bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2908: EDB+FN is an attractive therapeutic target in oncology: Insights from protein expression analysis of solid tumors
Authors: Lewandowski Sara , Diao Liyang , Quigley Alyssa , Crochiere Marsha , Pinkas Jan
Published: March 2024

Stroma plays a major role in the initiation, growth, survival, and drug-resistance of solid tumors, yet few therapeutics specifically target tumor-associated stroma. Extra-domain-B fibronectin (EDB+FN) is an oncofetal splice variant of fibronectin upregulated in solid tumor stroma, which is associated with tumor growth, angiogenesis, and metastases. Here we developed an immunohistochemistry (IHC) assay to assess EDB+FN protein expression in the stroma of tumor and normal tissues to characterize the potential of EDB+FN as a therapeutic target for solid tumors with high unmet need. We validated a primary detection antibody and titrated assay conditions to achieve specificity and a broad dynamic range of EDB+FN expression levels across indications, including thyroid cancer, head and neck squamous cell carcinoma, hepatocellular carcinoma, soft tissue sarcoma, pancreatic cancer, non-small cell lung cancer, ovarian cancer, and renal cancer. Considering the stroma-specific expression pattern of EDB+FN, we developed a scoring algorithm weighting both the intensity and distribution of EDB+FN expression specifically in the stroma compartment and separately in tumor cells. Using this assay and scoring approach, we screened more than 200 tumor samples from 10 solid tumor indications and found EDB+FN to be highly differentially expressed in tumor-associated stroma with little to no expression on tumor cells and trace to undetectable levels in healthy tissue. EDB+FN was expressed across the indications evaluated with a wide range of expression both within and between indications. Stromal EDB+FN expression was not correlated with stromal density, which also varied widely within and across indications. In parallel, we developed an algorithm using digital pathology to approximate pathologist scoring of stromal density and EDB+FN expression, allowing streamlined screening of preclinical samples for in vivo studies and indication selection. The disease-specific expression pattern of EDB+FN and high incidence of expression across indications make EDB+FN an ideal target for high-unmet-need solid tumors. The specificity and dynamic range of our IHC assay for detection of EDB+FN protein expression position it as a robust potential biomarker assay for EDB+FN-targeting therapeutics.

Citation Format: Sara Lewandowski, Liyang Diao, Alyssa Quigley, Marsha Crochiere, Jan Pinkas. EDB+FN is an attractive therapeutic target in oncology: Insights from protein expression analysis of solid tumors [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 2908.
Abstract 2917: Purifying cancer-associated fibroblasts (CAFs) from glioblastoma and defining their role in therapeutic resistance
Authors: Sati Ankita , Mathur Aakriti , Lad Meeki , Saha Atul , Aghi Manish K.
Published: March 2024

Glioblastoma (GBM), a challenging brain tumor, necessitates the development of new therapies due to poor patient prognoses, with a median survival of 14-16 months. Standard of care, as established almost 20 years ago, remains to be surgical resection followed by chemotherapy and radiation and till date there is no defined standard of care for recurrent GBM, highlighting the urgent need for the development of novel therapies. Recent studies have implicated the tumor microenvironment in these poor prognoses. While cancer associated fibroblasts (CAFs) are a key cellular component of the microenvironment of many systemic tumors, their presence in GBM had been doubted until we recently developed intriguing data identifying cells in GBM that express fibroblast markers, have fibroblast-like morphology, and, most importantly, transcriptomically resemble CAFs from systemic cancers rather than other stromal cells that express similar surface markers such as pericytes (Jain et al. 2023). Similar to other solid cancers, GBM CAFs increase tumor growth and drive immunosuppression. The role of CAFs in regulating these processes could have significant implications in response to standard of care therapy as well as novel immunotherapies. While our initial CAF isolation had just 50% purity, we have developed a novel flow-sorting algorithm for CAF enrichment driven by our bioinformatic data. Through this protocol, we have successfully established, the first of its kind, a biobank of patient derived GBM CAFs with greater than 90% purity. These CAFs are now being utilized to investigate their contribution in conferring resistance to chemotherapy (Temozolomide) and radiotherapy. The CAFs are also being assessed for their role in suppressing T cell function and resistance to immunotherapies. In parallel, the origin of GBM CAFs and their development trajectory is being analyzed to find molecular markers to specifically target CAFs in the GBM microenvironment. The work put together will provide insight on mechanisms employed by CAFs in altering the GBM microenvironment and a basis for developing novel combination approaches, alleviating therapeutic resistance caused due to the presence of CAFs in the GBM microenvironment. The results of this study have the potential to significantly attenuate therapeutic resistance in GBM and provide much needed treatment options and improvement in survival, for what remains one of the most dismal diagnoses in the clinic.

Citation Format: Ankita Sati, Aakriti Mathur, Meeki Lad, Atul Saha, Manish K. Aghi. Purifying cancer-associated fibroblasts (CAFs) from glioblastoma and defining their role in therapeutic resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2917.
Abstract 2929: Multiplexed somatic genome editing to model and investigate advanced colorectal cancer
Authors: Mastel Manuel , Jackstadt Rene , Meier Jasmin , Diamante Gabriele
Published: March 2024

Colorectal cancer (CRC) is among the deadliest cancers worldwide, with advanced CRC being the leading cause of death. For the development of novel therapy options, it is crucial to investigate mechanisms of advanced CRC in a bona fide way. However, little is known about the impact of distinct genomic alterations on cancer progression. The assessment of the function and role of the putative drivers in tumor progression via sequencing data remains challenging, due to the complexity and possible combinations of the candidates. Hence, genetically engineered mouse models (GEMMs) represent the mainstay for the investigation of the role of oncogenes and tumor suppressor genes in cancer progression. However, particularly in CRC, they are limited by imprecise modeling of cancer-associated changes, challenging scalability, and development of tumors in anatomically incorrect places. To tackle these issues, we developed SOmatic CRISPR-mediated genome Alterations of Tumor suppressors with Exploratory single cell Sequencing (SOCRATES) to analyze advanced CRC. We multiplexed CRISPR-Cas systems, packaged them into lentiviral particles, and delivered them to enterocytes via colonoscopy-guided submucosal injection. With this innovative approach, SOCRATES enables rapid and direct in vivo genome engineering for the modeling of advanced CRC with distinct mutational patterns and the investigation of the cancer cell states and tumor microenvironment (TME) upon editing the genes of interest. Similar to the Greek philosopher Socrates, who established a form of argumentized dialogue between individuals, SOCRATES facilitates the understanding of previously undiscovered communication between cancer cells and TME. We analyzed the influence of the most recurrent tumor suppressor mutations (Fbxw7, Ptprt, Arid1a, Atrx, Atm, Smad4, Pten) on the cancer cell state and TME in advanced CRC. Further, we created a TS-TME interaction atlas and revealed novel mechanistic insights into how the TS mutations rewire cell states and cell-cell communications. With this generated knowledge, SOCRATES will contribute to our understanding of complex tumor ecosystems and foster the improvement of diagnostic and therapeutic approaches.

Citation Format: Manuel Mastel, Rene Jackstadt, Jasmin Meier, Gabriele Diamante. Multiplexed somatic genome editing to model and investigate advanced colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2929.
Abstract 2971: A cytosolic growth factor receptor serves as a convergent core of condensates for anabolic activity in cancer and senescence
Authors: Kim Taegyun , Choi Haebeen , Yoon Taeyoung , Kang Chanhee
Published: March 2024

Anabolic activity, driven by growth factor signaling, is essential for cellular activities, including cell growth, proliferation, and protein synthesis. Dysregulation of growth factor signaling has been implicated in numerous human pathological conditions, including cancer and aging. Interestingly, cancer cells and senescent cells - two completely different cell fates - are reported to have an increased anabolic activity. Here, we show endosomal condensation of a growth factor receptor as a molecular switch for such anabolic enhancement. Endosomal condensates of a growth factor receptor (ecGFR) exhibit liquid-liquid phase separation (LLPS), acting as a signaling hub locked in the ‘ON’ state by preventing their lysosomal degradation. Furthermore, we identify a regulatory circuit that operates in both cancer and senescence to facilitate the formation of ecGFR and its physicochemical properties. Pharmacological and genetic resolution of ecGFR corrects aberrant anabolism in cancer and senescence, thereby suppressing cancer growth and senescence-associated hyperinflammation in vitro as well as in vivo. Thus, our study provides a convergent anabolic core between cancer and senescence that could be exploited as a therapeutic vulnerability for human pathological conditions associated with aberrant anabolism.

Citation Format: Taegyun Kim, Haebeen Choi, Taeyoung Yoon, Chanhee Kang. A cytosolic growth factor receptor serves as a convergent core of condensates for anabolic activity in cancer and senescence [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 2971.
Abstract 2978: Extracellular ATP induced senescence in human lung cancer cells
Authors: Ward Ryan A. , Hunt Arabella , Anderson Nora , Chen Xiaozhuo
Published: March 2024

In tumors, extracellular ATP (eATP) concentrations are 1,000 to 10,000 times higher than is found in normal tissues and eATP is up taken through macropinocytosis leading to a large increase in intracellular ATP levels. eATP is also linked to the TGF-β signaling pathway as exocytosis of ATP is induced that is then used in an autocrine fashion activating the P2 × 7 purinergic receptor1. Through these mechanisms, eATP has also been recently shown to induce EMT, CSC formation, and drug resistance1. One of the mechanisms through which these processes may be induced is a senescent cell precursor2. Senescence is a generally irreversible epigenetically controlled process characterized by a complete exit from the cell cycle in response to either DNA damage, stressful conditions, or aging. Recent mounting evidence has shown that senescence can be a cancer promoting mechanism by entering this state in response to stress such as during chemotherapy, but they can utilize it to enhance their malignant capabilities, including the ability to escape their senescent state with heightened stem cell characteristics, which can lead to a higher chance of relapse after treatment2. Senescent cells have recently been named a hallmark of cancer3. This study shows the time dependent induction of a senescent like state in human lung cancer A549 cells after only 2 hours of treatment with 0.5mM eATP, the concentration found in the tumor microenvironment, through analysis of transcriptional markers using total polyA RNAseq as well as chromogenic and flow cytometric assays for senescence associated beta-galactosidase activity. Additionally, inhibitors of macropinocytosis and purinergic receptors have been used to gain insight into the mechanisms of action that this pathway takes. This demonstrates a novel use of ATP within the tumor microenvironment for aiding in cancer progression and drug resistance. After EMT, CSC formation, and drug resistance, senescence is added to the long list of eATP mediated cancer promoting processes.

1. Song J, Qian Y, Evers M, Nielsen CM, Chen X. Cancer Stem Cell Formation Induced and Regulated by Extracellular ATP and Stanniocalcin-1 in Human Lung Cancer Cells and Tumors. IJMS. 2022;23(23):14770. doi:10.3390/ijms232314770 2. Zhang D, Monteiro MJ, Liu J, Gu W. Mechanisms of cancer stem cell senescence: Current understanding and future perspectives. Clin Exp Pharma Physio. 2021;48(9):1185-1202. doi:10.1111/1440-1681.13528 3. Hanahan D. Hallmarks of Cancer: New Dimensions. Cancer Discovery. 2022;12(1):31-46. doi:10.1158/2159-8290.CD-21-1059

Citation Format: Ryan A. Ward, Arabella Hunt, Nora Anderson, Xiaozhuo Chen. Extracellular ATP induced senescence in human lung 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 2978.
Abstract 2990: Differential micro-RNA expression in circulating exosomes of pancreatic ductal adenocarcinoma patients
Authors: Kaur Rupinder , Bhoriwal Sandeep , Gautam Promod Kumar
Published: March 2024

Pancreatic ductal Adenocarcinoma (PDAC) is a highly lethal solid tumor with 5-year survival rate of 5-8%. Extracellular vesicles like exosomes circulating in the blood are crucial mediators of intracellular communication, immunomodulation and tumor progression. The microRNAs being the major cargo of exosomes, are the primary carriers of intracellular information. The role of exosomal-miRNA (exoMIR’s) in regulating the pathogenesis of tumors is well-established in oncology but its potential is still unexplored. To the best of our knowledge no study has yet explored the contrasting exoMIR expression in cancer patients before and after their surgery. In this study, differential exoMIR’s profile of three pancreatic ductal adenocarcinoma patients at three stages: pre-surgery, post-surgery, and follow-up was established using small RNA sequencing on the Illumina platform. In blood samples taken before and after surgery total of 181, 201 and 201 microRNAs were dysregulated in circulating exosomes of three different patients viz. P_1, P_9 & P_11 (Patient identifiers) respectively. Out of the total dysregulated microRNAs in post-op samples 76 were upregulated and 105 downregulated in P_1, 95 upregulated and 106 downregulated in P_9 & 69 upregulated and 132 downregulated in P_11 as compared to their Pre surgery samples. Further, when exoMIR’s of post-op samples were compared to that of follow-up samples after 6 months of surgery their expression profile changed notably such that a total of 184, 157 & 190 microRNAs dysregulated in follow-up of P_1, P_9 and P_11 respectively. Out of the total dysregulated microRNAs in follow up samples 93 were upregulated and 91 downregulated in P_1, 69 upregulated and 88 downregulated in P_9 & 96 upregulated and 94 downregulated in P_11 as compared to their post-op samples. On Venn diagram analysis 27 microRNAs were found to be commonly dysregulated in all 3 patients before surgery and 22 common micro RNAs were again dysregulated even after 6 months of surgery. Bioinformatic analysis of these

differentially expressed miRNAs and their respective protein targets revealed that their role in oncogenic molecular pathways is very prominent, thus highlighting their potential use in cancer therapeutics, diagnostics as well as prognosis.

Citation Format: Rupinder Kaur, Sandeep Bhoriwal, Promod Kumar Gautam. Differential micro-RNA expression in circulating exosomes of pancreatic ductal adenocarcinoma patients [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 2990.
Abstract 3015: HD-PTP mediates tumor suppression via modulation of anti-tumor immunity
Authors: Guo Chenxu , Sun Sheng , Thimmiah Nayana , Maccio Agustina , Koh Siang , Ellisen Leif
Published: March 2024

The role of circulating extracellular vesicles in cancer biology is an area of intense research interest. Here, we reveal a tumor suppressor mechanism of HD-PTP (His Domain Protein Tyrosine Phosphatase, encoded by PTPN23), a protein associated with ESCRT (endosomal sorting complex required for transport), a complex that controls endosome sorting and exosome secretion. While loss of HD-PTP is known to be tumorigenic in mice and is frequently observed in human cancers including Triple Negative Breast Cancer (TNBC), the relevant pathways have remained obscure. We find that inhibition of HD-PTP in vivo promotes tumor progression selectively in a syngeneic, immune-competent TNBC model but not in a matched immune-deficient model. Through systematic profiling of the exosomal proteome in HD-PTP proficient and deficient cells, we identify PD-L1 as a key exosomal cargo selectively enriched due to loss of HD-PTP. Mechanistically, we show that inhibition of HD-PTP results in PD-L1 stabilization, its co-localization with the exosomal marker CD63, the enrichment of endosomal PD-L1 and subsequent increase in ExoPD-L1 release. Exosomes produced post HD-PTP loss inhibits antigen-dependent T cell activity in vitro, and HD-PTP inhibition in a syngeneic TNBC model promotes non-cell-autonomous, exosome- and PD-L1-dependent tumor progression, associated with reduced T cell infiltration and altered macrophage polarization. Consistent with these findings, low HD-PTP levels in human solid tumors are associated with decreased tumor infiltrating lymphocytes, poor response to immune checkpoint inhibition and inferior overall survival. Taken together, our studies unveil a novel tumor suppressor pathway controlling PD-L1 trafficking and ExoPD-L1 secretion, highlighting the critical roles of HD-PTP and ESCRT in anti-tumor immunity.

Citation Format: Chenxu Guo, Sheng Sun, Nayana Thimmiah, Agustina Maccio, Siang Koh, Leif Ellisen. HD-PTP mediates tumor suppression via modulation of anti-tumor immunity [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 3015.
Abstract 3020: The tumor suppressive role of methylthioadenosine phosphorylase in melanoma
Authors: Hsiao Jennifer J. , Andreu-Perez Pedro , Kemény Lajos V. , Hejna Miroslav , Nsengimana Jérémie , Allouche Jennifer , Emran Abdullah Al , Bishop D. Timothy , Jönsson Göran B. , Newton-Bishop Julia , Song Jun , Fisher David E.
Published: March 2024

Methylthioadenosine phosphorylase (MTAP) is an enzyme that is expressed in virtually all tissues but lost in many cancers. MTAP deficiency can be due to either deletion of the MTAP gene or methylation of the MTAP promoter. In normal cells, MTAP catalyzes the conversion of methylthioadenosine (MTA), produced during polyamine biosynthesis, to adenine and 5-methylthioribose-1-phosphate, which is subsequently converted to methionine. MTAP deficiency results in intracellular accumulation of MTA. Although recent genome wide association studies (GWAS) have associated the MTAP locus with melanoma risk, the molecular mechanisms linking MTAP loss to increased tumorigenesis are not yet fully understood. In this study, we hypothesized that loss of MTAP and the resulting accumulation of MTA would dysregulate microphthalmia transcription factor (MITF), a master transcriptional regulator of melanocytes that is also an amplified or mutated oncogene in melanoma. We identify a novel signaling mechanism in which MTA accumulation from MTAP deficiency aberrantly induces MITF expression via inhibition of the cAMP phosphodiesterase PDE4D3 in melanocytes. Inhibition of PKA abolishes this MITF induction, suggesting that the PKA pathway is hyperactivated upon MTAP deficiency. Downregulation of MTAP leads to increased proliferation of melanoma cells in vitro and increased melanoma tumor growth in vivo. We also show that MTAP deficient melanoma cells are more resistant to the BRAF inhibitor vemurafenib and observe MTAP downregulation in BRAF inhibitor resistant melanoma clinical specimens. Furthermore, MTAP downregulation via decreased expression and/or genomic loss corresponds to significantly worse outcomes in early-stage cutaneous melanomas from multiple datasets, thereby identifying a clinically important sub-category of “thin-lethal” tumors.

Citation Format: Jennifer J. Hsiao, Pedro Andreu-Perez, Lajos V. Kemény, Miroslav Hejna, Jérémie Nsengimana, Jennifer Allouche, Abdullah Al Emran, D. Timothy Bishop, Göran B. Jönsson, Julia Newton-Bishop, Jun Song, David E. Fisher. The tumor suppressive role of methylthioadenosine phosphorylase in 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 3020.
Abstract 3034: Krüppel-like factors in regulation of gastric cancer progression
Authors: Kakkat Sooraj , Suman Prabhat , Goswami Sandeep , Basu Sujit , Heslin Martin J. , Turbat-Herrera Elba A. , Alcantara Veronica Ramirez , Sarkar Chandrani , Chakroborty Debanjan
Published: March 2024

Introduction: Gastric cancer (GC) is the third leading cause of cancer-associated mortality and the fifth most frequently diagnosed cancer worldwide. The development and progression of GC is a complicated multistage process subjected to dynamic changes in gene regulation. Investigating the effects of these changes is therefore critical for improving our knowledge about GC initiation and progression. Krüppel-like factors (KLFs) are evolutionarily conserved zinc finger-containing transcription factors with altered expressions and diverse regulatory functions in GC. We previously reported that there is loss of KLF4 in GC. Here we report that KLF4 is a crucial regulator of KLF5 expression and vice versa and together they regulate GC cell behavior.

Methods: The Cancer Genome Atlas (TCGA) and pan cancer data of differential expressions of KLFs in GC was analyzed. TCGA RNAseq and clinical data for the differential expression status of KLF genes in normal and cancerous tissues and the clinicopathological association was accessed from the UALCAN web portal. The expressions of KLF4 and KLF5 in human normal stomach and GC and orthotopic xenografts were detected by immunohistochemistry (IHC). KLF4, KLF5 cross regulation was evaluated by gene manipulation of each gene individually and checking the expression of the other factor in GC cells. The effect of KLFs on GC cell proliferation, migration, and invasion was determined by Ki67 staining of tissues, PrestoBlue cell viability assay, scratch wound and transwell cell invasion assays.

Results and Conclusion: Our results indicated that not only KLF4 and KLF5 have contrasting expressions and effects in GC but also these two factors cross regulate each other. While lower expressions of KLF4 was found in human GC and orthotopic xenografts, increased expression of KLF5 was found in both human GC tissue and orthotopic xenografts. KLF4 silencing and CRISPR/Cas9 knockdown in human GC cells resulted in increased expression of KLF5 which was associated with increased GC cell proliferation and invasiveness. Interestingly, KLF5 knockdown by CRISPR/Cas9 in human GC cells on the other hand resulted in increased expression of KLF4, which was associated with decreased GC cell growth. Our data therefore suggests that the differential expressions of KLF4 and KLF5 might serve as valuable prognostic markers in GC.

Citation Format: Sooraj Kakkat, Prabhat Suman, Sandeep Goswami, Sujit Basu, Martin J. Heslin, Elba A. Turbat-Herrera, Veronica Ramirez Alcantara, Chandrani Sarkar, Debanjan Chakroborty. Krüppel-like factors in regulation of gastric cancer progression [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 3034.
Abstract 3042: Unraveling the mechanism of YAP toxicity in neuroendocrine solid tumors: Insights from Merkel cell carcinoma
Authors: Bahar Furkan , Frost Thomas C. , Ananthapadmanabhan Varsha , Schnabel Julia L. , Thakuria Manisha , DeCaprio James A.
Published: March 2024

The Hippo pathway, a pivotal regulator orchestrating organ size and tissue growth, has emerged as a central player in cancer biology. The downstream transcription factor YAP within this pathway has been implicated in diverse oncogenic processes. YAP activation contributes to drug resistance, metastasis, and poor clinical outcomes in many solid tumors. Conversely, YAP exhibits growth-suppressive effects in neuroendocrine (NE) solid cancers, a paradox that remains poorly understood. Analysis of RNAseq data from the Cancer Cell Line Encyclopedia (CCLE) revealed a distinct classification of tumors into YAP1-expressing (YAPon) and non-expressing (YAPoff) subgroups, with hematopoietic malignancies and NE solid tumors featured prominently in the latter. Merkel cell carcinoma (MCC) is a rare, high-grade, NE carcinoma of the skin with two distinct etiologies. Virus-positive MCC contains integrated Merkel cell polyomavirus that expresses the viral T antigens and virus-negative MCC caused by sunlight exposure and extensive UV damage. Bulk RNAseq performed with more than 60 MCC tumors revealed that YAP expression displayed an inverse correlation with an NE gene expression signature. To gain insight into why YAP expression is so low in MCC, we generated MCC cell lines with inducible expression of YAP. Expression of YAP led to growth arrest and cell death. We performed a genome-wide CRISPR-Cas9 screen to identify genes that when lost enable MCC cells to tolerate YAP expression. Functional enrichment analysis of the positively selected genes uncovered a variety of signaling pathways. Intriguingly, the CRISPR screen revealed a positive enrichment of non-canonical BAF complex members, including BRD9 and SMARCD1. To validate this finding, we treated MKL-1 cells with a BRD9 inhibitor, observing a substantial reduction in YAP toxicity. These findings open avenues for the development of targeted therapeutic strategies for high grade NE cancers, addressing a critical gap in our understanding of YAP biology in the context of MCC and beyond.

Citation Format: Furkan Bahar, Thomas C. Frost, Varsha Ananthapadmanabhan, Julia L. Schnabel, Manisha Thakuria, James A. DeCaprio. Unraveling the mechanism of YAP toxicity in neuroendocrine solid tumors: Insights from Merkel cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3042.
Abstract 3057: The TARZN complex binds to de novo enhancer mutations and promotes oncogenic expression in T-ALL
Authors: Anuar Nurkaiyisah Zaal , Goh Chai Yeen , Chua Boon Haow , Tan Shi Hao , Costa Joana R. , Mansour Marc R. , Sanda Takaomi , Kappei Dennis
Published: March 2024

TAL1 is overexpressed in 40-60% of T-cell acute lymphoblastic leukaemia (T-ALL) cases and forms an oncogenic core regulatory circuit (CRC) with other transcription factors such as LMO1, LMO2 and GATA3. In 5% of T-ALL cases an insertion of a consensus GT dinucleotide is observed upstream of the TAL1 gene, termed the “Mutation of TAL1 enhancer” (MuTE), driving TAL1 overexpression. Using an in vitro reconstitution DNA pull-down assay combined with quantitative mass spectrometry, we identified nine candidate proteins that preferentially bound to the MuTE sequence compared to the WT sequence. Among the candidates, we demonstrate by reciprocal immunoprecipitation experiments coupled to quantitative mass spectrometry that the RNA methyltransferase TARBP1 and the zinc finger proteins ZBTB2, ZBTB25 and ZNF639 formed a complex that we term TARZN. Interestingly, the TARZN complex also bound to de novo super enhancer sites upstream of the LMO1 and LMO2 genes in T-ALL cells, indicating a putative common mechanism between these different non-coding driver mutations. Furthermore, knock-down of all TARZN members resulted in lower TAL1 protein expression in MuTE-positive but not in MuTE-negative T-ALL cells. Overall, these data suggest that the TARZN complex cooperatively promotes oncogenic expression in T-ALL.

Citation Format: Nurkaiyisah Zaal Anuar, Chai Yeen Goh, Boon Haow Chua, Shi Hao Tan, Joana R. Costa, Marc R. Mansour, Takaomi Sanda, Dennis Kappei. The TARZN complex binds to de novo enhancer mutations and promotes oncogenic expression in T-ALL [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 3057.
Abstract 3070: CDK12 is a novel therapeutic target in glioblastoma
Authors: Mun Jeong-Yeon , Shu Chang , Gao Qiuqiang , Westhoff Mike-Andrew , Karpel-Massler Georg , Siegelin Markus D.
Published: March 2024

Glioblastoma (GBM), the most common primary brain tumor in adults carries a highly unfavorable prognosis of only one to two years despite treatment with the standard of care, involving surgery, temozolomide and radiation. Patient-derived xenograft (PDX) GBM cultures were assessed for their susceptibility to loss of CDK12 function, which was either mediated genetically (shRNA) or by the novel inhibitor, SR-4835. GBM metabolism was measured by utilizing extracellular flux analysis as well as LC/MS based carbon tracing analyses. In vivo efficacy was determined by orthotopic GBM models in mice. Based on Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) and shRNA library screens in multiple GBM cell cultures we identified CDK12 as essential for the growth of GBM. Consistently, loss of function of CDK12 (genetically and pharmacologically) led to a reduction of growth of GBM patient-derived xenograft (PDX) lines in vitro. Notably, SR-4835 reduced GBM growth in the low nanomolar range and synergistically enhanced the potency of temozolomide. Extracellular flux analysis and metabolite screening analyses, including carbon tracing (U13C-Glucose, U13C-Glutamine) suggested that loss of function of CDK12 elicited a substantial inhibition of cellular respiration, causing energy deprivation with subsequent cell death with apoptotic features. On the molecular level, loss of function of CDK12 increased ATF4 along with pro-apoptotic Noxa, whereas anti-apoptotic Mcl-1 decreased. In turn, adenoviral mediated ectopic expression of Mcl-1 inhibited cell death mediated by loss of function of CDK12 in GBM cells. In an orthotopic murine PDX model of GBM animals receiving treatment with SR-4835 had a significantly longer overall survival without induction of toxicity as compared to mice treated with vehicle. In summary, these findings suggest that CDK12 is a novel treatment target for GBM and that CDK12 is an important driver of energy metabolism in GBM to partially mediate apoptotic resistance. Moreover, SR-4835 enhanced the potency of temozolomide in GBM models. Therefore, the novel CDK12 inhibitor, SR-4835 should be tested in a clinical trial in patients suffering from GBM.

Citation Format: Jeong-Yeon Mun, Chang Shu, Qiuqiang Gao, Mike-Andrew Westhoff, Georg Karpel-Massler, Markus D. Siegelin. CDK12 is a novel therapeutic target in glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3070.
Abstract 3073: ACTL6a drives metabolic reprogramming and chemoresistance in head and neck squamous cell carcinoma
Authors: Monavarian Mehri , Finegersh Andrey
Published: March 2024

Actin like protein 6A (ACTL6a), a subunit of the SWI/SNF chromatin remodeling complex, is amplified in a third of all squamous cell carcinomas including head and neck (HNSCC) cancers. Recent studies implicate ACTL6a as an oncogenic driver that potentiates SWI/SNF-related chromatin remodeling; however, the underlying mechanisms in HNSCC progression yet to be elucidated. Using the HNSCC cell lines FaDu, SCC90, and SCC2, ACTL6a knockdown (siACTL6a) led to a significant reduction in cell proliferation compared to control when measured by sulforhodamine B but not resazurin, suggesting up-regulation of oxidative phosphorylation with siACTL6a. We used RNA-seq datasets of siACTL6a in FaDu cells and found that there was a significant up-regulation of components of complex I and IV of the electron transport chain compared to control. Gene set enrichment analysis also demonstrated a significant up-regulation in glycolysis in ACTL6a amplified tumors within the HNSCC TCGA dataset. Since metabolism is a key driver of chemotherapy resistance, we studied effects of ACTL6a expression on cisplatin-mediated cytotoxicity. Compared to control, siACTL6A of the HNSCC cell lines FaDu and SCC2 had significantly decreased IC50 to cisplatin, indicating ACTL6a mediates toxicity. We also observed significantly decreased migration in a transwell migration assay in siACTL6A FaDu and SCC2 cells compared to control. We are studying the effects of shRNA directed against ACTL6a using a syngenic in vivo tumor model with a mouse oral cavity (MOC2) cell line that grows in C57BL/6J mice. Subcutaneous injection of MOC2 cells demonstrated significantly decreased tumor growth in shACTL6a cells compared to control. We are performing additional studies to identify specific mechanisms of ACTL6a mediated metabolic reprogramming in tumor cells. In conclusion, ACTL6A amplification is common in HNSCC and facilitates metabolic reprogramming, which drives tumor proliferation, cell migration, and drug resistance.

Citation Format: Mehri Monavarian, Andrey Finegersh. ACTL6a drives metabolic reprogramming and chemoresistance in head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3073.
Abstract 3081: Targeting lipid kinases to enhance autophagy inhibition for the treatment of pancreatic cancer
Authors: Schechter Elyse G. , DeLiberty Jonathan M. , Stalnecker Clint A. , Bryant Kirsten L.
Published: March 2024

Pancreatic ductal adenocarcinoma (PDAC) is characterized as the most KRAS-addicted cancer type, with KRAS mutations found in >95% of cases. Mutant KRAS relies on dysregulated metabolism to support growth. One dysregulated pathway upregulated in PDAC is autophagy, a lysosome-mediated process that degrades proteins and organelles to supply macromolecules for growth. Our lab and others have shown that inhibition of KRAS or the mitogen activated protein kinase (MAPK) components, MEK or ERK, further increases PDAC dependency on autophagy as a resistance mechanism. Cotreatment with ERK MAPK inhibitors and the autophagy inhibitor chloroquine (CQ) decreased autophagic flux, inhibited proliferation, and induced apoptosis in PDAC cells. CQ is the only FDA-approved autophagy inhibitor, and it demonstrates low potency in vivo, motivating our studies to identify strategies to improve autophagy inhibition in PDAC. We utilized a CRISPR-Cas9 loss-of-function screen to identify sensitizers to CQ in PDAC and identified 25 autophagy-related targets.

We hypothesize that targeting the autophagy pathway at multiple nodes will increase the efficacy of CQ treatment in PDAC. To validate hits identified in the CRISPR-Cas9 screen, I designed an siRNA array that contained three distinct oligos for each target. I quantified changes in proliferation in a panel of four PDAC cell lines after siRNA-mediated suppression of the target genes following 3- or 6-day time points.

I hypothesized that targets identified to be non-essential on their own would allow for potential synthetic lethality with CQ. To test this, I performed a 3-day knockdown followed by 3-day exposure to a dose response of CQ. I found that suppression of lipid kinases PIP4K2A, PIP4K2C, or PIK3C3 shift the dose response to CQ in a panel of PDAC lines. This indicates that loss of those targets sensitizes PDAC cells to CQ treatment. Furthermore, we found that pharmacological inhibition of VPS34, the lipid kinase encoded by PIK3C3 by the ATP-competitive inhibitor SAR-405 synergizes with CQ.

My future studies will be focused on validating other targets identified in the loss-of-function CRISPR-Cas9 screen. I will measure changes in autophagic flux and apoptosis due to the loss of validated targets. The long-term goal of this project is to enhance the translatability of autophagy inhibition for patient care through identifying combinational approaches to improve CQ response in PDAC.

Citation Format: Elyse G. Schechter, Jonathan M. DeLiberty, Clint A. Stalnecker, Kirsten L. Bryant. Targeting lipid kinases to enhance autophagy inhibition for the treatment 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 3081.
Abstract 3087: The m6A methyltransferase RBM15 drives the growth of triple-negative breast cancer cells through the stimulation of serine and glycine metabolism
Authors: Park Su Hwan , Park Yun-Yong , Lee Jong-Ho
Published: March 2024

N6-adenosine methylation (m6A) is critical for controlling cancer cell growth and tumorigenesis. However, the function and detailed mechanism of how m6A methyltransferases modulate m6A levels on specific targets remains unknown. In the current study, we identified significantly elevated levels of RBM15, an m6A writer, in basal-like breast cancer (BC) patients compared to non-basal like BC and linked it to worse clinical outcome. Gene expression profiling uncovered correlations between RBM15 and serine and glycine metabolism genes including PHGDH, PSAT1, PSPH, and SHMT2. RBM15 influences overall m6A levels and, specifically, m6A of serine and glycine metabolism genes via direct binding to target RNA. Further RBM15 effects on cell growth were largely dependent on serine and glycine metabolism. Thus, RBM15 coordinates cancer cell growth through altered serine and glycine metabolism suggesting RBM15 as a new therapeutic target in BC.

Citation Format: Su Hwan Park, Yun-Yong Park, Jong-Ho Lee. The m6A methyltransferase RBM15 drives the growth of triple-negative breast cancer cells through the stimulation of serine and glycine metabolism [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 3087.
Abstract 3104: A NanoBRET target engagement assay for querying domain selectivity at full-length polymerase theta in live cells
Authors: Edenson Steven , Slater Michael , Corona Cesear , Beck Michael , Vasta James , Teske Kelly , Michaud Ani , Robers Matthew
Published: March 2024

In HR-deficient cells, Polymerase Theta (Pol-theta) serves to repair double strand breaks and has emerged as a therapeutic target in HR-deficient cancers. Encoded by the POLQ gene, Pol-theta is a large (290 Kda) protein with two distinct functional domains (polymerase, helicase), separated by an unstructured region. Each domain of Pol-theta has proven vulnerable to small molecule inhibitors, with a number of molecules undergoing clinical evaluation. Unlike the helicase domain, target engagement at the polymerase domain requires cooperativity with DNA fragments. Here we describe a novel NanoBRET Target Engagement assay that enables domain-specific analysis of small molecule occupancy in live cells. To observe the high affinity-state of small molecule inhibitors to the polymerase domain, we have developed a cell-permeable pol domain NanoBRET probe, along with a novel work flow to introduce small DNA fragments into live cells. Together these components form a nucleoprotein complex with full length polymerase theta. This assay method can be used to quantify and rank-order engagement to the polymerase domain in live cells. To enable domain-selectivity analysis, we have developed a second NanoBRET probe directed to the helicase domain. Together these two NanoBRET probes allow for the mechanism of action studies at Pol-theta in living cells.

Citation Format: Steven Edenson, Michael Slater, Cesear Corona, Michael Beck, James Vasta, Kelly Teske, Ani Michaud, Matthew Robers. A NanoBRET target engagement assay for querying domain selectivity at full-length polymerase theta in live 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 3104.
Abstract 3143: The ADC payload PNU-159682 is highly active in a wide range of cancer indications by inducing DNA damage and cell death via a distinct mode of action
Authors: Kaiser Monika , Fiedler Ulrike , Gerlach Daniel , Kraut Norbert , Bammert Lukas
Published: March 2024

During the last decade antibody-drug-conjugates (ADCs) have become an important and validated treatment modality for cancer patients. Here, we introduce a unique next generation ADC platform based on Sortase-mediated antibody conjugation (SMAC-Technology) yielding in very homogenous and stable drug conjugates with limited systemic, but powerful anti-tumor activity. The highly potent payload used is a proprietary derivative of the Anthracycline PNU-159682. Our PNU-159682-based ADCs are known to not only induce DNA damage in the target cell, but importantly also trigger immunogenic cell death and thus, stimulating anti-tumor immunity offering untapped combination potential. ADCs based on the SMAC-Technology platform currently undergo clinical development. In this work, we present functional studies that were performed to further elucidate the mode of action (MoA) of the ADC payload PNU-159682 and to investigate any potential liabilities with respect to sensitivity, which could limit treatment options for cancer patients. Flow cytometry-based readouts verified that PNU-EDA, a derivative of PNU-159682, is a highly potent inducer of DNA damage, cell cycle arrest and cell death. Interestingly, PNU-EDA arrests cells and inhibits DNA synthesis in S-phase in contrast to other Anthracyclines such as Doxorubicin, which leads to a block in the G2/M-phase. High-throughput cell line panel sensitivity screens confirmed that the activity of PNU-EDA is broad and not restricted to specific cancer indications. Notably, a correlation between lower potency and increased ABCB1 (MDR1) expression levels was observed for PNU-EDA, but not for parental PNU-159682. More detailed mechanistic insights were obtained by performing a genome-wide CRISPR-Cas9 KO screen, which revealed a partial dependency of the PNU-EDA potency on the proficiency of the TC-NER DNA damage repair mechanism. This finding further highlights a distinct MoA of PNU-159682 compared to Doxorubicin or other DNA-targeting compounds such as Cisplatin. Overall, our screens and mechanistic studies verified that PNU-159682-based ADCs efficiently kill cancer cells via a particular MoA and thereby, offer highly promising therapeutic options to a diverse and large population of cancer patients.

Citation Format: Monika Kaiser, Ulrike Fiedler, Daniel Gerlach, Norbert Kraut, Lukas Bammert. The ADC payload PNU-159682 is highly active in a wide range of cancer indications by inducing DNA damage and cell death via a distinct mode of action [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 3143.
Abstract 3173: Impact of hypoxia on the integrated stress response activated by imipridones ONC201 and ONC206 in pediatric diffuse midline glioma cells
Authors: Roady Tyler J. , Stubbs Nolan , Chen Josephine , Xia Yutong , Uruchurtu Ashley Sanchez Sevilla , Tian Xiaobing , Zhou Lanlan , El-Deiry Wafik S.
Published: March 2024

Diffuse midline gliomas (DMGs) are highly aggressive, high-grade gliomas which typically arise in children and young adults. With currently approved treatments the median survival from time of diagnosis for pediatric DMG is 8-10 months with only 10% of children living to 2 years post diagnosis. Despite being only 15% of the cases it makes up 40% of the pediatric brain cancer deaths making it the leading cause of death for all pediatric glioma cases. Two recent clinical studies, NCT03416530 and NCT03134131, have shown the clinical efficacy of Dordaviprone (ONC201/TIC10) for the treatment of DMG; increasing median survival to 22 months in patients following radiation treatment prior to recurrence. Imipridone ONC206, a chemical derivative of ONC201, is under clinical development for treatment of pediatric and adult patients with primary brain tumors (NCT04732065 and NCT04541082). To further improve treatment, we must continue to study how the tumor microenvironment impacts the efficacy of imipridones. One crucial aspect of all brain cancers is hypoxia, so the IC50s of the SU-DIGP-25, SU-DIPG-XIII and SU-DIPGIV pediatric DMG cell lines treated with ONC201 or ONC206 were measured using the CellTiter-Glo assay under conditions of hypoxia and normoxia. Imipridones mediate apoptosis through the upregulation of the TRAIL death receptor DR5 and the activation of the integrated stress response (ISR), so western blots were used to show changes in the ISR protein expression in ONC201 treated DMG cells at multiple different degrees of hypoxia. To understand how hypoxia inducible factors (HIFs) play a role in resistance and susceptibility to ONC201 or ONC206, HIF-1a, HIF-2a, and HIF-3a were knocked down showing altered ISR protein expression after treating with the imipridones under hypoxic and normoxic conditions.

Citation Format: Tyler J. Roady, Nolan Stubbs, Josephine Chen, Yutong Xia, Ashley Sanchez Sevilla Uruchurtu, Xiaobing Tian, Lanlan Zhou, Wafik S. El-Deiry. Impact of hypoxia on the integrated stress response activated by imipridones ONC201 and ONC206 in pediatric diffuse midline glioma 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 3173.