bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2960: Deciphering the role of miRNA146-a and its crosstalk with cellular redox state in senescence escape in breast cancer cells
Authors: Pervaiz Shazib , Liew Angeline Q. , Clement Marie-Veronique
Published: March 2024

Senescence serves as a double-edged sword in cancer as studies revealed that senescence exhibits both tumor-suppressing and tumor-promoting effects. A subpopulation of cancer cells that enters senescence can evade senescence to proliferate, thereby resulting in tumor regrowth, which has been associated with chemoresistance and tumor aggressiveness. Unlike senescent cells, the senescence-escaped cells harbor low levels of reactive oxygen species (ROS), however, the mechanism(s) underlying this redox dichotomy in senescence and senescence evasion remains elusive. In this regard, recent reports have highlighted the pivotal role of miRNAs in regulating cellular senescence. To that end, miR-146a has been reported as a biomarker of senescence probably via modulating pro-inflammatory and antioxidant pathways. We set up a model of doxorubicin-induced senescence in MDA-MB-231 breast carcinoma cells to study the role and involvement of miRNA146a in senescence induction and its regulation. Senescence induction was confirmed by upregulation of p21, increase in senescence-associated beta galactosidase and C12FDG staining, as well as propidium iodide positivity. We show that, following the initial phase of apoptotic cell death, as evidenced by increased yH2AX and cleaved caspase 3, a population of senescent cells escaped growth arrest to re-enter cell cycle and proliferate. Senescence-escaped cells harbored lower ROS levels compared to senescent cells, which correlated with upregulation of antioxidant enzymes such as MnSOD and CuZnSOD as well as increased transcription of NRF2 and NQO1. Our results also provide evidence for a novel senescence associated redox state, which implicates intracellular peroxynitrite as a driver of cellular senescence. Interestingly, in our model system, p21 upregulation was not associated with intracellular ROS accumulation, which was reported in earlier findings. Interestingly, these changes coincided with a significant increase in miR-146 expression (during senescence), which was previously shown to downregulate ROS in other model systems. While modulating miR-146a did not seem to change ROS levels upon doxorubicin-induced senescence in MDA-MB231 cells, the precise crosstalk between cellular ROS, miR146-a and senescence evasion is currently being pursued.

Citation Format: Shazib Pervaiz, Angeline Q. Liew, Marie-Veronique Clement. Deciphering the role of miRNA146-a and its crosstalk with cellular redox state in senescence escape in 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 2960.
Abstract 3009: ATRX loss blocks the differentiation of mesenchymal stem cells and promotes undifferentiated sarcoma development
Authors: Cai Yiming , Yao Jun , Pan Dean N. , Jin Yanqiang , You James M. , Yao Wantong , Ying Haoqiang
Published: March 2024

Soft tissue sarcomas (STSs) are a collection of rare tumor types originated from the mesenchymal tissues. Among the over 70 histological subtypes of STS, undifferentiated sarcoma (US), which lacks any discernible morphological features of differentiated tissues, accounts for over 20% of all STSs and is correlated with high tumor grade and poor prognosis. Recent genomic profiling in US has identified p53 and ATRX among the most frequently mutated or deleted genes. ATRX is a SWI/SNF2 type of chromatin remodeling factor which functions in a histone variant H3.3-specific chaperone complex to orchestrates replication-independent nucleosome assembly at repetitive heterochromatic DNA regions including telomeres. Loss-of-function mutations occur frequently in many tumor types and is associated with the development of alternative lengthening of telomere (ALT). However, how loss of ATRX function may contribute to tumorigenesis is largely unknown. Here, we demonstrated that ATRX is required for the terminal differentiation of mouse mesenchymal stem cells (MSCs) into multiple lineages, such as adipocytes and osteocytes. Targeted deletion of Atrx in mouse MSCs, but not terminally differentiated mesenchymal lineage cells, accelerated sarcoma initiation induced by loss of p53 and significantly shortened the overall survival. Atrx-deficient tumors express high level of MSC markers such as CD44 and CD29 and exhibit pathological features highly reminiscent of human high-grade US. Transcriptomic analysis indicates that Atrx deficiency is associated with enhanced proliferation. Together, our data indicates that ATRX deficiency contributes to undifferentiated sarcoma development by inhibiting mesenchymal stem cell differentiation.

Citation Format: Yiming Cai, Jun Yao, Dean N. Pan, Yanqiang Jin, James M. You, Wantong Yao, Haoqiang Ying. ATRX loss blocks the differentiation of mesenchymal stem cells and promotes undifferentiated sarcoma development [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 3009.
Abstract 3041: The small MAF transcription factor MAFG is a potent driver of melanoma
Authors: Vera Olga , Martinez Michael , Soto-Vargas Zulaida , Xu Xiaonan , Karreth Florian
Published: March 2024

While common mutations in potent proto-oncogenes and tumor suppressors induce melanoma formation, no recurrent mutations associated with the late stages of melanomagenesis have been identified. Instead, non-mutational mechanisms such as the deregulation of transcriptional or epigenetic programs typically promote the malignant progression and metastasis of melanoma. We have previously identified the small MAF transcription factor MAFG as a critical target of the melanoma suppressor miRNA miR-29, prompting an in-depth evaluation of the role of MAFG in melanoma. MAFG expression is elevated in melanoma compared to melanocytes and increases with tumor stage. Ectopic expression of MAFG in human melanocytes and melanoma cells enhances proliferation in vitro and promotes melanoma growth in vivo. Moreover, MAFG overexpression in BrafV600E; PtenFL/+ mice accelerated melanomagenesis, significantly shortening overall survival. Despite being a critical NRF2 dimerization partner, NRF2 was dispensable for the effects of MAFG. Moreover, MAFG overexpression in melanoma cells had no effect on the activity of NRF2 transcriptional reporters, nor did it induce transcriptional programs associated with NRF2. RNA sequencing and pathway analysis revealed MAFG-mediated effects on melanoma-associated processes such hypoxia, the PI3K/AKT pathway, and pigmentation. Indeed, MAFG induced HIF1a under normoxic conditions, enhanced AKT phosphorylation, and downregulated MITF and its target genes in the pigmentation pathway in melanoma cells. Interestingly, MAFG also potently enhanced AXL expression, suggesting that MAFG may promote melanoma, at least in part, by affecting the MITF/AXL balance that is associated with melanoma phenotype switching. We next analyzed whether MAFG is required for melanoma. Interestingly, silencing MAFG in human melanoma cells robustly inhibited growth in vitro. Moreover, the CRISPR/Cas9-mediated knockout of MAFG in an aggressive BrafV600E; PtenFL/FL model potently prevented melanoma formation. Given the mild phenotype of MAFG whole-body knockout mice, our results suggest targeting of MAFG or its downstream pathways as a viable therapeutic approach in melanoma. In conclusion, our study establishes MAFG as a potent driver of melanoma development and nominates it as a therapeutic target.

Citation Format: Olga Vera, Michael Martinez, Zulaida Soto-Vargas, Xiaonan Xu, Florian Karreth. The small MAF transcription factor MAFG is a potent driver of melanoma [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 3041.
Abstract 3061: A positive feedback loop between GLS1 and c-Myc drives tumor aggressiveness
Authors: Yang Jianqiang , Chen Fanghui , Yang Fan , Teng Yong
Published: March 2024

Both GLS1 and c-Myc are upregulated in head and neck squamous cell carcinoma (HNSCC) primary tumors and further increased in metastatic tumors. However, the regulation between these two molecules remains largely unknown. GLS1 is a critical enzyme that regulates glutamate, which plays an important role in cancer metabolism that supports cancer growth and survival. Our bioinformatic analysis of the TCGA HNSCC cohort revealed a strong correlation between c-Myc and GLS1 expression. We describe the importance of c-Myc in regulating GLS1 and vice versa. c-Myc protein directly binds to the promoter of the GLS1 gene and upregulates its expression at the transcriptional level. Interestingly, blocking GLS1 signaling in HNSCC cells by lentiviral shRNA knockdown or CB-839 treatment downregulates USP1, one of the best characterized human DUBs, which in turn reduces c-Myc protein stability via the ubiquitin-proteasome pathway. The GLS1-c-Myc axis thus represents a novel positive feedback loop that is critical for driving the aggressiveness of HNSCC. As the treatment of HNSCC remains a major challenge, these novel findings provide the molecular basis for combining GLS1-specific inhibitors with c-Myc-targeted therapy for the treatment of HNSCC patients.

Citation Format: Jianqiang Yang, Fanghui Chen, Fan Yang, Yong Teng. A positive feedback loop between GLS1 and c-Myc drives tumor aggressiveness [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 3061.
Abstract 3075: Different roles of EPAC1 and EPAC2 in ovarian cancer: Implications for precision targeting in cancer therapy
Authors: Gao Zhengyin , Yuan Wanjun , Lee Leo T.O.
Published: March 2024

There are two distinct functional isoforms of Exchange proteins directly activated by cAMP (EPACs), EPAC1 and EPAC2, which exhibit fundamental distinctions in structure, expression patterns, signaling specificity, and subcellular localization. This diversity suggests that EPAC1 and EPAC2 can operate independently, synergistically, or antagonistically, contributing to the wide range of reported functions and impacts in different cancers and studies. We compared the function of EPAC1 and EPAC2 in ovarian cancer using in vitro and in vivo models and further explored the underlying mechanism in the regulation of metabolism reprogramming. Selective inhibition of EPAC1 and EPAC2 markedly reduced proliferation in ovarian cancer cell lines, leading to cell death and cycle arrest. RNA-seq analysis indicated different downstream signaling pathways triggered by EPAC1 and EPAC2, with EPAC2 specifically linked to functions in energy metabolism. Treatment with an antagonist or knockdown of EPAC2 resulted in attenuation of both glycolysis and oxidative phosphorylation (OXPHOS), while EPAC1 did not induce such effects. Furthermore, inhibition of EPAC2 induced mitochondrial dysfunction, manifested by reduced ATP production, decreased mitochondrial membrane potential, and increased burden of reactive oxygen species (ROS). Our data also revealed that EPAC2 governs the MAPK pathway and mediates the mitochondrial unfolded protein response (UPRmt) in ovarian cancer cells. By delineating the distinctions between EPAC1 and EPAC2 within ovarian cancer cells, this project revised the prevailing understanding of EPACs and suggests the potential for precise targeting of EPAC isoforms as a viable strategy in cancer therapy.

Citation Format: Zhengyin Gao, Wanjun Yuan, Leo T.O. Lee. Different roles of EPAC1 and EPAC2 in ovarian cancer: Implications for precision targeting in 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 3075.
Abstract 3095: A high-throughput phenotypic screen to identify small molecule inhibitors of Werner helicase
Authors: Moomau Christine A. , Lu Yipin , Zhang Xiaobin , Zhai Xiang , Gu Lina , Sheng Qing , Li Fang , Chen Yaoyu
Published: March 2024

Werner helicase (WRN) is a RecQ DNA helicase involved in genome maintenance and DNA damage repair. It has recently been shown to be essential to cancer cells with high microsatellite instability (MSI-H). In MSI-H cancer cells, WRN depletion was shown to induce DNA damage and disrupt mitoses, resulting in a distinct phenotype of enlarged and fragmented nuclei. Here, we present a high-throughput phenotypic screen to identify compounds that selectively induce enlarged nuclei in MSI-H cancer cells. In HCT116, an MSI-H colorectal cancer cell line, approximately 40% of cells exhibited enlarged nuclei when WRN was depleted using siRNA. In contrast, fewer than 10% of control cells displayed this phenotype. In HT29, a microsatellite stable (MSS) cancer cell line, no such difference in nuclear morphology was observed, suggesting that the phenotype is specific to MSI-H cells. We used high content imaging to screen our in-house diversity library of approximately 175,000 compounds in 384-well format. 4,260 compounds induced enlarged nuclei in HCT116 cells, a 2.4% hit rate. After re-screening hits in HCT116 along with two additional MSI-H cancer cell lines, SW48 and SNU-407, and counter-screening in HT29 cells, 144 hits were confirmed to specifically enlarge nuclei in MSI-H but not MSS cells. Using the ADP-Glo Kinase Assay, two of these compounds were confirmed to inhibit WRN ATPase activity, suggesting WRN inhibition as a potential mechanism for their specific effects in MSI-H cells. This screen will also identify compounds which selectively kill MSI-H cells through mechanisms beyond direct inhibition of WRN, including interaction with WRN complex members or other members of DNA damage repair pathways. Validation studies including the assessment of cell viability and DNA damage in a panel of MSI-H and MSS cell lines will be performed. Our study proposes a phenotypic screening strategy for identifying small molecules with the potential to target WRN and uncover additional novel mechanisms for treating MSI-H cancers.

Citation Format: Christine A. Moomau, Yipin Lu, Xiaobin Zhang, Xiang Zhai, Lina Gu, Qing Sheng, Fang Li, Yaoyu Chen. A high-throughput phenotypic screen to identify small molecule inhibitors of Werner helicase [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 3095.
Abstract 3109: Development of novel mono and bivalent nanobodies against EGFR for targeted cancer therapy
Authors: Cortes Diana C. Aguilar , Heitrich Mauro O. , Fernandez Marisa M. , Werbajh Santiago , Canziani Gabriela , Zylberman Vanesa , Malchiod Emilio L. , Podhajcer Osvaldo L. , Vinzón Sabrina E.
Published: March 2024

Introduction: The epidermal growth factor receptor (EGFR) plays a central role in the tumorigenesis of various solid tumors, rendering it a noteworthy target for cancer therapy. Nanobodies (Nbs) offer an appealing therapeutic approach due to their low immunogenicity, rapid clearance, and high targeting specificity. The aim of this study is to isolate, design, and characterize Nbs directed against EGFR.

Methods: The Nb library was constructed following llama immunization with cells overexpressing EGFR. After three rounds of panning the phage-display library (both in solid phase and solution), individual clones were screened for EGFR reactivity using ELISA against Virus-Like Particles. Positive clones were sequenced, cloned into an expression vector, and then purified by immobilized metal affinity chromatography (IMAC). The Nbs were characterized through immunofluorescence (IF), flow cytometry (FACS), and surface plasmon resonance (SPR). The most promising candidates were used to design bivalent constructs, which were subsequently characterized by SPR and in a cell proliferation assay.

Results: We successfully constructed an EGFR-targeted Nb library, which allowed the selection of multiple EGFR-specific Nbs following the optimization of the panning strategy. Two of the candidates exhibit strong binding to native EGFR in cells and outperform the gold standard anti-EGFR Nb 7D12. They demonstrate enhanced binding parameters in surface plasmon resonance (SPR) assays, with fast association and slow dissociation rates. The homo/heterodimeric bivalent constructs show improved affinity and the ability to inhibit cancer cell proliferation.

Conclusion: We were able to develop novel mono and bivalent nanobodies with enhanced binding properties which can be used for targeted cancer therapy.

Citation Format: Diana C. Aguilar Cortes, Mauro O. Heitrich, Marisa M. Fernandez, Santiago Werbajh, Gabriela Canziani, Vanesa Zylberman, Emilio L. Malchiod, Osvaldo L. Podhajcer, Sabrina E. Vinzón. Development of novel mono and bivalent nanobodies against EGFR for targeted 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 3109.
Abstract 3113: Development of HTS enzymatic assays for WRN helicase and exonuclease functions
Authors: Pham Ha , Ali Mahbbat , Martinez Anibal Ramos , Lowery Robert
Published: March 2024

WRN, a double strand break repair enzyme with ATP-dependent DNA-helicase and 3’- >5’ exonuclease activities, is under intense focus as a therapeutic target because of its synthetic lethality in tumors with microsatellite instability. To accelerate discovery of WRN inhibitors, we developed and validated homogenous, fluorescence-based high throughput assays for WRN helicase and exonuclease enzymatic activities using the Transcreener HTS Assay platform, which relies on highly selective antibodies to detect nucleotides in a homogenous (mix-and-read) format with far red fluorescent readouts. We produced the WRN helicase domain (aa 500-946, N-terminal 6xHis) in BaV-infected insect cells and optimized detection of its dsDNA-dependent ATPase activity using the Transcreener ADP2 Assay in FP, TR-FRET, and FI detection modes. Optimal reaction conditions included 50 μM ATP (approximate Km) and saturating concentration (100 nM) of a 3’ flapped duplex DNA oligomer; these conditions yielded a good signal with 250 pM WRN, a kcat of 300 min−1, and a Z’ of 0.85. An IC50 of 35 nM was determined for the probe inhibitor NSC-617145, and a 1,280 compound pilot screen (Tocris 2.0 Micro) identified multiple hits that were confirmed in dose response experiments. We produced the WRN 3’-5’ exonuclease domain (aa 1-133-6xHis) in E. coli and used the Transcreener dAMP Exonuclease Assay to allow direct, FP-based detection of dAMP monomers released from a 52 bp dsDNA oligomer with a 5’ overhang. With saturating DNA present (1 μM), the assay produced a good signal with 1 nM enzyme; the Z’ value was 0.89. There are no published inhibitors for the WRN exonuclease, but suramin inhibited with an IC50 of approximately 100 nM. These assays allow sensitive, robust, quantitative detection of WRN ATPase and exonuclease activities using an extensively validated HTS platform; they should be valuable tools for screening and optimizing small molecules targeting specific WRN functions.

Citation Format: Ha Pham, Mahbbat Ali, Anibal Ramos Martinez, Robert Lowery. Development of HTS enzymatic assays for WRN helicase and exonuclease functions [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 3113.
Abstract 3133: A novel bispecific antibody-drug conjugate targeting HER2 and Trop-2 displays potent antitumor activity in a variety of tumor models with promising preclinical characteristics
Authors: Zhong Haihong (Helen) , Xiong Yan , Huang Han , Pan Yuming , Wang Na , Sun Bin , Liu Shen , Yuan Wei , Liu Dingguo , Fang Jan , Bao Haifeng
Published: March 2024

Antibody-drug conjugates (ADCs) have exhibited considerable advancements in cancer therapy, though their efficacy is often confined to specific patient subsets or results in modest clinical responses due to low and heterogenous expression of drug targets in tumors. Targeting more than one tumor-associated antigens (TAAs) represents a new strategy to broaden treatment applicability and minimize on-target toxicity of ADC. Our analysis of co-expression of HER2 and Trop-2, two clinically validated ADC targets, in tumors of various histological malignancies manifests the great potential for an ADC simultaneously targeting these two antigens. We describe here a novel bispecific ADC (BIO-201) designed to co-target HER2 and Trop-2. This compound comprises a bispecific anti-HER2/Trop-2 antibody conjugated with a novel topoisomerase I inhibitor via a cleavable linker. BIO-201 demonstrates increased or comparable cell binding and internalization compared to parental antibodies. In in vitro cytotoxicity assays, BIO-201 effectively kills cancer cells with an IC50 in the sub nM range, irrespective of whether they co-express HER2 and Trop-2 or express only one antigen. Co-culture studies reveal that BIO-201 possesses a good bystander killing effect on drug target-negative tumor cells. In vivo studies further demonstrate the superior anti-tumor activity of BIO-201 in various tumor xenograft models, including those expressing different levels of HER2 and/or Trop-2, as well as models resistant to HER-2-targeting therapies. Moreover, BIO-201 exhibits favorable plasma stability, preclinical pharmacokinetics (PK), and toxicity profiles. In conclusion, these findings suggest that the anti-HER2/Trop-2 bispecific ADC, BIO-201, holds significant promise as an effective therapy for a diverse range of cancers, especially those expressing heterogenous levels of HER2 or Trop-2, and has the potential to benefit a broad patient population.

Citation Format: Haihong (Helen) Zhong, Yan Xiong, Han Huang, Yuming Pan, Na Wang, Bin Sun, Shen Liu, Wei Yuan, Dingguo Liu, Jan Fang, Haifeng Bao. A novel bispecific antibody-drug conjugate targeting HER2 and Trop-2 displays potent antitumor activity in a variety of tumor models with promising preclinical characteristics [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 3133.
Abstract 3274: Trefoil factor 1 suppresses stemness and enhances chemosensitivity of pancreatic cancer
Authors: Yamaguchi Junpei , Kokuryo Toshio , Yokoyama Yukihiro , Sunagawa Masaki , Baba Taisuke , Ebata Tomoki
Published: March 2024

Background and Aims: Pancreatic cancer is one of the most lethal malignancies, partly due to resistance to conventional chemotherapy. The chemoresistance of malignant tumors is associated with epithelial-mesenchymal transition (EMT) and the stemness of cancer cells. The aim of this study is to investigate the availability and functional mechanisms of trefoil factor family 1 (TFF1), a tumor-suppressive protein in pancreatic carcinogenesis, to treat pancreatic cancer.

Methods: To investigate the role of endogenous TFF1 in human and mice, specimens of human pancreatic cancer and genetically engineered mouse model of pancreatic cancer (KPC/TFF1KO; Pdx1-Cre/LSL-KRASG12D/LSL-p53R172H/TFF1−/−) were analyzed by immunohistochemistry (IHC). To explore the efficacy of extracellular administration of TFF1, recombinant and chemically synthesized TFF1 were administered to pancreatic cancer cell lines, a xenograft mouse model and a transgenic mouse model.

Results: The deficiency of TFF1 was associated with increased EMT markers of cancer cells (Snail and Zeb1) in mouse models of pancreatic cancer, KPC. Analysis of the survival of patients who underwent chemotherapy for recurrent pancreatic cancer revealed that the expression of TFF1 in cancer cells was associated with better survival. Also, in the mouse model of pancreatic cancer, KPC mice showed improved survival when treated with gemcitabine, the KPC/TFF1KO mice did not. Pancreatic cancer cell lines were administered with gemcitabine and/or chemically synthesized TFF1, revealing that addition of TFF1 downregulated gemcitabine-induced EMT markers (Snail, Slug, ZEB1, and αSMA), Wnt pathway activation (β-catenin, TCF7, and EPHB3). In addition, TFF1 inhibited the expression of cancer stemness markers (CD133 and NANOG3) and the ability to form tumor sphere. Importantly, TFF1 accelerated the apoptosis of cancer cells induced by gemcitabine in vitro. In vivo, combined treatment of gemcitabine and subcutaneous administration of TFF1 arrested tumor growth in xenograft mouse model. Also, KPC mice with combined treatment showed the better survival rather than gemcitabine-alone treatment, with lower expression of CD133, high expression of ZEB1, and lower nuclear translocation of β-catenin.

Conclusion: These results indicate that TFF1 can contribute to establishing a novel strategy to treat pancreatic cancer patients by enhancing chemosensitivity.

Citation Format: Junpei Yamaguchi, Toshio Kokuryo, Yukihiro Yokoyama, Masaki Sunagawa, Taisuke Baba, Tomoki Ebata. Trefoil factor 1 suppresses stemness and enhances chemosensitivity of 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 3274.
Abstract 3279: MUC1 is necessary for the inflammatory memory response to osimertinib resistance in NSCLC cells
Authors: Haratake Naoki , Bhattacharya Atrayee , Nakashoji Ayako , Ozawa Hiroki , Shimokawa Mototsugu , Kufe Donald
Published: March 2024

Emergence of resistance is an invariable outcome in cancer progression that may involve memory of cancer cells to treatment. The oncogenic MUC1-C protein confers pleotropic resistance of cancer cells to diverse cytotoxic and targeted agents by unclear mechanisms. We demonstrate that MUC1-C regulates the interferon (IFN) type I/II pathways in H1975 non-small cell lung cancer (NSCLC) cells selected for osimertinib resistance (H1975-OR). Targeting MUC1-C in H1975-OR cells suppressed STAT1 and inflammatory IFN signaling in association with reversing the osimertinib-resistant phenotype. Studies of H1975-OR cells selected for growth in the absence of osimertinib demonstrate that revertant H1975-RT cells retain MUC1-C-dependent memory necessary for recalling osimertinib resistance. Mechanistically, osimertinib treatment of H1975-RT cells activates the MUC1 gene at a (i) promoter-like signature (PLS) by MUC1-C and STAT1, and (ii) proximal enhancer-like signature (pELS) by PBAF and JUN/AP-1. Targeting MUC1-C in osimertinib-treated H1975-RT and MGH170 NSCLC MET-amplified cells isolated from a patient refractory to osimertinib treatment suppressed induction of STAT1 and downstream IFN-stimulated genes (ISGs) encoding MX1, OAS1 and ISG15. Targeting MUC1-C, STAT1, PBRM1/PBAF and JUN/AP-1 further confirmed their dependencies for reemergence of osimertinib resistance in H1975-RT and MGH170 cells. In support of these results, high MUC1-C protein expression analyzed by IHC is associated with shorter progression free survival for patients treated with osimertinib. These findings and the demonstration that MUC1-C is upregulated in NSCLC cells from patients refractory to osimertinib indicate that MUC1-C drives osimertinib resistance in NSCLC cells by promoting an inflammatory memory response.

Citation Format: Naoki Haratake, Atrayee Bhattacharya, Ayako Nakashoji, Hiroki Ozawa, Mototsugu Shimokawa, Donald Kufe. MUC1 is necessary for the inflammatory memory response to osimertinib resistance in NSCLC 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 3279.
Abstract 3289: APOBEC3A drives tumor evolution through activation of ERVs in non small cell lung cancer
Authors: Isozaki Hideko , Sakhtemani Ramin , Nikpour Naveed , Monroe Susanna , Lawrence Michael , Hata Aaron
Published: March 2024

Acquired drug resistance to even the most effective anti-cancer targeted therapies remains an unsolved clinical problem. Although many drivers of acquired drug resistance have been identified, the underlying molecular mechanisms shaping tumor evolution during treatment are incompletely understood. We recently demonstrated that lung cancer targeted therapies commonly used in the clinic induce the expression of cytidine deaminase APOBEC3A (A3A), leading to sustained mutagenesis in drug-tolerant cancer cells persisting during therapy. Preventing therapy-induced A3A mutagenesis by gene deletion decreased the chromosomal aberration events and delayed the emergence of drug resistance. Thus, inhibition of A3A may represent a potential therapeutic strategy to prevent acquired resistance. Understanding the regulatory mechanisms of A3A may provide alternative approaches to inhibit A3A mutagenesis. Using a panel drug screen, we found that DNA methyltransferase (DNMT) inhibitor remarkably induces A3A in non-small cell lung cancer cells. RNA-seq profiling revealed that targeted therapy as well as DNMT inhibitor treatment activate expression of distinct classes non-coding repetitive RNA elements, including endogenous retrovirus (ERVs), in drug-tolerant persister cells. Activation of intracellular viral sensing pathways by introduction of exogenous nucleic acids mimicking viral elements induced A3A expression. While the transcription factor NFkB was acutely activated by targeted therapy, TBK1-IRF3 signaling was activated at later time points. These findings suggest that reactivation of ERVs may underlie A3A mutagenic activity and tumor evolution during targeted therapy.

Citation Format: Hideko Isozaki, Ramin Sakhtemani, Naveed Nikpour, Susanna Monroe, Michael Lawrence, Aaron Hata. APOBEC3A drives tumor evolution through activation of ERVs in non small cell lung 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 3289.
Abstract 3313: Discovery of a potent, selective, and orally available small molecule for disruption of the SOS1-RAS interaction
Authors: Ki Dong Hyuk , Yu Hana , Kim Donggeon , Jeon Yeejin , Jo Seongin , Nam Joonwoo , Kim Eun-Jung , Kim Sungeun , Choi Hunmi , Kim Jieun , Yu Jihyun , Choi Sungpil , Han Wooseok
Published: March 2024

KRAS mutations represent one of the most common genetic alterations in many cancers including non-small cell lung cancer (NSCLC), pancreatic ductal adenocarcinoma (PDAC), and colorectal cancer (CRC). While Sotorasib and Adagrasib, KRAS G12C inhibitors, have received approval, they exhibit limited responsiveness in clinical trials and are not applicable to various other KRAS mutation types. SOS1 (Son of Sevenless 1) functions as a guanine nucleotide exchange factor (GEF) on RAS, facilitating the transition of inactive GDP-bound RAS to its active GTP-bound state. In addition, SOS1 plays a pivotal role in negative feedback by actively contributing to the reactivation of ERK during treatment with inhibitors targeting the RTK/RAS/MAPK pathway. Inhibiting SOS1, which impedes the reactivation of ERK, has the potential to enhance the effectiveness of inhibitors targeting the RTK/RAS/MAPK signaling cascade and prevent the emergence of resistance mechanisms via H-RAS and N-RAS bypass pathways. Therefore, combining the inhibition of SOS1 with inhibitors targeting the RTK/RAS/MAPK pathway may enhance outcomes and mitigate relapse associated with observed resistances. Here, we present the discovery of a potent, selective, and orally bioavailable small molecule SOS1 inhibitor that effectively disrupts the interaction between SOS1 and RAS. It has demonstrated remarkable synergy effects with RTK/RAS/MAPK pathway inhibitors, significantly impeding the growth of tumors carrying KRAS or EGFR mutations in vivo. Overall, our development candidate has demonstrated significant therapeutic potential in combination with inhibitors targeting the RTK/RAS/MAPK pathway for cancers bearing activating mutations in this pathway.

Citation Format: Dong Hyuk Ki, Hana Yu, Donggeon Kim, Yeejin Jeon, Seongin Jo, Joonwoo Nam, Eun-Jung Kim, Sungeun Kim, Hunmi Choi, Jieun Kim, Jihyun Yu, Sungpil Choi, Wooseok Han. Discovery of a potent, selective, and orally available small molecule for disruption of the SOS1-RAS interaction [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 3313.
Abstract 3350: The pan-quadruplex drug QN-302 targets up-regulated genes in pancreatic cancer and in other cancer types and correlate with poor patient prognosis
Authors: Neidle Stephen , Ahmed Ahmed A. , Arshad Tariq
Published: March 2024

We have previously disclosed (Ahmed et al, ACS Med Chem Lett, 2020) a novel small molecule G-quadruplex binding compound, QN-302, that is highly potent in pancreatic ductal adenocarcinoma (PDAC) cells and in several in vivo models for this disease. QN-302 was invented at University College London UK and has been subsequently developed by Qualigen Therapeutics Inc. It was cleared by the FDA in August 2023 for clinical evaluation and is currently in a Phase 1 clinical trial at select oncology centers in the USA. Genes that are significantly down-regulated by QN-302 are mostly up-regulated genes in human PDAC. We report here that some of these genes are also up regulated in other cancer types, whose expression frequently correlates with poor patient prognosis. We have used human cancer data from https://www.proteinatlas.org which contains pathology information based on mRNA and protein expression data from 17 different forms of human cancer, together with millions of in-house generated immunohistochemically stained tissue sections, images and Kaplan-Meier plots showing the correlation between mRNA expression of each human protein gene and cancer patient survival. We have revisited the RNA-seq data for QN-302 in PDAC MIA-PACA2 cells exposed to QN-302 for 24 hrs. (GSE151741 at https://www.ncbi.nlm.nih.gov/geo/) in detail and now identify a small group of eleven down-regulated genes, all with >3-fold expression changes. Interestingly all these genes and their gene products have been previously identified as playing a role in human PDAC (they also have varying roles in other cancer types). Some have been validated as anticancer targets. 10/11 of these genes (https://www.proteinatlas.org/) have been previously reported as being over-expressed in significant fractions of large (>150) groups of human cancer patients from The Cancer Genome Atlas (TCGA) project. Members of the PDAC susceptible gene panel are mostly disfavored in prostate, lung and breast cancer. However, the patient data does not discriminate between cancer sub-types nor does it show resistant data. They are especially favored in colorectal, liver and renal cancers, suggesting that QN-302 may have anticancer effects in these cancers as well as in PDAC. We also do not exclude the strong possibility that each cancer type also has its own group of G-quadruplex containing genes that are sensitive to QN-302.

Citation Format: Stephen Neidle, Ahmed A. Ahmed, Tariq Arshad. The pan-quadruplex drug QN-302 targets up-regulated genes in pancreatic cancer and in other cancer types and correlate with poor patient prognosis [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 3350.
Abstract 3405: CT-assessed body composition and tumor immunologic characteristics in patients with non-small-cell lung cancer
Authors: Cheng Ting-Yuan David , Mahenge Cuthbert Mario , Akasheh Rand T. , Yilmaz Ayse Selen , Kinder Ben , Nguyen Xuan , Pietrzak Maciej , Presley Carolyn J. , Shields Peter G.
Published: March 2024

Objectives: Obesity is associated with higher immunotherapy efficacy, but body mass index is a convoluted marker of adipose and muscle tissue. We conducted a discovery scale study to assess the association of skeletal muscle and adipose tissue areas annotated on computed tomography (CT) scan images with selected tumor immunologic characteristics among patients with non-small-cell lung cancer (NSCLC).

Methods: We analyzed publicly available data from 102 patients (mean age = 67.2, 47.1% female, and 70.6% stage I-II) who had diagnostic CT images in The Cancer Image Archive. All patients had the 12th thoracic vertebra (T12) image, and a subset (62 patients) had the 3rd lumber vertebra (L3) image. Paravertebral muscle areas on T12 and skeletal muscle and adipose tissue areas on L3 were annotated using Slice-O-Matic. RNA-seq data were provided by The Cancer Genome Atlas and Clinical Proteomic Tumor Analysis Consortium; percentages of CD8, regulatory T cells, and activated NK cells were identified using the CIBERSORT. ESTIMATE algorithm was used to derive the stromal score and the immune score. Differences in the immune markers were examined using ANOVA adjusting for stage, histology, and study.

Results and Conclusion: Patients with higher paravertebral muscle area (3rd tertile) had the lowest stromal scores, compared to the 2nd and 1st tertile (P<0.05). Patients in the 2nd tertile of paravertebral muscle areas had the highest immune score and CD274 (PD-L1) gene expression. Among the body composition types classified using L3 images, low muscle/high adiposity was associated with lower stromal scores, and low muscle was associated with lower immune scores, compared to high adiposity and high muscle/low adiposity types. Other immunological markers did not differ across the body composition types.

Significance: These findings suggest associations between deconvoluted skeletal and adipose tissue components and tumor markers relevant to immune checkpoint inhibitor efficacies in NSCLC. Further validation using immune phenotyping in a large patient sample is warranted. Funding: The study is in part supported by NIH/NCI R37CA248371 and OSU Comprehensive Cancer Center - James.

Citation Format: Ting-Yuan David Cheng, Cuthbert Mario Mahenge, Rand T. Akasheh, Ayse Selen Yilmaz, Ben Kinder, Xuan Nguyen, Maciej Pietrzak, Carolyn J. Presley, Peter G. Shields. CT-assessed body composition and tumor immunologic characteristics in patients with non-small-cell lung 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 3405.
Abstract 3436: Circadian rhythm dysregulation with risk of gastrointestinal cancers: A large-scale prospective analysis
Authors: Kang Yi , Mok Shinghei , Zong Xiaoyu , Cao Yin
Published: March 2024

Introduction: The incidence of multiple gastrointestinal (GI) cancers has been rising among younger adults with unknown etiology. Circadian rhythm dysregulation due to increasing exposures to artificial lighting, irregular work hours, and frequent travel, has been recently linked with multiple diseases. Disruption of the circadian clock drives Apc LOH to hyperactivate Wnt signaling and enhances MYC-dependent glycolytic metabolism to accelerate colorectal cancer progression. However, the association between circadian rhythm dysregulation, quantified by relative amplitude (RA)–a parameter derived from rest-activity patterns, and risk of colorectal and other GI cancers has not been evaluated in epidemiologic studies.

Methods: We prospectively examined the associations between RA and risk of incident GI cancers among 87,653 UK Biobank participants who wore an Axivity AX3 triaxial accelerometer over 7 days (2013-15) with follow-up to 2021. RA was derived and averaged across all valid days, using the difference between the mean activity levels during the most active 10-hour period and the least active 5-hour period. Cox models were used to estimate relative risks (RRs) and 95% confidence intervals (CIs).

Results: During 512,074 person-years, 1,079 incident GI cancer cases occurred. After multivariable adjustment, lower RA was associated with an increased risk of overall GI cancer (RR per SD [standard deviation] = 1.12, 95% CI 1.04-1.21, P for trend = 0.01). Compared to individuals in the highest tertile (T1), those with RA in the lowest tertile (T3) had a 25% increased risk of overall GI cancer (RR = 1.25, 95% CI 1.05-1.50). The positive associations with GI cancers were mainly driven by gastric cancer (RR per SD = 1.33, 95% CI 1.02-1.74, P for trend= 0.04) and colon cancer (RR per SD = 1.13, 95% CI 1.00-1.28, P for trend = 0.03).

Conclusion: In this large-scale, prospective analysis of accelerometer data, circadian rhythm dysregulation was associated with subsequent risk of GI cancers, primarily gastric and colon cancer. To our knowledge, this is among the first population-based studies reporting the positive link between circadian rhythm dysregulation with cancer risk.

Citation Format: Yi Kang, Shinghei Mok, Xiaoyu Zong, Yin Cao. Circadian rhythm dysregulation with risk of gastrointestinal cancers: A large-scale prospective 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 3436.
Abstract 3518: Next generation H&E cell modeling: Using same-slide multiplex immunofluorescence (mIF) data to train H&E
Authors: Arbiv Becky , Bart Amit , Dankovich Tal , Elran Ron , Bookstein Shai , Laniado Avi , Dicker Tomer , Dagan Sun , Puig Oscar , Bloom Kenneth , Markovits Ettai
Published: March 2024

Haematoxylin & Eosin (H&E)-based deep learning algorithms require a large number of human-based cell annotations for model training, and are limited by what a human eye can see. Multiplex immunofluorescence (mIF) offers a more comprehensive and accurate method for classifying cells because annotations are based on cell status, i.e. whether a cell expresses certain markers or not. In this study, we leverage mIF-based cell type predictions1 to enhance H&E model performance.We used a publicly available CODEX/PhenoCycler dataset2 consisting of 140 tissue cores obtained from 35 patients with colorectal cancer, which were stained with 56 protein markers and subsequently with H&E. mIF data was used to create over 60,000 prediction-based annotations on the corresponding H&E-stained images that were used to train deep learning H&E classifiers.

The final model performance reached AUC of 0.91 when evaluated on the H&E test annotations and 0.90 on the mIF predictions. Notably, the mIF annotations-based H&E model surpassed the manual annotations-based H&E model in effectively identifying challenging cell types, demonstrating its superior performance. These findings highlight the potential of leveraging mIF cell type predictions to train accurate and automated H&E models.

1Markovits et al, BioRxiv, https://doi.org/10.1101/2022.11.09.5157762Schürch et al, Cell. 2020,182(5): 1341-1359.PMID: 32763154

Citation Format: Becky Arbiv, Amit Bart, Tal Dankovich, Ron Elran, Shai Bookstein, Avi Laniado, Tomer Dicker, Sun Dagan, Oscar Puig, Kenneth Bloom, Ettai Markovits. Next generation H&E cell modeling: Using same-slide multiplex immunofluorescence (mIF) data to train H&E [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 3518.
Abstract 3537: Assessing machine learning models of drug response predictions using orthotopic patient-derived xenograft
Authors: Chien Yuan-Hung , Pippa Raffaella , Andrews Warren , Rodriguez Javier , Buck Kristen , Gorospe Derrick , Valencia Elizabeth , Carapia Bianca , Eastwood Emily , Sperry Jantzen , Nakashima Jonathan , Do Long
Published: March 2024

Accurate prediction of drug response using machine learning (ML) remains a significant challenge in drug development as well as in personalized cancer therapy. Furthermore, there is a scarcity of rigorous external validation studies for evaluating drug response prediction models. Even when available, such validations are often confined to in-vitro studies. Orthotopic patient-derived xenograft (O-PDX) mice serve as essential preclinical models that closely replicate the human tumor microenvironment and assess the therapeutic response to cancer treatments. We present CertisAITM, a novel ensemble of machine learning models that have been trained on a vast array of experimental high-throughput screenings of both monotherapies and combination therapies, incorporating over 4500 investigational and FDA-approved drugs across 10 major cancer indications. The results of our ML drug response prediction models show an average R2 of 0.75 and RMSE of 0.62 (across internal 5-fold cross-validation) for all 10 cancer prediction models. Our evaluation of CertisAI's drug response predictions within O-PDX pharmacology studies has shown a notable overall correlation between actual observed tumor growth inhibition (TGI) and predicted TGI, with an r value of 0.45 across seven indications. The most accurate prediction model achieved an r value of 0.7 for colorectal cancer, encompassing 37 treatments in 6 O-PDX studies. Altogether, these results highlight CertisAI’s potential in enhancing pre-clinical model selection as well as personalized treatment strategies in oncology.

Citation Format: Yuan-Hung Chien, Raffaella Pippa, Warren Andrews, Javier Rodriguez, Kristen Buck, Derrick Gorospe, Elizabeth Valencia, Bianca Carapia, Emily Eastwood, Jantzen Sperry, Jonathan Nakashima, Long Do. Assessing machine learning models of drug response predictions using orthotopic patient-derived xenograft [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 3537.