bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 6911: Expanding reported molecular characteristics for the NCI Patient-Derived Models Repository
Authors: Timme Cindy R. , Evrard Yvonne A. , Das Biswajit , Chang Ting-Chia , Chen Alice , Chen Li , Crespo-Eugeni Michelle A. , Jiwani Shahanawaz , Karlovich Chris A. , Pauly Rini , Wu Peter I-Fan , Newton Dianne L. , Williams P. Mickey , Hollingshead Melinda G. , Doroshow James H.
Published: March 2024

The National Cancer Institute’s Patient-Derived Models Repository (NCI PDMR; https://pdmr.cancer.gov) has developed a national repository of Patient-Derived Models (PDMs) comprised of patient-derived xenografts (PDXs), in vitro patient-derived tumor cell cultures (PDCs) and cancer associated fibroblasts (CAFs) as well as patient-derived organoids (PDOrg). These PDMs are clinically annotated with molecular information available in an easily accessible database for the extramural community. To ensure the data and models remains pertinent to current translational efforts, NCI actively reviews and adds new molecular features to the public database for researchers to use. While these data could be obtained through analysis of the available NextGen sequencing files in the PDMR database, many laboratories do not have the bioinformatics support to run these assessments for models that are of research interest. Therefore, new pipelines for an array of additional model and molecular characteristics present in PDX, PDOrg, and PDC models have been validated and are reported in the public database in a searchable format. Current model characteristics include addition of OncoTree Codes as a second histologic classifier, use of the PDXNet Consortium’s inferred ancestry caller to better represent Native/Latin American populations, human leukocyte antigen (HLA) typing, molecular classification of tumors (e.g. CMS subtyping of colorectal adenocarcinoma, PAM50 signature based subtyping of breast carcinoma), microsatellite instability (MSI) assessment, and identification of clinically relevant fusions. SOPs for the pipelines used are available on the public website to allow for independent validation and use by other laboratories. Funded by NCI Contract No. HHSN261200800001E

Citation Format: Cindy R. Timme, Yvonne A. Evrard, Biswajit Das, Ting-Chia Chang, Alice Chen, Li Chen, Michelle A. Crespo-Eugeni, Shahanawaz Jiwani, Chris A. Karlovich, Rini Pauly, Peter I-Fan Wu, Dianne L. Newton, P. Mickey Williams, Melinda G. Hollingshead, James H. Doroshow. Expanding reported molecular characteristics for the NCI Patient-Derived Models Repository [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 6911.
Abstract 6943: Evolutionary dynamics under chemotherapy in small cell lung cancer: Insights from patient-derived xenotransplant models
Authors: Kaiser Laura C. , Schmiel Marcel , Ruminska Agnieszka , Alavinejad Nazanin , Müller Christian , Valiulis Justinas , Peifer Martin , Cartolano Maria , Thomas Roman K. , George Julie
Published: March 2024

Introduction: The treatment of patients with small cell lung cancer (SCLC) represents a major medical challenge due to aggressive tumor growth and the poor 5-year overall survival rate of only 5%. SCLC tumors typically are remarkably sensitive to chemotherapy at the beginning; however, the subsequent rapid relapse of therapy-resistant tumors is a severe obstacle. We therefore aimed to decipher the molecular patterns guiding processes of evolutionary adaptation in SCLC as a consequence of therapeutic interventions.

Methods: Over 100 patient-derived xenotransplant models were generated from clinical SCLC specimens capturing a wide range of genetic and molecular features as well as clinical phenotypes with regard to chemotherapy response. We recapitulated chemotherapy response in vivo for 32 models, and performed in-depth genome and single-cell transcriptome sequencing to thus dissect genomic evolutionary trajectories and transcriptional plasticity of therapy-naïve and relapsed tumors, which includes the study of multiregional and longitudinal samples.

Results: The response to chemotherapy in vivo reflected the clinical response of the patients; however, several models of relapsed patients remained sensitive to treatment. Genomic studies of clonal dynamics indicated selection of subclones as a result of therapeutic pressure. In contrast, chemo-refractory tumors maintained their clonal composition after therapy. In agreement with genomic profiles, single-cell transcriptome data revealed a tremendous shift in expression profiles and composition of subpopulations. Furthermore, subclonal genomic events including copy number alterations were found to shape the transcriptional heterogeneity in tumors.

Conclusion: Here, we demonstrate a comprehensive functional characterization of multi-regional tumor sites and longitudinal specimens acquired from patients with SCLC, in which we elucidate genomic and transcriptional heterogeneity as a consequence of therapy response. Overall, our data points to a complex interplay between sub-clonal genomic changes and transcriptional plasticity shaping therapy response in which pre-existing genomic alterations impact selection under therapy.

Citation Format: Laura C. Kaiser, Marcel Schmiel, Agnieszka Ruminska, Nazanin Alavinejad, Christian Müller, Justinas Valiulis, Martin Peifer, Maria Cartolano, Roman K. Thomas, Julie George. Evolutionary dynamics under chemotherapy in small cell lung cancer: Insights from patient-derived xenotransplant models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6943.
Abstract 6980: GOLGA7 is essential for NRAS trafficking from the Golgi to the plasma membrane but not for its palmitoylation
Authors: Liu Chenxuan , Jiao Bo , Wang Peihong , Zhang Baoyuan , Gao Jiaming , Li Donghe , Xie Xi , Yao Yunying , Yan Lei , Qin Zhenghong , Liu Ping , Ren Ruibao
Published: March 2024

RAS GTPases play a crucial role as oncogenic drivers in multiple cancer types. Targeting their localization to the plasma membrane (PM) is a promising strategy for cancer therapy, as RAS signaling requires PM localization. While KRAS traffics through a Golgi-independent route, palmitoylated RAS isoforms are transported to PM from the Golgi via a secretory pathway that is not yet fully understood. GOLGA7 is a Golgi-resident protein known as an accessory protein stabilizing the palmitoyltransferase ZDHHC9 for the palmitoylation of NRAS and HRAS. In this study, we found that among all four RAS isoforms, NRAS uniquely requires GOLGA7 for its association with the PM. Interestingly, the mislocalization of NRAS is achieved without detectable changes in its palmitoylation level in GOLGA7 deficient cells. We further observed that loss of GOLGA7 inhibit the anterograde trafficking of GFP-NRASG12D proteins and result in the accumulation of NRAS in the cis compartment of the Golgi apparatus. Moreover, targeting GOLGA7 suppresses cell proliferation by downregulating RAS signaling in a variety of NRAS-mutant cancer cells. Finally, GOLGA7 depletion attenuated the oncogenic transformation induced by NRASG12D in mice. These findings reveal a specific intracellular trafficking route mediated by GOLGA7 and have identified GOLGA7 as a potential therapeutic target for NRAS-driven cancers.

Citation Format: Chenxuan Liu, Bo Jiao, Peihong Wang, Baoyuan Zhang, Jiaming Gao, Donghe Li, Xi Xie, Yunying Yao, Lei Yan, Zhenghong Qin, Ping Liu, Ruibao Ren. GOLGA7 is essential for NRAS trafficking from the Golgi to the plasma membrane but not for its palmitoylation [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 6980.
Abstract 6984: Investigating the function of the OSM-OSMR axis in pancreatic ductal adenocarcinoma (PDAC)
Authors: Sui Yuan , Hunter Tony
Published: March 2024

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal forms of cancer, characterized by a low survival rate and a significant global mortality impact. The interaction between PDAC and the immune system is complex and plays a crucial role in the progression of the disease. PDAC creates an immunosuppressive tumor microenvironment, which hampers the ability of immune cells to effectively infiltrate the tumor and mount an anti-cancer immune response. Additionally, there is an imbalance of cytokines, with an overabundance of immunosuppressive factors and a deficiency in pro-inflammatory cytokines. This hostile immunological landscape contributes to the aggressive nature of PDAC and hinders the success of immunotherapies and adjuvant treatments. One cytokine of particular interest is oncostatin M (OSM), a member of the interleukin-6 (IL-6) family. OSM has been implicated in the regulation of cancer and has been associated with poor overall survival in pancreatic cancer and other malignancies. Similar to other cytokines, OSM is secreted by immune cells and acts as a regulator of the inflammatory microenvironment surrounding the tumor. The levels of OSM in this milieu can potentially influence cancer development and regulation through multiple mechanisms. Despite the growing understanding of cytokines in cancer, research on the role of OSM in PDAC is still limited and requires further investigation to identify potential therapeutic targets. Therefore, there is a critical need to delve deeper into the functions of OSM and its receptor, oncostatin M receptor (OSMR), in the initiation and progression of pancreatic cancer. As such, our goal is to examine the functions of OSM and its receptor (OSMR) in initiating and advancing pancreatic cancer to better comprehend the role of the OSM-OSMR axis in PDAC, both in vivo and in vitro.

Citation Format: Yuan Sui, Tony Hunter. Investigating the function of the OSM-OSMR axis in pancreatic ductal adenocarcinoma (PDAC) [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 6984.
Abstract 6985: The oncogenic functions and action mechanism of UTP14A, a subunit required for 18S rRNA synthesis, in head and neck cancer
Authors: Wu Li-Wha , Chang Chen-Ni , Biswas Pulak K. , Tsai Sen-Tien
Published: March 2024

Head and neck cancer (HNC) is the sixth common malignancy in the world and > 90% of HNC cases are squamous cell carcinoma in origin. Oral cancer is one major HNC subtype. Despite the recent advancements in cancer diagnostics and therapeutics, the 5-yr survival rate of advanced HNC patients remains <50%. Ribosomes are the cellular factories responsible for making proteins. The hyper-activation of ribosome biogenesis initiated by oncogene gain or tumor suppressor gene loss plays a critical role in cancer initiation and progression. Ribosome biogenesis is a complex and energy intensive process that involves hundreds of factors. UTP14A gene encodes a member of the uridine triphosphate 14 family and is an essential component of a large ribonucleoprotein complex bound to the U3 small nucleolar RNA. Previous studies have demonstrated that UTP14A plays a key role in the synthesis of ribosomes and 18S rRNA, and is overexpressed in several malignancies. However, the biological functions and underlying mechanisms of UTP14A in HNC remain elusive. We found not only the increase of UTP14A mRNA expression in TCGA-HNC database but also its negative impact on patient clinical outcome. UTP14A depletion significantly impaired HNC cell proliferation, migration and invasion in vitro. Ectopic overexpression had the opposite effect, suggesting an oncogenic role for UTP14A in HNC. Through gene set enrichment analysis of pairwise RNA sequencing results, several genes involved in the process of epithelial mesenchymal transition (EMT) were potentially associated with manipulated UTP14A expression. We also detected a concordant change of lipid droplet numbers and its surface marker expression in UTP14A-manipulated cells, respectively, by BODIPY staining and immunhistochemical staining. Western blot analysis validated a positive relationship of EMT markers and COX-2, a potential mediator of lipid metabolism and EMT, with altered UTP14A expression. The involvement of COX2 in UTP14A mediation was confirmed by using both pharmacological inhibition and genetic manipulation. We also identified p38 as a central downstream effector but acting upstream from COX-2 in UTP14A mediation in oral cancer cells. We believe that our study of UTP14A-mediated oncogenic signaling axis can potentially be harnessed as a novel therapeutic target against HNC although more mechanistic studies may be needed.

Citation Format: Li-Wha Wu, Chen-Ni Chang, Pulak K. Biswas, Sen-Tien Tsai. The oncogenic functions and action mechanism of UTP14A, a subunit required for 18S rRNA synthesis, in head and neck 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 6985.
Abstract 7022: Whole genome and reduced representation enzymatic methyl-seq enable cost effective methylomes
Authors: Panchapakesa Vaishnavi , Ponnaluri Chaithanya , Evanich Daniel , Erijman Ariel , Langhorst Bradley , Williams Louise
Published: March 2024

DNA methylation is an epigenetic regulator of gene expression with important functions in development and diseases such as cancer. Traditionally, sodium bisulfite conversion was used to distinguish 5-methylcytosines (5mC) and 5-hydroxymethylcytosines (5hmC) from cytosines. However, this method damages DNA and introduces significant sequencing bias. NEBNext® Enzymatic Methyl-seq (EM-seq™) is an enzymatic conversion approach that minimizes DNA damage therefore enabling longer insert sizes, lower duplication rates and a more accurate quantification of methylation in DNA samples with inputs ranging from 10 ng to 200 ng. An improved enzymatic conversion method, EM-seq v2, has a more streamlined workflow and an expanded DNA input range of 100 pg to 200 ng. Libraries made using NA12878 genomic DNA show improved yields, consistent global methylation and an even GC bias representation. The increased library yields subsequently reduces sequencing duplications and costs. Sequencing costs are an important consideration when performing whole genome methylome analysis as this often needs high sequencing depth to attain meaningful coverage to accurately call methylation. Reduced representation libraries, a commonly used method to investigate DNA methylation, relies on enrichment of CpGs within libraries digested using MspI. These CpGs are commonly found in regulatory regions. Although lacking comprehensive CpG coverage, for many researchers this method provides enough cost effective CpG methylation coverage for their studies. Reduced Representation EM-seq libraries (RREM-seq) and Reduced Representation Bisulfite libraries (RRBS) were made using 200 ng to 100 pg of NA12878 DNA. EM-seq adaptors were ligated to MspI digested DNA followed by conversion using either EM-seq v2 or sodium bisulfite. Libraries were PCR amplified and sequenced on an Illumina NovaSeq platform. RREM-seq resulted in higher yields and reproducible results regardless of input amounts compared to RRBS libraries. RREM-seq libraries also identified a higher number of CpGs with even coverage facilitating accurate methylation calling. RREM-seq libraries have superior sequencing metrics resulting in robust methylation profiling. Focusing on a subset of the genome generates higher coverage DNA methylation data at a lower DNA sequencing cost.

Citation Format: Vaishnavi Panchapakesa, Chaithanya Ponnaluri, Daniel Evanich, Ariel Erijman, Bradley Langhorst, Louise Williams. Whole genome and reduced representation enzymatic methyl-seq enable cost effective methylomes [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 7022.
Abstract 7041: Tumor-immune interactions and cisplatin resistance in localized muscle-invasive bladder cancer
Authors: De Carvalho Filipe La Fuente , Lee Jihyun , Bi Kevin , Titchen Breanna , Stawiski Konrad , Park Jihye , Garza Amanda , Michaud Daniel , Guerriero Jennifer , Mittendorf Elizabeth , Mouw Kent , Van Allen Eliezer
Published: March 2024

Background: Cisplatin-based chemotherapy followed by radical cystectomy remains the standard-of-care treatment for patient with localized muscle-invasive bladder cancer (MIBC). Neoadjuvant clinical trials studying the combination of cisplatin-based chemotherapy and immune checkpoint blockade (ICB) in MIBC reported encouraging pathologic complete response rates. However, the molecular mechanisms and cellular programs involved in response and resistance to cisplatin and ICB in MIBC remain incompletely characterized. Our goal is to define cellular transcriptional programs and chromatin accessible regions in cancer cells and infiltrating immune cells associated with response and resistance to neoadjuvant systemic therapy.

Methods: We performed single-cell Multiome ATAC and Gene expression sequencing (simultaneous identification of gene expression and open chromatin regions within the same cell) of tumors that had a complete response – “responders” – and tumors that had no response or progressed – “non-responders” – through neoadjuvant cisplatin-based chemotherapy (n=15). Single cell suspensions were prepared following the 10x Genomics protocol. Cell Ranger ARC was used for sequence alignment, peak calling, and generation of count matrices. Downstream single-cell gene expression analysis was performed with Scanpy and ATAC-seq with Seurat.

Results: We identified two distinct urothelial cell populations in "responders" vs "non-responders" based on single cell gene expression and genome wide chromatin accessibility regions. Cancer cells in “non-responders” preferentially express basal cell gene expression signatures. “Non-responders” were significantly enriched in suppressive tumor-associated macrophages (TAMs). Interestingly, SPP1+ TAMs known to have a pro-tumoral role and promote resistance to ICB were exclusively identified in “non-responders”.

Conclusion: Single cell and genome wide chromatin accessibility regions identify heterogenous urothelial cell populations expressing basal cell markers in tumors resistant to neoadjuvant cisplatin-based chemotherapy. “Non-responders” are significantly enriched with TAMs implicated in resistance to ICB. Future studies will better define the implications of these findings in cancer therapeutics for patients with MIBC.

Citation Format: Filipe La Fuente De Carvalho, Jihyun Lee, Kevin Bi, Breanna Titchen, Konrad Stawiski, Jihye Park, Amanda Garza, Daniel Michaud, Jennifer Guerriero, Elizabeth Mittendorf, Kent Mouw, Eliezer Van Allen. Tumor-immune interactions and cisplatin resistance in localized muscle-invasive bladder 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 7041.
Abstract 7044: Transcriptome and TCR repertoire in human telomerase reverse transcriptase peptide vaccine treated metastatic prostate cancer patients
Authors: Nätkin Reetta , Simensen Julia Elisabeth , Engedal Nikolai , Ellingsen Espen Basmo , Westhrin Marita , Westgaard Ingunn , Hovig Eivind , Lilleby Wolfgang , Nykter Matti , Urbanucci Alfonso
Published: March 2024

Human telomerase reverse transcriptase (hTERT) vaccine has found to be effective for most of the participated de novo metastatic prostate cancer patients in clinical studies. Nevertheless, the molecular mechanisms behind the immune response induced by the hTERT vaccine are not fully elucidated. Among the cohort of 21 patients treated with androgen deprivation therapy, radiotherapy and hTERT vaccine, we used RNA-sequencing and TCR-sequencing (20 and 14 pre-treatment and 20 and 21 post-treatment samples, respectively) to inspect the changes in transcriptome and TCR-repertoire after the hTERT vaccine treatment and differences between patients that had early response and patients that had late or no response. We found multiple hallmarks being shifted after the treatment and being different between early and late responders. Also, a change in activity of multiple gene set signatures was detected after the treatment and activity of part of the gene set signatures predicted survival. Deconvolution of cell type composition from RNA-sequencing data revealed changes in immune cell abundances after the treatment. TCR-sequencing revealed changes in composition and diversity of TCR repertoires after the treatment and these differed between early and late responders. The results of this study will help to predict patients’ responses to the cancer vaccine and to further understand the mechanisms behind successful cancer vaccines.

Citation Format: Reetta Nätkin, Julia Elisabeth Simensen, Nikolai Engedal, Espen Basmo Ellingsen, Marita Westhrin, Ingunn Westgaard, Eivind Hovig, Wolfgang Lilleby, Matti Nykter, Alfonso Urbanucci. Transcriptome and TCR repertoire in human telomerase reverse transcriptase peptide vaccine treated metastatic prostate cancer 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 7044.
Abstract 7054: L1-ATP8B1 exacerbates high-level reduction-oxidation homeostasis to promote carcinogenesis via affecting PHB1 sumoylation in LUSC
Authors: Zhang Rui , Zhang Xiao , Sun Zeguo , Liu Pengpeng , Chen Guidong , Zhang Weijia , Yu Jinpu
Published: March 2024

Long Interspersed Nuclear Element-1 (LINE-1, L1) plays important roles in carcinogenesis. However, the function of LINE-1 in lung squamous cell carcinoma (LUSC) remains unclear. Here we found that L1-ATP8B1 was overexpressed in LUSC patients with short survival and associated with mitochondrial dysfunction in both the TCGA dataset and the TJMUCH cohort. Overexpression of L1-ATP8B1 promoted cell proliferation and invasion in vitro and facilitated LUSC xenograft growth in vivo. L1-ATP8B1 affected mitochondrial complex enzyme I activity via affecting cardiolipin-dependent PHB1 sumoylation and promoting PHB1 ubiquitination, inducing high-level cellular reduction-oxidation (redox) homeostasis. Synergetic therapy with an L1 inhibitor and an antioxidant dramatically interfered with redox homeostasis and restored mitochondrial function, abolishing L1-ATP8B1-induced growth and metastasis of LUSC xenografts in vivo. In conclusion, we for the first time demonstrated that metabolic disorder plays a vital role in L1-related carcinogenesis and identified L1-ATP8B1 as a promising prognostic biomarker and therapeutic target for LUSC.

Citation Format: Rui Zhang, Xiao Zhang, Zeguo Sun, Pengpeng Liu, Guidong Chen, Weijia Zhang, Jinpu Yu. L1-ATP8B1 exacerbates high-level reduction-oxidation homeostasis to promote carcinogenesis via affecting PHB1 sumoylation in LUSC [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 7054.
Abstract 7093: Prediction of overall survival in stage II and III colon cancer through machine learning of rapidly-acquired proteomics
Authors: Xu Kailun , Yin Xiaoyang , Guo Tiannan , Zheng Shu , Shao Yingkuan
Published: March 2024

The use of adjuvant therapy in stage II-III colon cancer (CC) has been controversial for decades. No markers or models now is satisfactory enough to be adopted widely by the medical community. Here, we analyzed the proteomics of paraffin-embedded tissue (FFPE) biopsy samples from 230 CC patients (stages II-III) with up to 10 years of survival by using pressure cycling technology (PCT) and data-independent acquisition (DIA) mass spectrometry. Using machine learning, we established a novel and practical protein-based clinical classification system for CC prognosis which was further verified in an independent validation cohort. Using the nine protein-based clinical model, we improved the area under the curve (AUC) value to 0.926 in the training cohort and 0.872 in the validation cohort. Our promising model will be a potential approach to prognostication to aid in rational follow-up schedule-making and risk-adaptive individualized therapies.

Citation Format: Kailun Xu, Xiaoyang Yin, Tiannan Guo, Shu Zheng, Yingkuan Shao. Prediction of overall survival in stage II and III colon cancer through machine learning of rapidly-acquired proteomics [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 7093.
Abstract 7131: Base excision repair regulation of replication stress induced poly(ADP-ribose) checkpoints
Authors: Ibrahim Md , Khan Md Maruf , Al-Rahaleh Rasha Q. , Clark Jennifer , Hayat Faisal , Fang Qingming , Koczor Christopher A. , Migaud Marie E. , Sobol Robert W.
Published: March 2024

PARP-inhibitors (PARPi) have been developed to treat homology-directed repair deficient cancers such as BRCA1/2-defective breast and ovarian tumors. However, acquired resistance to PARPi is now common, suggesting the need to identify new protein targets. To that end, a missed opportunity is found in the PARP1/PARP2 activation mechanism in response to DNA damage and replication stress and the resulting protein complexes and enzymes that depend on and coordinate PARP-mediated DNA repair processes. We have found that PARP1/PARP2 activation, whether from acute DNA damage, from replication stress or both triggers a temporal and coordinated interplay of base excision repair and single-strand break repair (BER/SSBR) proteins and enzymes. In turn, the recruitment of these BER and SSBR proteins suppresses PARP1/PARP2 activation, thereby functioning as a network of PARP1/PARP2 regulators, modulating the PARP-mediated response to replication stress. To that end, we find that loss of expression of these key BER/SSBR proteins releases a break on replication-stress induced PARP1/PARP2 activation, triggering un-restrained PARP1/PARP2 activation and elevated levels of replication-dependent poly(ADP-ribose) (PAR). We next confirmed that the loss of these downstream BER enzymes render cancer cells responsive to PARPi’s when the BRCA1/2 pathways are restored. Further, we show that BER expression regulates the cellular response to inhibitors of the PAR degrading enzyme PARG, suggesting that XRCC1-dependent BER proteins regulate replication-stress dependent PAR accumulation. The increase in PAR due to PARG inhibition, that is further regulated by BER, drives a strong intra-S phase response, indicated by activation of ATR and CHK1 signaling. As the checkpoint governed by ATR and CHK1 functions as a protective mechanism, we show that PARG inhibition is synthetically lethal with ATR and CHK1 inhibition and this may be explained by our demonstration of PARGi-mediated trapping of essential BER proteins at the site of damage and PAR accumulation. Together, these studies reveal a significant role for BER/SSBR proteins in regulating replication stress induced PARylation and the resulting intra-S phase checkpoint.

Citation Format: Md Ibrahim, Md Maruf Khan, Rasha Q. Al-Rahaleh, Jennifer Clark, Faisal Hayat, Qingming Fang, Christopher A. Koczor, Marie E. Migaud, Robert W. Sobol. Base excision repair regulation of replication stress induced poly(ADP-ribose) checkpoints [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 7131.
Abstract 7156: Targeting the β-catenin signaling axis in osteosarcoma
Authors: Curcic Marina , Gaikwad Shreyas , Srivastava Sanjay K
Published: March 2024

Osteosarcoma, an aggressive bone malignancy predominantly affecting children, poses a formidable challenge for therapeutic interventions. Here we evaluated a recently approved FDA drug, PCT, for potential anti-cancer effect in osteosarcoma model. Initial assessments of cytotoxicity encompassing various human and murine osteosarcoma cell lines—OS-17, OS-25, U2OS, SAOS2, MG63, and K7M3—revealed an IC50 ranging 1-3 µM. Subsequent investigations demonstrated significant anti-clonogenic activity and G2M phase cell cycle arrest. Annexin-PI assay showed a notable apoptotic effect of PCT, shedding light on the mode of cell death. Given the pivotal role of β-catenin signaling in human osteosarcoma pathogenesis and metastasis, targeting β-catenin components holds promise for therapeutic intervention. In silico docking studies suggested that PCT may have similar anti-cancer effect compared to β-catenin inhibitors (e.g., MSAB, ICG001). Our western blot analyses in multiple osteosarcoma cell lines demonstrated that PCT inhibits β-catenin pathway. Fluorescence microscopy and PCR analyses substantiated PCT's ability to hinder the nuclear translocation of β-catenin, providing mechanistic insights into its anti-tumor properties. Our preliminary data also suggests that AXL, an upstream regulator of β-catenin pathway, was modulated by PCT. In summary, our findings indicate that PCT exhibits therapeutic potential against osteosarcoma by targeting the β-catenin pathway. Further mechanistic studies are currently underway in our lab.

Citation Format: Marina Curcic, Shreyas Gaikwad, Sanjay K Srivastava. Targeting the β-catenin signaling axis in osteosarcoma [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 7156.
Abstract 7160: Germline predictors for bevacizumab induced hypertensive crisis in ECOG-ACRIN 5103 and BEATRICE
Authors: Shen Fei , Jiang Guanglong , Philips Santosh , Cantor Erica , Gardner Laura , Xue Gloria , Cunningham Geneva , Kassem Nawal , Oneil Anne , Cameron David , Suter Thomas , Miller Kathy , Sledge George , Schneider Bryan
Published: March 2024

Introduction: Bevacizumab is a beneficial therapy in several advanced cancer types. Predictive biomarkers to better understand which patients are destined to benefit or experience toxicity are needed. Associations between bevacizumab induced hypertension and survival have been reported but with conflicting conclusions.

Methods: We performed post-hoc analyses to evaluate the association in 3,124 patients from two phase III adjuvant breast cancer trials, E5103 and BEATRICE. Differences in invasive disease-free survival (IDFS) and overall survival (OS) between patients with hypertension and those without were compared. Hypertension was defined as systolic blood pressure (SBP) ≥ 160 mmHg (n=346) and SBP ≥ 180 mmHg (hypertensive crisis) (n=69). Genomic analyses were performed to evaluate germline genetic predictors for the hypertensive crisis.

Results: Hypertensive crisis was significantly associated with superior IDFS (p = 0.015) and OS (p = 0.042), but only IDFS (p = 0.029; HR = 0.28) remained significant after correction for prognostic factors. SBP ≥ 160 mmHg was not associated with either IDFS or OS. A common single-nucleotide polymorphism, rs6486785, was significantly associated with hypertensive crisis (p = 8.4 × 10−9; OR = 5.2).

Conclusion: Bevacizumab-induced hypertensive crisis is associated with superior outcomes and rs6486785 predicted an increased risk of this key toxicity.

Citation Format: Fei Shen, Guanglong Jiang, Santosh Philips, Erica Cantor, Laura Gardner, Gloria Xue, Geneva Cunningham, Nawal Kassem, Anne Oneil, David Cameron, Thomas Suter, Kathy Miller, George Sledge, Bryan Schneider. Germline predictors for bevacizumab induced hypertensive crisis in ECOG-ACRIN 5103 and BEATRICE [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 7160.
Abstract 7167: Impact of patient specific factors on exposures of tarlatamab, a half-life extended DLL3-directed bispecific T-cell engager in patients with advanced small cell lung cancer
Authors: Kong Stephanie M. , Minocha Mukul , Chen Po-Wei , Martinez Pablo , Anderson Erik S. , Parkes Amanda , Houk Brett E. , Lin Chih-Wei
Published: March 2024

Background: Tarlatamab is a first in class, half-life extended delta-like ligand (DLL3) targeted bispecific T-cell engager (BiTE) immunotherapy that has shown antitumor activity with durable objective responses and promising survival outcomes in the ongoing studies in patients with previously treated small-cell lung cancer (NCT03319940, NCT05060016) (Ahn et al, 2023; Paz-Ares et al, 2023). Here we describe the effects of patient specific factors [age, sex, bodyweight, ethnicity, estimates of renal and hepatic function, prior lines of therapy, baseline disease status, emergence of anti-drug antibodies (ADA)] on tarlatamab exposures.

Methods: Tarlatamab serum concentrations were available from 420 subjects (8509 samples) pooled across the ongoing Phase 1 DeLLphi-300 study (dose range 0.003 mg to 100 mg Q2W and 200 mg Q3W) and Phase 2 DeLLphi-301 study (10 mg and 100 mg Q2W). The data were analyzed using a nonlinear-mixed effects modeling approach implemented in NONMEM (v7.5) software. Model selection and evaluation was guided by standard statistical and graphical approaches. Impact of key baseline demographic variables on tarlatamab clearance and volume of distribution were evaluated.

Results: Tarlatamab exposures increased in a dose-proportional manner and were not impacted by age, sex, ethnicity, estimates of renal and hepatic function, prior lines of therapy or baseline disease status. Asian race resulted in 14% higher peak serum concentrations relative to Caucasian subjects. Higher body weight (99 kg; 90th percentile) was associated with a 24% decrease in Day 28 pre-dose concentration (Ctrough) relative to median bodyweight (73 kg). Lower body weight (54 kg; 10th percentile) was associated with a 27% increase in Ctrough relative to median bodyweight. Positive ADA status resulted in a 24% decrease in Ctrough. However, at the recommended dose of 10 mg Q2W, neither body weight nor ADA status had a clinically relevant impact on tarlatamab efficacy or safety measures (Ahn et al, 2023).

Conclusion: Overall, based on these analyses, no dose adjustment for tarlatamab is required based on age, sex, bodyweight, ethnicity, estimates of renal and hepatic function, prior lines of therapy, baseline disease status or emergence of ADA.

Citation Format: Stephanie M. Kong, Mukul Minocha, Po-Wei Chen, Pablo Martinez, Erik S. Anderson, Amanda Parkes, Brett E. Houk, Chih-Wei Lin. Impact of patient specific factors on exposures of tarlatamab, a half-life extended DLL3-directed bispecific T-cell engager in patients with advanced small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7167.
Abstract 7219: Preclinical investigations of concomitant tumor treating fields (TTFields) with cisplatin for treatment of cervical cancer
Authors: Frechtel-Gerzi Roni , Gerasimova Daria , Zeevi Einav , Monin Roni , Fishman Hila , Schlachet-Drukerman Inbar , Mumblat Helena , Martinez-Conde Antonia , Engelman Rotem , Dor-On Eyal , Tzchori Itai , Haber Adi , Giladi Moshe , Weinberg Uri , Palti Yoram , Palmer Greg M. , Secord Angeles Alvarez
Published: March 2024

Introduction: Cervical cancer, although largely preventable, continues to be a significant health concern. Early-stage treatment is commonly surgery; while advanced, recurrent, or metastatic disease often requires systemic therapy. Chemotherapy, mainly cisplatin is the backbone of first-line therapy. TTFields are electric fields that disrupt cellular processes critical for cancer cell viability and tumor progression. In other tumor types, TTFields applied with cisplatin has exhibited benefit. This in vitro study assessed the preclinical efficacy of TTFields for cervical cancer and explored efficacy for concurrent use with cisplatin.

Methods: Effects on cell count in cervical cancer cell lines exposed to TTFields (0.5 V/cm for Ca Ski cells, 1 V/cm RMS for HeLa and SiHa cells; 72 h) across a range of frequencies (100-400 kHz) were evaluated. TTFields (200 kHz) were then applied with varying cisplatin doses followed by cell count, colony formation, and apoptosis assays. Overall effect was calculated as the product of percent reductions in cell count and colony formation. TTFields-treated cells were evaluated for formation of the DNA damage marker γH2AX using fluorescent microscopy; and for the expression of Fanconi Anemia (FA)-BRCA pathway proteins through Western blotting.

Results: TTFields treatment reduced cell count in all cervical cancer cell lines tested. Cisplatin exhibited dose-response effects, which were enhanced when TTFields were co-applied. TTFields led to downregulated expression of FA-BRCA pathway proteins, which are involved in repairing cisplatin-induced DNA damage, resulting in increased DNA damage.

Conclusions: These preclinical results suggest that TTFields should be further explored as a potential treatment for cervical cancer. TTFields-induced downregulation of the FA-BRCA pathway possibly explains the enhanced efficacy when TTFields are applied together with cisplatin, providing mechanistic insight.

Citation Format: Roni Frechtel-Gerzi, Daria Gerasimova, Einav Zeevi, Roni Monin, Hila Fishman, Inbar Schlachet-Drukerman, Helena Mumblat, Antonia Martinez-Conde, Rotem Engelman, Eyal Dor-On, Itai Tzchori, Adi Haber, Moshe Giladi, Uri Weinberg, Yoram Palti, Greg M. Palmer, Angeles Alvarez Secord. Preclinical investigations of concomitant tumor treating fields (TTFields) with cisplatin for treatment of cervical 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 7219.
Abstract 7228: In-vitro efficacy of Dordaviprone/GSK126 combination therapy on castration resistant and neuroendocrine prostate cancer
Authors: Purcell Connor , Srinivasan Praveen , Pinho-Schwermann Maximilian , MacDonald William , Ding Elizabeth C. , Tajiknia Vida , El-Deiry Wafik
Published: March 2024

Neuroendocrine prostate cancer (NEPC) is an aggressive histologic subtype associated with poor prognosis that commonly arises in later stages as a mechanism of treatment resistance. Activation of oncogenic drivers, in combination with epigenetic changes (such as EZH2 overexpression and DNA methylation) further promotes tumor proliferation and expression of downstream neuroendocrine lineage pathways (in part controlled by transcription factors, including SOX2, ASCL1, and BRN2). Importantly, EZH2 inhibitors (EZH2i) can restore AR expression in CRPC (Ku et al., 2017). Imipridones, including Dordaviprone (ONC201), show promise in treating neuroendocrine tumors by interacting with DRD2 and CLpP (Anderson et al., 2022). These results warrant investigation into the potential for synergism in imipridone/EZH2i combination therapies.

In the PCa cell lines LNCap, PC3, 22Rv1, and DU145 the combination of ONC201 and EZH2i GSK126 was assessed. Cell viability data after treatment with ONC201 and GSK126 reveals several dose ranges with potential synergistic activity after 72h. Preliminary western blots after 72 hours of GSK126 treatment indicate modulation of proteins relevant to the mechanism of action of imipridones, specifically DR5 and CLpP, in LNCap, PC3, and 22Rv1. Notably, the decrease in DR5 expression warrants investigation into the effects of EZH2i on TRAIL sensitivity and whether imipridones may rescue DR5 expression to maintain TRAIL sensitivity.

Subsequent experiments will investigate dosing and time point-based effects on viability and protein expression, in addition to assessing the synergy of other imipridones and EZH2i’s. Further, while the cell lines PC3, 22Rv1, and DU145 are castration-resistant, the neuroendocrine prostate cell line NCI-H660 will be used as a positive control as it expresses higher neuroendocrine features, including DRD2. Additionally, the modulation in DR5 expression warrants inquiry into the effects of combination therapy on tumor-immune cell interactions. Further, we will manipulate the expression of neuroendocrine transcription factors to assess changes in therapy sensitivity.

Citation Format: Connor Purcell, Praveen Srinivasan, Maximilian Pinho-Schwermann, William MacDonald, Elizabeth C. Ding, Vida Tajiknia, Wafik El-Deiry. In-vitro efficacy of Dordaviprone/GSK126 combination therapy on castration resistant and neuroendocrine prostate 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 7228.
Abstract 7230: A novel platform for identifying therapeutic index in pancreatic cancer
Authors: Pantazopoulou Vasiliki , Engle Dannielle
Published: March 2024

Pancreatic ductal adenocarcinoma (PDA) remains highly aggressive with a mere 12% 5-year survival rate, which underscores the urgent need for improved therapeutic approaches. The current standard of care primarily includes surgery and chemotherapy. However, existing therapies often result in severe side effects and offer limited success. The limitations are not only due to the development of treatment resistance but also due to the killing of normal cells, and as such a low therapeutic index. Targeted therapies aimed at the primary drivers of PDA, such as the KRASG12D mutation or the activated ErbB pathway, have shown promise in providing novel treatment options. We have previously demonstrated that combining targeted therapies, specifically KRASG12D and EGFR inhibitors, results in reduced tumor growth in both human and murine PDA organoid models in vitro. However, less is known about how these targeted therapies affect normal cells. Here, we are using co-cultures of normal pancreas and PDA organoids to create a platform that allows us to identify combinations of targeted therapies that can achieve a higher therapeutic index. Our goal is to identify treatment combinations that allow for the use of lower individual drug dose, while exhibiting enhanced anti-tumor efficacy and minimizing toxicities to normal organoids. This approach holds significant promise for improving patient outcomes and addressing the challenges associated with current PDA treatments.

Citation Format: Vasiliki Pantazopoulou, Dannielle Engle. A novel platform for identifying therapeutic index in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7230.
Abstract 7234: The second-generation high-fidelity base editor AccuBaseTM (ceBE) can proficiently modify multiple genes within a human primary T cell while minimizing Off-target effects
Authors: Ying Han , Li Guanglei , Wang Liling , Lu Chunju , Lai Qi , Yao Chao , Lv Fenghua , Zhu Shiguo , Xu Tianhong
Published: March 2024

Off target mutations, chromosomal rearrangements and Indels are the biggest limitation to the use of gene editing tools today. Base editing system provides an efficient method to modify the genome without double strand breaks (DSB). The biggest problem for base editing is the sgRNA-independent off-target. We utilize synthetic biology strategies to create a novel base editor AccuBaseTM (ceBE) that has the highest editing efficiency in the industry, with zero off target events. This was achieved by strategically inserting deaminases into Cas9 at specific, tolerance-verified sites, a process guided by an extensive transposon-based genetic screening, protein engineering, and direct evolution approach. AccuBaseTM protein forms a complex with the sgRNA, but it has not yet engaged with the target DNA and is not in contact with any non-targeting dsDNA. This mechanism avoids guide RNA independent indiscriminate off-target mutations that was a common problem of the first generation base editing tool. Upon guided by sgRNA, the AccuBaseTM protein associates with the target double-stranded DNA, triggering structural alterations within the AccuBaseTM protein. This results in the outward exposure of the deaminase domain, facilitating the editing of the target base. AccuBaseTM (ceBE) substantially reduces off-target effects while maintaining on-target editing when compared to BE4max. This improvement has been confirmed in multiple human cell lines, mouse cell lines, human primary T and NK cells, human embryonic stem cells, and in animal embryos. In this study, we apply AccuBaseTM to achieve multiplex gene modifications in primary human T cells, demonstrating its capacity for highly efficient multiplex gene disruption without inducing off-target effects. Importantly, the multiplex base-edited T cells exhibit enhanced ex-vivo cell expansion and do not exhibit the double-strand break-induced translocations observed in T cells edited with Cas9 nuclease.

Citation Format: Han Ying, Guanglei Li, Liling Wang, Chunju Lu, Qi Lai, Chao Yao, Fenghua Lv, Shiguo Zhu, Tianhong Xu. The second-generation high-fidelity base editor AccuBaseTM (ceBE) can proficiently modify multiple genes within a human primary T cell while minimizing Off-target effects [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 7234.