.

Citation Format: Krystal Rubi Santiago Torres, Carlos A. Casiano, Frankis Almaguel, Alfonso Duran, Kristen Whitley. Surface localization of enolase-1 (ENO-1) as an attractive theranostic target in docetaxel-resistant neuroendocrine-like prostate 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 4697.
Abstract 4705: Repetitive membrane potential oscillations enhance metformin's antiproliferative effect in glioblastoma stem cells
Authors: Verduci Ivan , Cannavale Gaetano , Rey Guido , Cianci Francesca , Fantin Alessandro , Mazzanti Michele
Published: March 2024

Glioblastoma (GB) is the most common and lethal brain tumor and there is a general agreement that GB stem cells (GSCs) are primarily responsible for its high aggressiveness and recurrence. It was recently reported that GSCs are enriched in the transmembrane form of CLIC1 protein (tmCLIC1) and its inhibition was shown to impair tumor growth both in vitro and in vivo. IAA94 hampers tmCLIC1 function but could not be used in clinics. However, tmCLIC1 is also sensitive to metformin, the most used drug to treat type-2 diabetes. Metformin has been demonstrated to have the same effect as IAA94 in in vitro experiments, resulting in an antitumoral action on cancer cells. Moreover, GB orthotopic mouse model treated with metformin shows a 50% survival compared to control animals, even if metformin concentration in the mice brain resulted in the nanomolar range. In this scenario, the main aim of this work is to enhance the effect of metformin able to reach the brain, improving its antitumoral activity in GB. The interaction between metformin and tmCLIC1 occurs only when this protein is in its open state. TmCLIC1 has the peculiarity of being a voltage-dependent ion channel that opens at depolarized voltages. Thus, our strategy is to apply electromagnetic field (EMF) stimulation to induce repetitive membrane depolarization, increasing metformin-tmCLIC1 binding. Our results show that EMF stimulation induces the close-to-open transitions of tmCLIC1, resulting in a 10-fold decrease of the operative concentration of Metformin. This was verified initially in vitro with GSC culture and spheroids model and afterward confirmed also in an in vivo model. The project’s long-term goal is to combine transcranial stimulation and metformin administration in patients as an adjuvant therapy able to target cells that are resistant to chemotherapy and drive tumor relapse.

Citation Format: Ivan Verduci, Gaetano Cannavale, Guido Rey, Francesca Cianci, Alessandro Fantin, Michele Mazzanti. Repetitive membrane potential oscillations enhance metformin's antiproliferative effect in glioblastoma stem 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 4705.
Abstract 4731: Targeting Lon protease as novel strategy to treat aggressive IDH mutant diffuse malignant astrocytoma
Authors: Douglas Christopher , Jain Shashi , Lomeli Naomi , Vu Thao , Pham James , Bota Daniela A.
Published: March 2024

While isocitrate dehydrogenase (IDH) wild-type and mutant malignant astrocytoma (IDHwt, IDHmt) are diffuse CNS tumors that have a high degree of parallelism with one another, including microvascular proliferation and necrosis, the IDHwt tumors clinically presents with a higher tumor grade and thus poorer prognosis and survival rate. Isocitrate dehydrogenase mutation (IDH) hinders the hypoxia response in gliomas and promotes an advantageous reduction in both tumor growth and treatment resistance. Since recurrence is high, adequate characterization and identification of potential novel molecular targets in IDHmt mutant diffuse glioma is integral for developing new therapeutic strategies for better control of tumor burden and, thus, improved outcomes. Our previous published work has shown that the hypoxia responsive LONP1 mitochondrial protease is involved in glioma growth and treatment resistance and that LONP1 inhibitors can augment the effect of chemotherapy in IDHwt models. Here, we highlight the downstream activity of LONP1 via the NRF2 pathway and how synergistically, along with the IDH mutation, LONP1 overexpression can promote the subsequent proneural to mesenchymal transition (PMT) induced by stress and other tumor microenvironment signals. By characterizing the interplay between LONP1 and IDH mutation in in-vitro models, we demonstrate that oxidative stress modulates both PMT and TMZ drug resistance. When translated to an in-vivo patient-derived, intracranial orthotopic xenograft model, LONP1 overexpression is associated with decreased survival.Based on our findings, future clinical translation includes the possibility of using LONP1 as a novel target to optimize the standard of care treatment in IDH mutant diffuse astrocytoma.

Citation Format: Christopher Douglas, Shashi Jain, Naomi Lomeli, Thao Vu, James Pham, Daniela A. Bota. Targeting Lon protease as novel strategy to treat aggressive IDH mutant diffuse malignant astrocytoma [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 4731.
Abstract 4756: Targeting DNA topoisomerase II to manage acquired resistance to third generation EGFR tyrosine kinase inhibitors in the treatment of EGFR mutant NSCLC
Authors: Chen Zhen , Vallega Karin A. , Wang Dongsheng , Quan Zihan , Fan Songqing , Wang Qiming , Leal Ticiana A. , Ramalingam Suresh S. , Sun Shi-Yong
Published: March 2024

Development of effective strategies to manage the inevitable acquired resistance to osimertinib, a 3rd generation EGFR inhibitor with proven clinical efficacy in prolonging survival of patients with EGFR mutant (EGFRm) non-small cell lung cancer (NSCLC), is an urgent and critical area of unmet need in the clinic. Effort toward this direction led us to find that the DNA topoisomerase II (Topo II) inhibitors, doxorubicin and etoposide (VP-16), but not other chemotherapeutic agents, synergistically decreased the survival of osimertinib-resistant cell lines when combined with osimertinib. The combination of osimertinib with either doxorubcin or VP-16 effectively induced DNA damage and apoptosis in osimertinib-resistant cells, suppressed the growth of osimertinib-resistant tumors, and delayed the emergence of acquired resistance to osimertinib. Mechanistic studies found that osimertinib as well other EGFR-TKIs effectively decreased Topo IIα levels in EGFRm NSCLC cells by facilitating its proteasomal degradation and induced DNA damage; these effects were lost in cell lines with osimertinib acquired resistance that possessed elevated basal levels of Topo IIα. In the majority of EGFRm NSCLC tissues relapsed from EGFR-TKI treatment, Topo IIα levels were substantially increased. Enforced expression of ectopic TOP2A genes in sensitive EGFRm NSCLC cells conferred resistance to osimertinib in inducing DNA damage and apoptosis, whereas knockdown of TOP2A in osimertinib-resistant cell lines restored their responses to undergo osimertinib-induced DNA damage and apoptosis. Together, these results reveal a previously undiscovered essential role of Topo IIα modulation in regulating the responses of EGFRm NSCLC cells to osimertinib, providing scientific rationale for targeting Topo II to manage acquired resistance to osimertinib and possibly other third generation EGFR-TKIs, thus warranting clinical validation of this strategy. (This study was supported by NIH/NCI R01 CA223220 and UG1 CA233259 and Emory Winship Cancer Institute lung cancer research pilot funds).

Citation Format: Zhen Chen, Karin A. Vallega, Dongsheng Wang, Zihan Quan, Songqing Fan, Qiming Wang, Ticiana A. Leal, Suresh S. Ramalingam, Shi-Yong Sun. Targeting DNA topoisomerase II to manage acquired resistance to third generation EGFR tyrosine kinase inhibitors in the treatment of EGFR mutant NSCLC [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 4756.
Abstract 4757: Combining PARP inhibitor with TACC3 inhibition overcomes PARP inhibitor resistance in ovarian cancer
Authors: Wu Yu , Wang Qilong , Deng Chaolin , Li Mo , Xiao Yinan
Published: March 2024

The treatment of ovarian cancer (OC) presents a significant challenge due to the emergence of resistance to poly (ADP-ribose) polymerase inhibitors (PARPi). Transforming acidic coiled coil containing protein 3 (TACC3) belongs to the TACC family, characterized by its coiled-coil domains. TACC3 plays a crucial role in cell division, particularly in the formation and stability of the mitotic spindle, which is essential for proper chromosome segregation. Mutations or changes in TACC3 have been associated with various cancers, making it an increasingly attractive target for anticancer therapy in recent years. Here, we demonstrated a significant upregulation of TACC3 in OC, correlating with adverse clinical outcomes. Notably, PARPi-resistant OC cells exhibited a marked sensitivity to TACC3 inhibition. This was evidenced by the induction of spindle defects and mitotic catastrophe in PARPi-resistant cells upon TACC3 suppression, achieved either genetically or pharmacologically. Moreover, we explored the therapeutic efficacy of combining TACC3 inhibitor with PARPi, specifically BO-264 with olaparib or niraparib. This combination exhibited a synergistic effect, markedly reducing cell viability in vitro and tumor growth in PARPi-resistant tumor xenograft models. Our study suggests a promising new method for treating ovarian cancer, especially for those resistant to current PARPi treatments, by simultaneously targeting TACC3 and PARPi, enhancing treatment efficacy and potentially improving patient outcomes.

Citation Format: Yu Wu, Qilong Wang, Chaolin Deng, Mo Li, Yinan Xiao. Combining PARP inhibitor with TACC3 inhibition overcomes PARP inhibitor resistance 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 4757.