bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1122: Pan-cancer analysis reveals roles of retrotransposon-fusion RNAs
Authors: Lee E. Alice , Lee Boram , Choi Yoonjoo , Park Junseok , Voshall Adam , Maury Eduardo , Kang Yeeok , Kim Yeon Jeong , Lee Jin-Young , Shim Hye-Ran , Kim Si-Cho , Chu Hoang Bao Khanh , Kim Da-Won , Kim Minjeong , Choi Eun-Ji , Ha Kyungsoo , Choi Jung Kyoon , Kim Yongjoon , Park Woong-Yang
Published: June 2023

Transposons comprise half of the human genome and some create novel insertions in human germ cells and somatic tissues of healthy and diseased individuals. These genetic elements may be an abundant yet underexplored source of immunogenic molecules that create chimeric transcripts composed of transposons and non-transposons. However, it remains challenging to accurately identify such transposon-fusion events from short RNA-seq reads mainly due to the repetitive nature of transposon sequences and error-prone read alignment near exon-intron junctions, and there are few existing methods for such detection. We developed a computational pipeline, rTea (RNA Transposable Element Analyzer) to detect transposons-fusion transcripts from RNA-seq data. Using rTea, we performed a pan-cancer analysis of 10,257 cancer samples across 34 cancer types as well as 2,994 normal tissue samples from the TCGA/ICGC, our unpublished colorectal cancer cohort, and the GTEx consortia. Among normal human tissues, higher fusion loads were found most notably in the testis and to a lesser extent in other tissues that have been characterized as immune-privileged. Somatic fusions found in cancer were enriched in known cancer genes, implicating their contribution to tumorigenesis. We also found distinct epigenetic and tumorigenic mechanisms underlying fusions from different transposon families. Through in silico immunogenicity modeling and experimental validation, we confirmed the MHC-I binding and CD8+ T cell activation by peptides derived from transposon fusions to the extent comparable to EBV viruses. Our findings highlight endogenous retroelements as novel therapeutic targets and a significant source of neoantigens.

Citation Format: E. Alice Lee, Boram Lee, Yoonjoo Choi, Junseok Park, Adam Voshall, Eduardo Maury, Yeeok Kang, Yeon Jeong Kim, Jin-Young Lee, Hye-Ran Shim, Si-Cho Kim, Hoang Bao Khanh Chu, Da-Won Kim, Minjeong Kim, Eun-Ji Choi, Kyungsoo Ha, Jung Kyoon Choi, Yongjoon Kim, Woong-Yang Park. Pan-cancer analysis reveals roles of retrotransposon-fusion RNAs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1122.
Abstract 1217: The FAM72 gene family promotes cancer development by disabling the base excision repair system
Authors: Feng Yuqing , Thakur Bhupesh , Bruce Jeffery , Mamand Sami , Shirdarreh Melika , Wong Matthew , Silvester Jennifer , Han Ming , Kashem Mohammad , Zia Amin , Cescon David , Pugh Tervor , Pezo Rossanna C. , Martin Alberto
Published: June 2023

Genetic lesions are central contributors to cancer development and progression, and understanding the sources of these lesions will provide a better understanding of the mechanisms of carcinogenesis. Our previous work showed that the uncharacterized murine Fam72a gene promotes mutagenic DNA repair during antibody maturation by causing the degradation of Uracil DNA glycosylase 2 (UNG2), a component of the base excision repair (BER) system. Humans encode four almost identical paralogues of FAM72 called FAM72A-D, which are absent in all other mammalian genomes, including those of non-human primates. The role of these four paralogues in human biology is unknown. Intriguingly, a previous report showed that FAM72A is over-expressed in many cancers. Since FAM72A promotes mutagenesis by degradation of UNG2, we hypothesized that overexpression of the FAM72 gene family might promote cancer development and progression. Here we show that FAM72A-D is overexpressed in many human cancers and inversely correlates with UNG2 protein levels in tumorigenic tissue. However, FAM72A but not FAM72B-D causes degradation of UNG2. Consistent with this effect, FAM72 expression correlates with a higher mutation load in many tumor types. Since genetic mutations are associated with cancer development and progression, we tested whether FAM72 expression is associated with disease outcomes. Indeed, we found that high FAM72 expression was associated with poorer survival in several cancers. To directly test if Fam72a is sufficient to promote cancer, we generated transgenic mice that overexpress Fam72a in multiple tissues. We observed that Fam72a overexpression promotes increased colonic polyps in the Apcmin background compared to controls. These data show that the novel FAM72 gene family are drivers of cancer development in both mice and humans and advances our understanding of the underlying molecular mechanisms that precipitate cancer development and progression. This work is supported by a grant from the CIHR (PJT-180269).

Citation Format: Yuqing Feng, Bhupesh Thakur, Jeffery Bruce, Sami Mamand, Melika Shirdarreh, Matthew Wong, Jennifer Silvester, Ming Han, Mohammad Kashem, Amin Zia, David Cescon, Tervor Pugh, Rossanna C. Pezo, Alberto Martin. The FAM72 gene family promotes cancer development by disabling the base excision repair system [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1217.
Abstract 1238: Loss of HSPD1 induces cellular plasticity in triple-negative breast cancer cells
Authors: Khodary Muhammad G. , Yirsaw Alehegne W. , Samuel Temesgen , Yates Clayton , Bedi Deepa
Published: June 2023

Abstract Background Unlike Breast cancer (BRCA) luminal subtypes, Triple negative breast cancer (TNBC) subtype lacks expression of estrogen receptor-α (ERα/ESR1), progesterone receptor (PGR) and/or epidermal growth factor (EGF) family receptor HER2/ERBB2 where patients do not benefit from endocrine and HER2 based therapies in addition to its poor differentiation that results in greater aggressiveness and poorer prognosis. The 60 KD Heat shock protein (HSP60) is a Mitochondrial protein that plays a role in stabilizing and refolding proteins and is regulated by HSPD1 gene. In normal cells, HSPD1 gene expression is controlled, however in TNBC, HSPD1 overexpression is common and is associated with poor cancer-specific survival. This study aims to understand downstream signaling pathways dependent on the function of HSPD1 in TNBC. Method To understand downstream signaling pathways dependent on the function of HSPD1, we analyzed the transcriptomic profiles of metastatic MDA-MB-231-WT and HSPD1-KD cells. Results Bioinformatics data analysis shows that HSPD1 is overexpressed in TNBC, particularly in basal subtype. High expression of HSPD1 related to low survival in breast cancer patients. HSPD1 KD in MDA-MB-231 cells identified several differentially regulated genes (DEG) as compared to WT MDA-MB-231 cells by RNA-seq analysis. Pathway analysis of DEG showed downregulation of mitochondrial respiration, thermogenesis, citric acid cycle, PD-1 signaling while upregulation of estrogen dependent gene expression, estrogen mediated signaling, nuclear receptor transcription pathway. These suggests that HSP60 overexpression in TNBC promotes basal type phenotype. Downregulation of HSP60 expression upregulated hormone receptors, particularly estrogen receptor (ESR1) and androgen receptor (AR) expression, thus inducing basal to luminal switch in MDA-MB-231 cells. These findings suggest that loss of HSPD1 significantly Induces plasticity in TNBC. Conclusion Our results suggest that loss of HSPDI in the context TNBC cells may promotes oncogenic transformation to an intermediary luminal progenitor phenotype that gains differentiation plasticity based on the upregulation of Estrogen-receptors signaling pathways. Ongoing analyses will be performed to identify the possible links between loss of HSPD1 and key transcription factors that define mammary epithelial cell differentiation.

Citation Format: Muhammad G. Khodary, Alehegne W. Yirsaw, Temesgen Samuel, Clayton Yates, Deepa Bedi. Loss of HSPD1 induces cellular plasticity in triple-negative breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1238.
Abstract 1242: Single cell multiomic map reveals regulatory landscape of human brain metastases
Authors: Klotz Remi , Zukowski Alexis , Kamal Mohamed , Attenelo Frank , Ramachandran Srinivas , Yu Min
Published: June 2023

Capturing comprehensive brain metastasis landscape is critical to the establishment of effective anti-tumor strategies. This study took advantage of single-cell multiomics sequencing to profile the molecular and cellular dynamics in tumor cells and associated microenvironment during brain metastasis. Among different primary cancer types, our data suggest that there are conserved yet distinct tumor cell subpopulations, governed by specific changes in gene expression, chromatin accessibility and tumor-stroma interactions. We characterized the conserved tumor subpopulations of brain metastasis with features of: (1) dormancy, (2) enhanced translation and migration, (3) cell death and (4) high proliferation rate. Dormant tumor cells in brain metastasis appear to limit cell-cell interactions with the surrounding microenvironment. In line with previous observations, dormant cells exhibit distinct stimulation for interferon, oxidative phosphorylation and HIPPO signaling. Despite a pronounced cell plasticity, trajectory analysis uncovered a cell progression pattern and its major sequential states and driving genes. Importantly, the tumor trajectory provides new insights into the regulatory landscape controlling the transition from dormant to proliferating tumor cells. Our findings also point to a valuable use of matched isolated circulating tumor cells and cell-free DNA to map the molecular and cellular dynamics of brain metastases. This work demonstrated that despite a pronounced intratumoral heterogeneity, brain metastases present conserved tumor subpopulations regardless of the patient and primary type. A novel and key finding in this study is the multiomics characterization of the regulatory landscape shaping human brain metatastases. Thus, we believe further understanding of these key regulatory elements could lead to novel tumor targets with broad translational potential.

Citation Format: Remi Klotz, Alexis Zukowski, Mohamed Kamal, Frank Attenelo, Srinivas Ramachandran, Min Yu. Single cell multiomic map reveals regulatory landscape of human brain metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1242.
Abstract 1244: Examining the differential roles of OSM and IL-6 in varying subtypes of breast cancer for novel therapeutic treatment
Authors: Wolf Cody L. , Tawara Ken , Jorcyk Cheryl L.
Published: June 2023

Breast cancer remains the second leading cause of cancer-related death in women, in large part due to distant metastasis to organs such as bone, lung, liver, and brain. Our laboratory has demonstrated that the IL-6-family cytokine oncostatin M (OSM) increases circulating tumor cell (CTC) numbers and metastases to lung in vivo, and that OSM stays active when bound to proteins in the extracellular matrix, thus “bioaccumulating” in the tumor microenvironment. These published findings are supported by our results demonstrating that OSM strongly promotes expression and secretion of IL-6 from breast cancer cells. Interestingly, the increased production of IL-6 by OSM occurs only in estrogen receptor-negative (ER-) cells. It is well known that patients with ER- breast cancer, specifically triple negative breast cancer (TNBC; ER- PR- HER2-), have limited therapeutic options. However, the divergent role OSM plays in ER+ and ER- breast cancer and the mechanism by which this occurs has yet to be fully understood. Thus, we aimed to fully elucidate the difference between OSM in ER+ versus ER- breast cancer. First, we performed RNA-Seq analysis on OSM-treated human ER+ T47D cells and ER- TNBC MDA-MB-231 cells and discovered significant differences in gene expression between both cell lines upon treatment with OSM, including alteration in DNA-replication and cell cycle pathway genes. Next, to better understand the mechanism by which OSM-mediated IL-6 secretion is repressed, we utilized a computational modeling approach and evaluated the direct inhibition of STAT3 and ER to identify theoretical dimerization complex for future studies. This research aims to elucidate the unique role OSM plays in ER+ and ER- breast cancer and will provide a molecular understanding of how this occurs and will provide detailed information on which patients will benefit most from anti-OSM therapeutics.

Citation Format: Cody L. Wolf, Ken Tawara, Cheryl L. Jorcyk. Examining the differential roles of OSM and IL-6 in varying subtypes of breast cancer for novel therapeutic treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1244.
Abstract 1307: The effect of circulating CXCL10 on osteosarcoma metastasis using orthotopic xenograft mouse models
Authors: Chen Xiang , Clement Margaret , Hicks John , Man Tsz Kwong
Published: June 2023

Osteosarcoma is the most common malignant bone tumor in children. Despite the use of chemotherapy and surgery, the survival of patients with metastasis is still dismal. We have previously reported that a high serum level of CXCL10 is associated with a poor prognosis and metastasis in osteosarcoma, suggesting that the chemokine may affect the development of metastasis. Nonetheless, the effect of endocrine signaling of CXCL10 is largely unknown. It is unclear if the prognostic effect of circulating CXCL10 is due to its metastasis-promoting effect or if CXCL10 is merely a biomarker. In this study, we employed orthotopic xenograft mouse models to examine the effect of circulating CXCL10 with respect to metastasis. We first injected luciferase-labeled 143B osteosarcoma cells into the tibia of NOD/SCID mice to generate an orthotopic xenograft mouse model. When the tumor was detectable by bioluminescence, we injected 1.5ug of CXCL10 protein or saline intravenously via the tail vein every day for two weeks. The development of pulmonary metastasis was monitored by bioluminescence. The mice were sacrificed at the endpoint when bioluminescence was detected in the lungs. The mouse lungs were then resected and examined by H&E staining for the detection of metastatic nodules. The mice in the experimental and control groups that developed lung metastases were compared. The results showed that no significant difference was observed between the two groups. The experiment was repeated one more time and similar results were observed. To investigate the influence of the cell line background, we analyzed another osteosarcoma cell line, MG63.3. No significant difference in metastasis development was observed between the mice injected with CXCL10 and the mice injected with saline. The results indicate that a higher level of circulating CXCL10 alone was not sufficient to promote pulmonary metastases in the orthotopic xenograft mouse models. We also showed that AKT phosphorylation was upregulated in the osteosarcoma cell lines incubated with CXCL10, ruling out that the CXCL10 protein used was biologically inactive. In summary, our results suggest that although an increased circulating level of CXCL10 is associated with a poor prognosis in osteosarcoma patients, it does not promote the development of pulmonary metastasis in xenograft mouse models. Circulating CXCL10 may only act as a prognostic biomarker, but not a metastatic driver. Alternatively, the CXCL10-CXCR3 axis may be necessary, but not sufficient, to cause metastasis.

Citation Format: Xiang Chen, Margaret Clement, John Hicks, Tsz Kwong Man. The effect of circulating CXCL10 on osteosarcoma metastasis using orthotopic xenograft mouse models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1307.
Abstract 1435: A GABP dominant negative approach to targeting tumor cell immortality
Authors: Stevers Nicholas O. , Collins Sara A. , Wu Samuel H. , Kasahara Noriyuki , Costello Joseph F.
Published: June 2023

Immortality is a hallmark of human cancer cells and therapeutic reversal is of great interest. Telomerase Reverse Transcriptase promoter (TERTp) mutations reactivate TERT expression, the rate limiting step in telomerase activity and cellular immortality. While prior telomerase blocking therapies lack tumor selectivity and were poorly tolerated, TERTp mutations and their regulation offer a unique opportunity for tumor specific reversal of cellular immortality. TERTp mutations are the most common non-coding mutation across all cancers, including glioblastoma (GBM), melanoma, urothelial carcinoma, and many others. The mutations generate a de novo E26 Transformation Specific (ETS) binding motif that recruits the GA-Binding Protein (GABP) multimeric complex to reactivate TERT expression. While GABP can form both a dimeric and tetrameric complex, we found that the tetrameric complex is responsible for reactivation of the mutant TERTp, suggesting selectively targeting the tetramer may induce telomere shortening and tumor cell death. However, through knocking out the tetramer, we found that the GABP dimer is sufficiently upregulated to maintain TERT expression. In the absence of the dimer and the tetramer isoform, many tumor cells senesce or undergo cell death. However, some escape this fate via upregulation of a second tetramer forming GABP paralogue that maintains TERT expression. Therefore, we devised a transactivation domain null GABP subunit that we hypothesized would act in a dominant negative manner to block the GABP dimer and both GABP tetramers. Introduction of the dominant negative construct into TERTp mutant GBM, meningioma, medulloblastoma, oligodendroglioma, and urothelial carcinoma cells significantly reduced TERT expression while not altering expression in TERTp wildtype GBM cells. Furthermore, the dominant negative is able to shorten telomere length in TERTp mutant GBM cells. While therapeutic targeting of the three GABP complexes seems particularly challenging, our initial dominant negative appears to do so. Ultimately the dominant negative could be delivered directly into tumors via clinically approved viral delivery systems such as retroviral replicating vectors.

Citation Format: Nicholas O. Stevers, Sara A. Collins, Samuel H. Wu, Noriyuki Kasahara, Joseph F. Costello. A GABP dominant negative approach to targeting tumor cell immortality [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1435.
Abstract 1440: Identification of a novel EGFR sparing brain penetrant ErbB2 inhibitor with activity against oncogenic ErbB2 mutations
Authors: Chicarelli Mark J , Bouhana Karyn , Brizendine Richard K. , Cable LouAnn , Crow Michelle , Fell Brad , Fischer John , Fulton Jennifer , Guarnieri Anna , Jalluri Ravi , Knox Hailey , Koch Keith A. , Rieger Rob , Robinson John , Stunkard Lee M. , Sullivan Francis , Turton Roy , Winski Shannon , Zhou Yeyun
Published: June 2023

Oncogenic driver mutations in ErbB2 (e.g., S310F/Y, L755S, V777L, V842I) are present in a variety of tumor types including gastric, uterine, urothelial carcinoma, non-small cell lung, breast, and colorectal, some of which are also known to metastasize to the CNS. These mutations can also emerge as mechanisms of acquired resistance to targeted therapies and as such represent a novel and actionable target mutation set across solid tumor indications. Current therapies that target ErbB2 have poor potency against these mutations or are limited in their utility due to inhibition of wild type epidermal growth factor receptors (WT EGFR). The inhibition of WT EGFR is associated with debilitating clinical effects that include diarrhea, stomatitis, and hepatotoxicity. Additionally, treatment of CNS metastases is especially challenging since the potential therapy must also cross the blood brain barrier to have a therapeutic effect. Next generation ErbB2 inhibitors that are active against ErbB2 mutations, spare WT EGFR, and that can penetrate the brain would provide improved target coverage with the potential for fewer off target side effects compared to current therapies and as well as the potential to exhibit superior clinical efficacy. Herein, we describe the pre-clinical in vitro and in vivo activity of a novel, brain penetrant ErbB2 inhibitor which retains potency against prevalent mutations while sparing WT EGFR.

Citation Format: Mark J Chicarelli, Karyn Bouhana, Richard K. Brizendine, LouAnn Cable, Michelle Crow, Brad Fell, John Fischer, Jennifer Fulton, Anna Guarnieri, Ravi Jalluri, Hailey Knox, Keith A. Koch, Rob Rieger, John Robinson, Lee M. Stunkard, Francis Sullivan, Roy Turton, Shannon Winski, Yeyun Zhou. Identification of a novel EGFR sparing brain penetrant ErbB2 inhibitor with activity against oncogenic ErbB2 mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1440.
Abstract 1468: MYC-C interacts with Aurora kinase A in Ewing sarcoma cells
Authors: McNae Molly , Burgess Selena G. , Bayliss Richard , Burchill Susan A.
Published: June 2023

EWSR1-ETS fusion genes result in upregulation and high expression of the oncogene MYC-C in Ewing sarcoma (ES). MYC-C is therefore an attractive therapeutic target in these aggressive cancers with limited treatment options. Unsuccessful efforts to target MYC-C proteins directly have resulted in the development of inhibitors to associated stabilizing proteins, such as Aurora kinase A (AURKA), to induce proteasomal degradation1. In this study we test the hypothesis that MYC-C and AURKA interact in ES. Peptide pull-down assays were performed using Strep-Tactin Sepharose beads and N-biotinyl MYC-C peptides. After incubation with AURKA, eluted proteins were analyzed by SDS-PAGE. Intracellular colocalization of proteins was examined by immunofluorescence of TC-32 and SK-N-MC cell lines using confocal microscopy (Zeiss LSM880) and high content imaging (CD7). Cells were stained with anti-MYC-C and anti-AURKA antibodies, and DAPI used to visualize nuclei. DuoLink® proximity ligation assays (PLA; Sigma) were performed on TC-32 and SK-N-MC cell lines. Images were captured on the confocal microscope and the number of nuclear foci quantified.MYC-C binds AURKA through its transcriptional activation domain (residues 1-155). Residues 10-34 of MYC-C are sufficient for binding with AURKA (residues 122-403) in cell-free peptide assays. Colocalization of MYC-C and AURKA was visualized in mitotic SK-N-MC cells, but not in TC-32 cells. The proteins colocalize at the spindle poles. PLA confirmed an interaction between MYC-C and AURKA in TC-32 and SK-N-MC ES cells. The number of foci per nucleus was significantly higher in the SK-N-MC p53-null cells compared to the wild-type p53 TC-32 cells (p<0.0001). In conclusion, MYC-C and AURKA colocalize and interact in the nucleus of ES cells. The frequency of interactions is greater in p53-null cells compared to cells with wild-type p53. Peptide pull-down assays identified residues 10-34 of MYC-C as the minimal AURKA interacting region. Disruption of this interaction by AURKA inhibitors may provide a mechanism for MYC-C degradation in ES, which could be exploited to develop novel therapeutic combinations to improve outcomes. 1Richards MW, Burgess SG, Poon E, Carstensen A, Eilers M, Chesler L, Bayliss R. Structural basis of N-Myc binding by Aurora-A and its destabilization by kinase inhibitors. Proc Natl Acad Sci U S A. 2016 ;113(48):13726-13731.

Citation Format: Molly McNae, Selena G. Burgess, Richard Bayliss, Susan A. Burchill. MYC-C interacts with Aurora kinase A in Ewing sarcoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1468.
Abstract 1474: Hippo-mediated control of the mutant TERT promoter via MYC and GABP
Authors: Stevers Nicholas O. , Mancini Andrew , Costello Joseph F.
Published: June 2023

Most cancers achieve replicative immortality through reactivation of telomerase reverse transcriptase (TERT), the rate limiting subunit in telomerase activity. Tumors from more than 50 distinct cancer types reactivate TERT expression via mutations in the TERT promoter. Understanding how the mutations lead to activation and immortality is a central question in cancer research. Oncogenic signaling pathways including EGFR/AMPK, MAPK, and C-MYC/ASL, have been linked to telomere maintenance via their regulation of the mutant TERT promoter. Two mutually exclusive point mutations in the TERT promoter generate a de novo E26 Transformation Specific (ETS) binding motif that recruits the GA-Binding Protein (GABP) multimeric complex to reactivate TERT expression (Bell et al, Science 2015). Recruitment of GABP to the mutant TERT promoter facilitates the recruitment of C-MYC to the promoter (Shi et al, Mol. Cell 2022), which aids in transcriptional activation. The Hippo pathway plays a key role in development, organ size determination, and homeostasis, and has been found dysregulated in numerous cancer types. GABP is a member of the Hippo pathway, with GABP activating the promoter of the Hippo transcriptional effector Yes-associated protein (YAP1) and the Hippo pathway core kinases stimulating GABP nuclear exit (Wu et al., Cell Reports 2013). We have found that YAP and its paralogue transcriptional coactivator with PDZ-binding motif (TAZ) are linked to mutant TERT promoter activation in glioblastoma via transcriptional activation of both GABPA and MYC. These observations suggest the Hippo pathway supports tumor immortality in glioblastoma. While immortality has proven to be an elusive target, further investigations of the signaling networks that converge on the activation of the mutant TERT promoter may reveal therapeutic targets that block tumor growth and have secondary benefit by their impact on tumor immortality.

Citation Format: Nicholas O. Stevers, Andrew Mancini, Joseph F. Costello. Hippo-mediated control of the mutant TERT promoter via MYC and GABP [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1474.
Abstract 1483: Development of FUBP1 inhibitors to reprogram pancreatic cancer cells into an anti-cancer phenotype
Authors: Bunea Alexandra , Polera Christopher , Dobrovolskaite Aiste , Moots Holly , Phanstiel Otto
Published: June 2023

The purpose of this project was to identify small molecules which reprogram tumor cells into an anticancer phenotype. Far upstream binding protein 1 (FUBP1) has been identified as a master regulator of a panel of genes involved in tumor survival including c-Myc and p21. FUBP1 controls gene expression by binding to specific far upstream element (FUSE) DNA sequences of the promoters of key tumor survival genes to regulate their transcription to provide a pro-tumor phenotype (high c-Myc, low p21). This makes FUBP1 a novel therapeutic target as its inhibition reprograms tumors to an anti-cancer phenotype (low c-Myc, high p21). This report describes the development of novel anthranilic acid derivatives which bind to FUBP1 (as shown by ChIP and gel shift assays) and modulate the mRNA and protein expression (qRT-PCR and Western) of FUSE-controlled genes (e.g., c-Myc and p21). The lead compound UCF699 was shown to reprogram pancreatic ductal adenocarcinoma (PDAC) cells into an anti-cancer phenotype in a dose-dependent manner and inhibit pancreatic cancer cell growth. In summary, the ability of UCF699 to control the expression of multiple FUSE-controlled genes and to reprogram tumor cells into an anti-cancer phenotype provides an exciting new way to treat pancreatic tumors.

Citation Format: Alexandra Bunea, Christopher Polera, Aiste Dobrovolskaite, Holly Moots, Otto Phanstiel. Development of FUBP1 inhibitors to reprogram pancreatic cancer cells into an anti-cancer phenotype [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1483.
Abstract 1537: DRIVE-Biologics: All the steps from discovery to development of novel biological entities
Authors: Fang Emily , Bunce Campbell , Payne Philip , Teran Rafael , Duchamp Olivier , Mignard Caroline , Bichat Francis , Viviani Fabrice
Published: June 2023

Biologics first revolutionized cancer treatment in the late 1900s with the approval of rituximab and trastuzumab, two monoclonal antibodies targeting antigens expressed on tumor cells. Another milestone was achieved in the early 2010s with the approval of antibodies targeting immune checkpoints. Nowadays, the discovery and development of new biological entities and biological therapeutic products represent a rapidly growing market in various therapeutic areas, with about 10 to 15 biologics being approved each year. We have built a premium expert ecosystem services - DRIVE-Biologics - to support and accelerate biologics drug discovery and development in oncology, immuno-oncology, and inflammatory diseases. The DRIVE-Biologics consortium provides a unique integrated solution with specialist services from strategic partners, to access market analysis, establish the ability to design, optimize, and develop novel biological entities addressing the therapeutic target of interest. DRIVE-Biologics supplies the high-level, IND-focused discipline to rigorously manage the integrated programs integrating CMC, manufacturing, regulatory affairs and clinical trial.

We will present the lead optimization and multiparameter preclinical evaluation process to select and assess biological candidates for downstream development and clinical studies:

-Custom cellular model development for discovery and potency analysis;

-In vitro screening, target engagement, and mechanism of action elucidation with cellular models ranging from tumor cell lines, immune cells or primary patient samples;

-In vivo efficacy and safety studies using refined and highly characterized syngeneic, xenogeneic, patient-derived xenograft or humanized mouse models up to non-human primates;

-DMPK capabilities to develop and validate bioanalytical methods (including GLP-compliancy) such as LBA and qPCR/RT-qPCR and also assess immunogenicity;

-Biodistribution and tumor specificity analysis of bioconjugated and radiolabeled biologics.

Herein, we provide DRIVE-BIO optimization and preclinical evaluation process to select promising biologics and list the key parameters to be checked.

We will present our recent results which highlight the importance to optimize these parameters to improve the efficacy of biologics.

Citation Format: Emily Fang, Campbell Bunce, Philip Payne, Rafael Teran, Olivier Duchamp, Caroline Mignard, Francis Bichat, Fabrice Viviani. DRIVE-Biologics: All the steps from discovery to development of novel biological entities [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1537.
Abstract 1586: The potential therapeutic effect of the Rac/Cdc42 inhibitor MBQ-167 in glioblastomain vitro
Authors: Almedina Derealise Garcia , Grafals-Ruiz Nilmary , Dharmawardhane Suranganie , Torres-Sanchez Anamaris
Published: June 2023

Glioblastoma is a highly aggressive astrocytoma known to form the most lethal type of primary brain tumor. Therapeutic options are limited because 94% of diagnosed patients survive less than five years. Glioblastoma malignancy is attributed to uncontrolled cellular proliferation, increased angiogenesis, apoptosis resistance, and local invasion. The Homologous small GTPases of the Rho family, Rac1 and Cdc42, are critical regulators of the invasion and migration of glioblastoma cells. Previous studies have found a correlation between the high expression of Rac and CDC42 and the highly invasive characteristics of GBM in vivo. Our group characterized the small molecule compound MBQ-167 as a potent dual inhibitor of Rac and Cdc42 in breast and pancreatic cancer and have shown its utility in cell and mouse models of metastasis. In this project, we tested the hypothesis MBQ-167 is also a valid therapy option for glioblastoma. The T98G glioblastoma cell line was treated with varying concentrations (62 nM to 1000 nM) of MBQ-167 for 24 hrs, and effects on Rac/PAK activation (at 24 hours) was determined through active GTP bound Rac pulldowns, cell viability (at 48 and 96 hours) through MTT assays, and cellular migration (at 12, 24, and 48 hours) through wound healing assays. Results show that 250 nM of MBQ-167 inhibits Rac and PAK activation by 50% as well as cell viability at both time points (48 and 96 hours). MBQ-167 (150 nM-500 nM) also blocked glioblastoma cell migration at 12, 24, and 48 hours. Taken together, these results confirm that MBQ-167 is a viable inhibitor in glioblastoma.

Citation Format: Derealise Garcia Almedina, Nilmary Grafals-Ruiz, Suranganie Dharmawardhane, Anamaris Torres-Sanchez. The potential therapeutic effect of the Rac/Cdc42 inhibitor MBQ-167 in glioblastomain vitro [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1586.
Abstract 1670: Sabizabulin shows anti-cancer efficacy in HER2+ breast cancer and novel sabizabulin derivatives overcome paclitaxel-resistance in triple negative breast cancer
Authors: Hartman Kelli L. , Krutilina Raisa I. , Oluwalana Damilola , Parke Deanna N. , Chen Hao , Miller Duane D. , Li Wei , Seagroves Tiffany N.
Published: June 2023

Of the four breast cancer molecular subtypes, the HER2 overexpressing subtype (HER2+) accounts for 15% of all breast cancer cases. Preferred frontline treatment relies on anti-HER2 therapies, such as trastuzumab and pertuzumab, combined with microtubule inhibitors, such as taxanes. However, the clinical efficacy of taxanes is limited by development of chemoresistance and hematological and neurotoxicities. Other agents that target tubulin, such as colchicine-binding site inhibitors (CBSIs) are a class of promising alternatives to taxane therapy due to their ability to overcome P-gp-mediated taxane resistance. Sabizabulin (formerly known as VERU-111) is a potent CBSI that is orally bioavailable, overcomes paclitaxel resistance, and inhibits tumor growth and distant metastases in triple negative breast cancer (TNBC). Here, we demonstrate sabizabulin’s anti-cancer efficacy in HER2+ breast cancer. We report that sabizabulin inhibits proliferation of HER2+ breast cancer, maintains a low nanomolar IC50 value, inhibits colony formation, and causes apoptosis in HER2+ breast cancer cell lines. Sabizabulin inhibits the primary tumor growth in an orthotopic HER2+ in vivo model, BT474, and in a patient-derived xenograft model, HCI-12. While sabizabulin shows promising results for treatment in HER2+ breast cancer, we further optimized the structure of sabizabulin to create a new class of anti-cancer molecules: 40a, CH-2-77, and 60c. Based on in vitro data, 60c showed higher potency in HER2+ breast cancer cell lines and was chosen as the lead compound to further study in a paclitaxel-resistant triple negative breast cancer in vivo study where it was able to effectively inhibit primary tumor growth compared to the vehicle group.

Citation Format: Kelli L. Hartman, Raisa I. Krutilina, Damilola Oluwalana, Deanna N. Parke, Hao Chen, Duane D. Miller, Wei Li, Tiffany N. Seagroves. Sabizabulin shows anti-cancer efficacy in HER2+ breast cancer and novel sabizabulin derivatives overcome paclitaxel-resistance in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1670.
Abstract 1671: Discovery of ETS-003, a potent and selective YAP/TAZ-TEAD PPI inhibitor with broad anti-tumor activity in Hippo-YAP aberrant cancers
Authors: Lu Jiajun , Gao Ming , He Hao , Feng Lijian , Gao Zhenting , Cui Wenqi , Yang Kun , Lu Jiting , Zheng Qiangang , Zhu Jidong , Guo Xin
Published: June 2023

Hippo/YAP is a conserved signaling pathway controlling organ development, tissue regeneration and immune modulation. Cascade of tumor suppressor genes (NF2, LATS1/2) and multiple signals from cellular microenvironment (mechano-transduction) regulate YAP/TAZ phosphorylation and degradation. The stabilized YAP/TAZ translocate from cytoplasm to nucleus, where they bind with TEADs for transcriptional activation. YAP/TAZ regulate numerous genes expression which play central roles in cell proliferation, apoptosis, tumor microenvironment remodeling, and drug resistance, making them appealing targets for cancer treatment. Disruption of YAP/TAZ-TEAD protein-protein interaction (PPI) has been regarded as an effective approach to abolish YAP/TAZ oncogenic activity. Previously we have reported the discovery of YAP/TAZ-TEAD PPI hit compounds bound at the Ω loop site of TEAD1. Here we report that the CADD-guided optimization of the hit compounds has yielded an orally available and potent YAP/TEAD PPI inhibitor ETS-003 with favorable ADME properties and robust anti-tumor efficacy. ETS-003 could potently block YAP/TAZ-TEAD PPI both in vitro and in cells, and disrupt YAP/TAZ genome-wide chromatin binding, resulting in on-target inhibition of YAP transcriptome. ETS-003 exhibited broad anti-proliferative activity in a variety of solid tumor cell lines. In Hippo-YAP dysregulated mesothelioma models, ETS-003 showed profound anti-tumor activity and good PK/PD/efficacy correlation. Moreover, when combined with MAPK pathway inhibitors (Osimertinib, Sotorasib and MRTX1133), ETS-003 could significantly enhance the anti-proliferative activity, suggesting multiple combination opportunities for ETS-003 in clinical investigations. The non-GLP studies of ETS-003 showed favorable safety margin, and warranted further clinical studies of ETS-003 in solid tumors.

Citation Format: Jiajun Lu, Ming Gao, Hao He, Lijian Feng, Zhenting Gao, Wenqi Cui, Kun Yang, Jiting Lu, Qiangang Zheng, Jidong Zhu, Xin Guo. Discovery of ETS-003, a potent and selective YAP/TAZ-TEAD PPI inhibitor with broad anti-tumor activity in Hippo-YAP aberrant cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1671.
Abstract 1690: Myc suppression permits entry into the cancer endocycle to evade toxic effects of chemotherapy
Authors: Loycano Michael , Pienta Kenneth J. , Amend Sarah R.
Published: June 2023

Recent advances in precision medicine and immunotherapy have made great strides in cancer treatment and care, but chemoresistance remains a major challenge. One method of chemoresistance employed by cancer cells is accession of the protective polyaneuploid cancer cell (PACC) state, in which cells enter a functionally dormant state upon environmental stress. Entry into the PACC state begins with a whole-genome duplication event followed by endocycling, where the cells are metabolically active and cycling through repeated G1, S and G2 phases of the cell cycle without dividing. While in this state, cells avoid the mitotic stress exerted by common chemotherapeutics and survive therapy, eventually undergoing a depolyploidization process to repopulate the tumor, driving cancer lethality. The mechanisms by which a cancer cell can switch between a mitotic cell cycle and an endocycle are unknown. Cancer is characterized by deregulated cell proliferation, often driven by mutation or amplification of genes that govern the cell cycle. C-myc, an oncogenic transcription factor, is dysregulated in roughly 70% of cancers and is clinically used as a negative prognostic factor for disease-free survival and metastasis. C-myc is responsible for the transcriptional activation of many cell cycle-related genes, and repression of cell cycle inhibitors. Our data indicate that endocycling cells in the PACC state downregulate c-myc expression. Transcriptomic analyses show repression of myc targets, along with supporting protein data that total c-myc protein levels are decreased. While myc downregulation is expected in non-proliferative cells, the compensatory mechanisms mediating the G1/S transition in the cancer endocycle remain unknown. These observations suggest the presence of underlying mechanisms to reprogram the mitotic cell cycle to access the PACC state. We hypothesize that myc downregulation is essential for cells to activate the cancer endocyle and enter the protective PACC state. Understanding the mechanisms that govern this transition is crucial to generate next-generation cancer therapeutics to block accession or disrupt this state.

Citation Format: Michael Loycano, Kenneth J. Pienta, Sarah R. Amend. Myc suppression permits entry into the cancer endocycle to evade toxic effects of chemotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1690.
Abstract 1714: CRACD/KIAA1211 loss drives cell plasticity and immune evasion of small cell lung cancer
Authors: Zhang Shengzhe , Kim Kee-Bum , Huang Yuanjian , Kim Dong-Wook , Kim Bongjun , Ko Kyung-Pil , Zou Gengyi , Zhang Jie , Jun Sohee , Kirk Nicole A. , Hwang Ye Eun , Ban Young Ho , Chan Joseph M. , Rudin Charles M. , Park Kwon-Sik , Park Jae-Il
Published: June 2023

Small cell lung carcinoma (SCLC) is a lethal neuroendocrine type of lung cancer with limited therapeutic options. Despite recent advances in cancer immunotherapy, its efficacy is limited to a small subset of SCLC patient tumors. The molecular origin of the refractoriness to immunotherapy remains elusive. CRACD (Capping protein inhibiting regulator of actin dynamics; KIAA1211/CRAD) gene is frequently mutated and transcriptionally downregulated in SCLC. Cracd knockout (KO) causes the transformation of preneoplastic neuroendocrine cells and significantly accelerates SCLC development in a mouse model initiated by the loss of Rb1, Trp53, and Rbl2 in the lung epithelium. Cracd KO induces tumor cell plasticity generating deregulated cell lineage trajectories of SCLC tumors. Strikingly, Cracd KO SCLC tumors display the complete loss of CD8+ T cells due to epigenetic suppression of the MHC-I pathway. Furthermore, single-cell transcriptomic analyses of SCLC patient samples classified SCLC by concurrent features: CRACD inactivation and tumor antigen presentation impairment. This study suggests CRACD as a tumor suppressor of SCLC that regulates proliferation and immune recognition of cells, providing novel insight into the mechanism of SCLC evading immune surveillance.

Citation Format: Shengzhe Zhang, Kee-Bum Kim, Yuanjian Huang, Dong-Wook Kim, Bongjun Kim, Kyung-Pil Ko, Gengyi Zou, Jie Zhang, Sohee Jun, Nicole A. Kirk, Ye Eun Hwang, Young Ho Ban, Joseph M. Chan, Charles M. Rudin, Kwon-Sik Park, Jae-Il Park. CRACD/KIAA1211 loss drives cell plasticity and immune evasion of small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1714.
Abstract 186: Cellos: High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology
Authors: Mukashyaka Patience , Kumar Pooja , Mellert Dave , Nicholas Shadae , Noorbakhsh Javad , Brugiolo Mattia , Anczukow Olga , Liu Edison T. , Chuang Jeffrey H.
Published: June 2023

Three-dimensional (3D) culture models, such as organoids, are flexible systems to interrogate cellular growth, multicellular spatial architecture, and morphology in response to drug treatment, including the potential to resolve the individual behaviors and interactions of mixed cancer cell populations. However, new computational methods to segment and analyze 3D models at cellular resolution are needed to realize these possibilities. Here we report Cellos (Cell Organoid Segmentation), an accurate, high throughput image analysis pipeline for 3D organoid and nuclear segmentation analysis. Cellos segments 3D organoids using classical algorithms and segments nuclei using a Stardist-3D convolutional neural network trained on a manually annotated dataset of 3,862 cells from 36 organoids confocally imaged at 5 μm z-resolution. To evaluate the capabilities of Cellos, we then analyzed 74,450 organoids with 1.65 million cells from multiple experiments on triple negative breast cancer organoids containing clonal mixtures with complex cisplatin sensitivity. Cellos was able to accurately distinguish cell ratios in organoids in 96-well plates to within 2.99% and was effective for fluorescently labelled nuclei and independent DAPI stained datasets. Cellos was able to recapitulate traditional luminescence based drug responses by analyzing 3D images, including parallel analysis of multiple cancer clones in the same well. Moreover, Cellos was able to identify organoid and nuclear morphology feature changes associated with treatment. Finally, Cellos enables 3D analysis of cell spatial relationships, which we used to detect ecological affinity between cancer cells, beyond expectations from local cell division or organoid composition. Cellos provides powerful tools to perform high throughput analysis for pharmacological testing and biological investigation of organoids based on 3D imaging.

Citation Format: Patience Mukashyaka, Pooja Kumar, Dave Mellert, Shadae Nicholas, Javad Noorbakhsh, Mattia Brugiolo, Olga Anczukow, Edison T. Liu, Jeffrey H. Chuang. Cellos: High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 186.