bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 6316: Minimizing ineffective treatment using an in vitro patient derived cancer cell screening platform for local oral squamous cell carcinoma patients in Pakistan
Authors: Zeb Sabaoon , Salim Khudeja , Zamir Hina , Shirdel Madina , Agha Momal , Qudrat Asma , Ahmad Sajjad , Faisal Muhammad , Munawar Muhammad Atif , Khattak Muhammad Mushtaq , Ahmad Mushtaq , Durrani Zubbair , Khan Faisal F.
Published: June 2022

According to GLOBOCAN’s 2020 report, in Pakistan, lip and oral cavity is the second most prevalent cancer with a low survival rate due to late detection and ineffective treatment regimens. To reduce ineffective treatment, this study aims to develop a cost-efficient in vitro drug screening platform using patient-derived primary cell lines to identify effective drugs against Oral Squamous Cell Carcinoma (OSCC) patients. Chemotherapeutic drugs to be screened were identified from NCCN guidelines as well as the local standard of care after oncologists from three tertiary care hospitals. These included 15 chemotherapeutic drugs along with 14 combinations. For this pilot study, tumor biopsies were collected, after relevant IRB approvals from consenting patients as part of the Oral Cancer Genomics Study project. Patient-derived primary cell lines were generated from tumor biopsies of 20 local OSCC patients recruited at Rehman Medical Institute and Hayatabad Medical Complex, Peshawar, Pakistan. Primary cell lines were derived from tumor biopsies within 30 minutes of resection and propagated till confluency using an optimized DMEM protocol. The readouts of our screen include cell viability, cell proliferation and cytotoxicity. This pilot screen presents a first of its kind dataset of the performance of drugs and drug combinations in primary cell lines derived from the tumors of local patients in Pakistan. This is not just an ideal platform to test novel and re-purposed drugs but also to develop into a service for personalized treatments, minimizing ineffective treatment and improving patient outcomes.

Citation Format: Sabaoon Zeb, Khudeja Salim, Hina Zamir, Madina Shirdel, Momal Agha, Asma Qudrat, Sajjad Ahmad, Muhammad Faisal, Muhammad Atif Munawar, Muhammad Mushtaq Khattak, Mushtaq Ahmad, Zubbair Durrani, Faisal F. Khan. Minimizing ineffective treatment using an in vitro patient derived cancer cell screening platform for local oral squamous cell carcinoma patients in Pakistan [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6316.
Abstract 6317: Molecular subtyping in prostate cancer associate with outcomes to abiraterone and ipatasertib treatment from the phase III IPATential150 trial
Authors: Shi Zhen , Nowicka Malgorzata , de Bono Johann , Chi Kim N. , Sweeney Christopher , Sternberg Cora N. , Olmos David , Bracarda Sergio , Massard Christophe , Matsubara Nobuaki , Garcia Josep , Chen Geng , Wongchenko Matthew , Sandhu Shahneen K.
Published: June 2022

Prostate cancer is a heterogeneous disease and genomic subtyping offers an opportunity to better understand underlying disease biology. Here, we performed transcriptional profiling by RNA-Seq (n=582) and targeted genomic sequencing by FoundationONE CDx (n=743) from prostate cancer tumor specimens in the phase III IPATential150 trial of first-line ipatasertib (Ipat) plus abiraterone (Abi) in metastatic castration-resistant prostate cancer (N=1101). Unsupervised transcriptomic analysis of the 582 samples with RNA-Seq with Nonnegative Matrix Factorization (NMF) reveals four consensus subtypes. This includes an immune/cell cycle-high, an AR signature/cell cycle-high, a stroma program-enriched, and an ERG fusion-enriched subtype. Subgroups of patients with immune/cell cycle-high and AR signature/cell cycle-high tumors had the shortest radiographic progression-free survival (rPFS) and were characterized by high MYC and cell cycle-related gene signatures. Patients with AR signature/cell cycle-high tumors showed the greatest increase in rPFS with Ipat + Abi vs. Placebo (Pbo) + Abi (HR = 0.58).

Cluster n Enriched processes Median rPFS (Pbo + Abi) (months, 95% CI) Median rPFS (Ipat + Abi) (months, 95% CI) HR (95% CI) NMF1 84 Immune processes, metabolism, cell cycle 10.3 (8.3 - 12.7) 13.9 (10.9 - 16.4) 0.77 (0.47 - 1.28) NMF2 165 Androgen response signature, cell cycle, MYC signature 11.9 (8.8 - 16.5) 20.9 (16.4 - NA) 0.58 (0.38 - 0.90) NMF3 156 Fibroblast, Wnt, Notch, Hedgehog, TGFb 20.0 (16.4 - NA) 22.3 (15.6 - 24.9) 0.96 (0.59 - 1.56) NMF4 177 ERG fusion 18.4 (13.8 - 23.8) 24.7 (16.2 - NA) 0.78 (0.50 - 1.20)

Citation Format: Zhen Shi, Malgorzata Nowicka, Johann de Bono, Kim N. Chi, Christopher Sweeney, Cora N. Sternberg, David Olmos, Sergio Bracarda, Christophe Massard, Nobuaki Matsubara, Josep Garcia, Geng Chen, Matthew Wongchenko, Shahneen K. Sandhu. Molecular subtyping in prostate cancer associate with outcomes to abiraterone and ipatasertib treatment from the phase III IPATential150 trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6317.
Abstract 6326: Reshaping immune lung populations to inhibit pulmonary fibrosis and cancer by activation of purinergic receptor P2RX7
Authors: Janho dit Hreich Serena , Ghinet Alina , Vouret-Craviari Valérie
Published: June 2022

Lung cancer is the most prevalent cancer worldwide with high mortality rate despite recent advances in therapies. Not only is fibrosis a major hallmark of lung cancer, it is also a risk factor for lung cancer development (mainly non-small cell lung cancer). In fact, patients diagnosed with idiopathic pulmonary fibrosis (IPF) are very likely to develop lung cancer. However, treatment and outcome of lung cancer patients with IPF is different than those without IPF despite their common genetic, molecular, cellular and immune properties. New therapeutic strategies are needed for improving outcome of patients bearing both diseases. To address this, we proposed that boosting the activation of P2RX7 with a positive modulator (HEI3090) would be a novel strategy to fight lung cancer. P2RX7 is a purinergic receptor activated by high extracellular ATP levels found in inflamed and tumor sites. It has anti-tumor and immunomodulatory properties by its ability to induce cell death and the release of IL-1b and IL-18. We showed previously that HEI3090 inhibits lung tumor growth by triggering an anti-tumor immune response that relies on IL-18. Indeed, HEI3090-release of IL-18 enhanced the cytotoxicity of NK cells and favored a Th1-biased immune response. Given that lung fibrosis is partly driven by inflammation with a dysregulated Th1/Th2/Th17 ratios and given the ability of HEI3090 to favor a Th1-biased immune response, we wondered if HEI3090 was able to inhibit fibrosis. To do so, we used the bleomycin mouse model where we show that activation of P2RX7 with HEI3090 inhibits lung fibrosis. HEI3090 targets P2RX7-expressing immune cells, decreases lung inflammation and favors an anti-fibrotic immune signature. Indeed, HEI3090 promotes the production of IFN-g by T cells and decreases pro-fibrotic IL-17A release by Th17 cells. Moreover, production of TGF-b, the key cytokine driving fibrosis, was greatly reduced in immune cells in HEI3090-treated mice. The antifibrotic effect of HEI3090 seems to rely on an increase of IL-18, known to induce the production of IFN-g by T cells. Overall, we show that reshaping lung immune phenotype by activation of P2RX7 is a promising strategy in lung fibrosis. HEI3090’s effect on cancer-related fibrosis is ongoing on a Kras mouse model. We highlight a new therapeutic strategy for patients with IPF that would ameliorate treatment and outcome of patients with both lung cancer and fibrosis

Citation Format: Serena Janho dit Hreich, Alina Ghinet, Valérie Vouret-Craviari. Reshaping immune lung populations to inhibit pulmonary fibrosis and cancer by activation of purinergic receptor P2RX7 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6326.
Abstract 6341: ImaGene: A robust AI-based software platform for tumor radiogenomic evaluation and reporting
Authors: Sukhadia Shrey S. , Tyagi Aayush , Venkatraman Vivek , Mukherjee Pritam , A.P. Prathosh , Divate Mayur , Gevaert Olivier , Nagaraj Shivashankar H.
Published: June 2022

The field of radiomics has undergone several advancements in approaches to uncovering hidden quantitative features from tumor imaging data for use in guiding clinical decision-making for cancer patients. Radiographic imaging techniques provide insight into the imaging features of tumor regions of interest (ROIs), while immunohistochemistry and sequencing techniques performed on biopsy samples yield omics data. These imaging and omics feature data can then be correlated and modeled using artificial intelligence (AI) techniques to highlight notable associations between tumor genotype and phenotype. Currently, however, the radiogenomics field lacks a unified and robust software platform capable of algorithmically analyzing imaging and omics features using modifiable parameters, detecting significant relationships among these features, and subjecting them to AI-based analysis. To address this gap, we developed ImaGene, a robust AI-based platform that uses omics and imaging features as inputs for different tumor types, performs statistical analyses of the correlations between these data types, and constructs AI models based upon significantly correlated features. It has several modifiable configuration parameters that provide users with complete control over their experiments. For each run, ImaGene produces comprehensive reports that can contribute to the construction of a novel radiogenomic knowledge base, in addition to enabling the deployment and sharing of AI models. To demonstrate the utility of ImaGene, we acquired imaging and omics datasets pertaining to Invasive Breast Cancer (IBC) and Head and Neck Squamous Cell Carcinoma (HNSCC) from public databases and analyzed them with this platform using specific parameters. In both cases, we uncovered significant associations between several imaging features and 11 genes: CRABP1, VRTN, SMTNL2, FABP1, HAND2, HAS1, C4BPA, FAM163A, DSG1, SMTNL2 and KCNJ16 for IBC, and 10 genes: CEACAM6, IGLL1, SERPINA1, NANOG, OCA2, PRLR, ACSM2B, CYP11B1, and VPREB1 for HNSCC. Overall, our software platform is capable of identifying, analyzing, and correlating important features from tumor scans, thereby providing researchers with a reliable and accurate tool for their radiogenomics experiments. We anticipate that ImaGene will become the gold standard for tumor analyses in the field of radiogenomics owing to its ease of use, flexibility, and reproducibility.

Citation Format: Shrey S. Sukhadia, Aayush Tyagi, Vivek Venkatraman, Pritam Mukherjee, Prathosh A.P., Mayur Divate, Olivier Gevaert, Shivashankar H. Nagaraj. ImaGene: A robust AI-based software platform for tumor radiogenomic evaluation and reporting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6341.
Abstract 6375: Augmented intelligence to define drug targets associated with triple negative breast cancer (TNBC) metabolic reprogramming
Authors: Jenna Sarah , Boucher Benjamin , Dudragne Liebaut , Diallo Abdoulaye Baniré
Published: June 2022

Introduction: Basal-like breast cancer (BLBC; TNBC) cells use aerobic glycolysis at a higher rate than Luminal A (LumA) cells. Metabolic reprogramming using aerobic glycolysis (Warburg effect), is correlated with increased aggressiveness of cancer cells and poor outcome in patients. Therefore, genes involved in this pathway are promising targets for developing cancer therapeutics.

Method: MIMs has developed a unique platform of augmented intelligence that combines bioinformatics, systems biology and artificial intelligence. It integrates multi-layered omics data with a knowledge-base that aggregates structured data from more than 140 databases as well as unstructured data from the scientific literature. Using this approach a genetic interaction graph (GI-Graph) is inferred per patient, capturing functional relationships between genes in the specific context of the tumor. The GI-Graphs are subsequently used to train supervised machine learning algorithms for predicting gene functionality and potential as a target. Preliminary analysis was performed on transcriptomic data from 321 LumA and 162 TNBC samples, from the TCGA Data Portal and a predictive model was developed using two GI-Graphs from the two subgroups. Briefly, subgraphs, containing genes with functional interactions with the known genes in OXPHOS and glycolysis pathways, were used to extract gene attributes, and to build an algorithm that predicts involvement of a gene in the Warburg effect. Using a testing gene set extracted from the literature the performance of the model was assessed, which showed a true positive rate of 18% and a false positive rate of 0.36%, and outperformed 5-times the classical bioinformatics tools.

Results: This model predicted 108 genes as the top 1% genes being involved in the metabolic reprogramming of TNBC. Additional information from MIMs’ platform, including differential gene expression between LumA and TNBC, gene pleiotropy and essentiality and the topological metrics, enabled the life scientists to further refine the gene lists, based on the expected characteristics of a good target in oncology. Following this process, 30 genes were selected as potential targets controlling the metabolic reprogramming of TNBC, among which 4 genes were already evaluated in TNBC clinical trials.

Conclusion: Our preliminary data strongly supports that the predictive model based on the GI-Graphs has the potential to identify promising therapeutic targets for TNBC.

Citation Format: Sarah Jenna, Benjamin Boucher, Liebaut Dudragne, Abdoulaye Baniré Diallo. Augmented intelligence to define drug targets associated with triple negative breast cancer (TNBC) metabolic reprogramming [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6375.
Abstract 6392: Predicting malignancy in indeterminate pulmonary nodules using quantitative CT imaging
Authors: Bloch Kate M. , Shi Xingyi , Duan Fenghai , Washko George R. , Spira Avrum , Aberle Denise R. , Estepar Raul S. , Billatos Ehab , Lenburg Marc E. ,   on behalf of the DECAMP Investigators
Published: June 2022

With an increasing number of positive lung cancer screening trials and the growing utilization of low dose CT screening, the detection of indeterminate pulmonary nodules is an important clinical problem. A biomarker that will be able to differentiate between benign andmalignant nodules would help to accelerate diagnosis and reduce unnecessary and invasive procedures. Here, we investigated the utility of quantitative radiomics to predict malignancy of small pulmonary nodules. Data including cancer status, age, gender, smokingstatus and CT radiomics data, from 242 patients accrued from the Detection of Early Lung Cancer Among Military Personnel (DECAMP1) consortium was used. DECAMP1 is a prospective study of 500 current or former smokers with indeterminate pulmonary nodules (0.7-3.0 cm). A total of 446 quantitative radiomic features were extracted from CT images of each patient. For the prediction models, various feature selection methods and machine learning algorithms including Random Forest, Gradient Boosting Machine and Support Vector Machine were used. Data was split into train and test set with tenfold cross-validation.Models were evaluated using; Accuracy, Sensitivity, Specificity and Area under the curve - a receiver operating characteristic curve (AUC-ROC). In terms of predictive performance, the AUC value was 0.64 (95% CI: 0.50-0.78) for the clinical model and 0.77 (95% CI: 0.64-0.90) for the radiomics model. Adding clinical features to the radiomics model (gender, age, smoking status) did not improve the model. We have also investigated the slice thickness and scanner (PET vs PET-CT) variables on the models’ performance and saw a modest improvement of the AUC values when using more homogenous data. In this study, we showed the potential of radiomics for lung cancer prediction in DECAMP1.For future work, we are planning to test whether incorporating bronchial gene expression data improves lung cancer detection and to validate these findings in separate, independent cohorts.

Citation Format: Kate M. Bloch, Xingyi Shi, Fenghai Duan, George R. Washko, Avrum Spira, Denise R. Aberle, Raul S. Estepar, Ehab Billatos, Marc E. Lenburg, on behalf of the DECAMP Investigators. Predicting malignancy in indeterminate pulmonary nodules using quantitative CT imaging [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6392.
Abstract 674: Tracking the transcriptome of lung cancer-associated fibroblasts within the TRACERx lung study from patient to culture models reveals phenotypic plasticity and instructive cues from cancer cells
Authors: Naito Yutaka , Hynds Robert , Novo David , Chakravarty Probir , Kelly Gavin , Swanton Charles , Honda Kazufumi , Sahai Erik ,   TRACERx Consortium
Published: June 2022

Cancer-associated fibroblasts (CAFs) play a pivotal role in cancer progression by enhancing extracellular matrix remodeling, cancer cell invasion, and mediating inflammatory environment. Therefore, CAFs have become targets for cancer therapies. However, a major hurdle to developing such therapies are the challenges of studying CAFs in culture - specifically it remains unclear which CAF functions and phenotypes are sustained during in vitro culture and the signaling pathways driving distinct CAF phenotypes.

We investigated whether CAF phenotypes and functions are sustained or changed during 2D CAF culture under in vitro systems, our analysis included early passage, late passage, and immortalized cultures, as well as CAFs in coculture with cancer cell lines. Transcriptomic analysis revealed that inflammatory-related gene expression programs were suppressed in late passage and immortalized CAFs compared with early passage equivalents. Direct co-culture with lung cancer cells can revert the inflammatory gene expressions in immortalized CAFs such that they partially resemble early passage CAFs. In contrast, indirect coculture with lung cancer cells - in which CAFs could not form cell-cell contacts with cancer cells - had a less significant effect on immortalized CAF inflammatory gene expression but could induce TGFβ regulated genes. Interestingly, inhibition of the TGFβ signaling pathway potentiated the inflammatory gene expression network induced by direct co-culture, suggesting that the signaling mediated by direct cellular interaction is antagonistic to the TGFβ signaling pathway.

These data further our understanding of cancer cell – CAF crosstalk and will help to develop in vitro assays that more closely maintain the state of CAFs observed in tissue.

Citation Format: Yutaka Naito, Robert Hynds, David Novo, Probir Chakravarty, Gavin Kelly, Charles Swanton, Kazufumi Honda, Erik Sahai, TRACERx Consortium. Tracking the transcriptome of lung cancer-associated fibroblasts within the TRACERx lung study from patient to culture models reveals phenotypic plasticity and instructive cues from cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 674.
Abstract 759: Analytical performance of a novel next generation sequencing assay for myeloid MRD
Authors: Zhang Hua , Peng Xinzhan , Luo Guobin , Kraltcheva Annie , Mandelman David , Swimley Michelle , Pazol Eli , Espinoza Jose , Mitchell Scott , Ding Bo , Singh Ratnesh , Fenger Doug , Li Na , Hatch Andrew , Mozhayskiy Vadim , Roman Steven , Rozenzhak Sophie
Published: June 2022

The detection of molecular measurable residual disease (MRD) for acute myeloid leukemia (AML) has shown promise as a prognostic for AML. To support clinical and translational research into potential strategies for MRD monitoring applications in the future, a next-generation sequencing (NGS) assay, the Oncomine Myeloid MRD Assay (RUO), was developed. This assay utilizes Unique Molecular Tags (UMT) and Ion AmpliSeq HD™ technology to detect ultra-low frequency genetic alterations from blood or bone marrow samples. The workflow includes manual AmpliSeq HD library construction, templating on Ion Chef™, and sequencing on Ion GeneStudio™ sequencers. The assay contains both DNA and RNA targeted panels to detect SNVs, indels, fusion markers, and microhaplotype. The DNA panel covers 1256 hotspots in 33 genes, including key mutations in NPM1, FLT3, DNMT3A and full gene coverage for CEBPA and TP53. The panel achieved a limit of detection (LOD) of 0.1% when tested on 27 reference genomic DNA samples and over 40 clinical research samples. The RNA panel detects 1003 fusion isoforms for 27 fusion driver genes, including BCR-ABL1, RUNX1, CBFB-MYH11, and KTM2A (MLL) partial tandem duplications (PTDs) and fusions. The assay also includes a Microhaplotyping panel to monitor chimerism. The workflow is analytically verified and includes an optimized analysis pipeline for sensitive and accurate MRD detection. Overall, this comprehensive Myeloid MRD (RUO) assay reliably identifies DNA mutations and fusions with high sensitivity and provides a new tool for myeloid MRD research. RUO: For Research Use Only. Not for use in diagnostic procedures.

Citation Format: Hua Zhang, Xinzhan Peng, Guobin Luo, Annie Kraltcheva, David Mandelman, Michelle Swimley, Eli Pazol, Jose Espinoza, Scott Mitchell, Bo Ding, Ratnesh Singh, Doug Fenger, Na Li, Andrew Hatch, Vadim Mozhayskiy, Steven Roman, Sophie Rozenzhak. Analytical performance of a novel next generation sequencing assay for myeloid MRD [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 759.
Abstract 774: Microdissected gene expression profiling of recurrent nasopharyngeal carcinoma
Authors: Tay Joshua , Teo Wei Keat , Goh Chuan Keng , Wu Bing Cheng , Loh Kwok Seng
Published: June 2022

Nasopharyngeal cancer (NPC) is an EBV-driven epithelial carcinoma with a recurrence rate of 30%. Biological pathways and predictive markers for recurrence remain understudied. Further, NPC tumors are associated with an intense inflammatory infiltrate, masking gene expression signals from the tumor epithelial compartment. We perform laser-capture microdissection on a preliminary cohort of 12 tumors, including primary tumors from recurrent and non-recurrent cases matched for stage of disease. Smart-3SEQ, a novel 3’ end RNA-Seq technique which allows for the accurate quantification of transcript abundance in FFPE samples, was performed to obtain gene expression libraries. Tumor epithelial and microenvironment regions from were separately microdissected, giving a total of 42 histologically-pure gene expression libraries. Raw reads were mapped to the human hg19 and EBV genomes and gene expression counts were obtained with Subread. Differential gene expression and gene set enrichment was performed in R with DESeq2 and fgsea respectively. We observed that primary NPC tumors that did not recur were significantly enriched for immune processes, including leukocyte mediated immunity, innate immune response and lymphocyte activation (padj < 1E-9 for all). The top differentially expressed genes in this group included mediators of inflammation such as STAT1 (padj = 0.0204). Critically, these gene expression changes were observed within the tumor epithelial compartment. In contrast, primary NPC tumors that eventually recurred were enriched for known oncogenes including BCL2 (padj = 0.000420). These findings suggest that heterogeneity in gene expression between NPC tumors play an important role in treatment response. Further work to define gene expression subtypes of NPC tumors will be helpful for patient stratification and personalized care.

Citation Format: Joshua Tay, Wei Keat Teo, Chuan Keng Goh, Bing Cheng Wu, Kwok Seng Loh. Microdissected gene expression profiling of recurrent nasopharyngeal carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 774.
Abstract 775: Evaluation of Erb-B2 expression from archival tumor tissue in early stage epithelial ovarian carcinoma patient prognosis
Authors: Rao Kavitha Advikolanu , Magliocco Anthony , Maksymiuk Andrew
Published: June 2022

In this retrospective study, Erb-B2 expression was assessed in 106 patients using Paraffin-Embedded Tissue (PET) to determine the prognostic value in Epithelial Ovarian Carcinoma (EOC) patients diagnosed at Saskatoon Cancer Center between the years 1983-1995. Relationship between Erb-B2 positivity and patient tumor characteristics was assessed for Overall Survival (OS) and Relapse-Free Survival (RFS) by Kaplan-Meier method. Based on the intensity of stain with a polyclonal antibody (A485, 1/400 dilution), cases with markedly intense cytoplasmic and membranous immunoreactivity were classified as Erb-B2 over-expressors. Erb-B2 was overexpressed in 13 (12%) cases. The mean age of the patients was 56 years (range 18-84 years). The patient population consisted of 64 Stage I and II, Early Stage (ES) and 36 cases with Stage III and IV Advanced Stage (AS). Data on histologic grade was available in 81 cases. 58 patients received platinum-containing regimen, 13 melphalan, and in 9 cases combination chemotherapy. Erb-B2 expression did not influence OS and RFS in these patients. Similarly, there was no significant relation to OS and RFS between Erb-B2 and age, grade, and patients with No Evidence of Disease (NED). Of the 64 cases with ES disease, 16 cases had Grade 2 tumor with Erb-B2 over-expression in 4 cases. Grade 2 tumors with Erb-B2 overexpression indicated significant relationship to OS and RFS, p=0.01, (median = 30 months, CI: 26 - 68) and p=0.05, (median = 15 months, CI: 13 - 68). Furthermore, in 21 cases with ES, Endometrioid histology and Erb-B2 expressors 6/21 (28%) experienced significantly shorter OS compared to non-expressors p=0.005, (median = 48 months, CI: 22 - 74) (mean = 134 months, CI: 124 - 144). In conclusion, Erb-B2 overexpression could be detected in only limited EOC cases in PET and appears to have no prognostic influence. Additionally, endometrioid carcinoma and grade 2, ES certainly reflect the importance of sub-group analysis. In ovarian carcinoma distribution of stage, histology, and grading of tumor cells are conventional markers for prognosis. Finally, Erb-B2 status detected by immunohistochemistry, in a subgroup of patients with high-degree of HER2 positivity/focal amplification may likely have better clinical outcome with anti-HER2 agents.

Citation Format: Kavitha Advikolanu Rao, Anthony Magliocco, Andrew Maksymiuk. Evaluation of Erb-B2 expression from archival tumor tissue in early stage epithelial ovarian carcinoma patient prognosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 775.
Abstract 799: HLTF and SHPRH in mismatch repair and cancer
Authors: Miller Anna Kristin , Mao Guogen , Rahal Christine , Putnam Christopher , Goellner Eva
Published: June 2022

Colorectal cancer (CRC) is one of the leading causes of cancer deaths, with an increasing rate of CRC diagnosis in younger individuals. MMR is the DNA repair mechanism that repairs DNA mispairs and small insertions or deletions remaining after replication. MMR is also required for apoptosis after certain types of exogenous DNA damage that result in damage-associated mispairs. MMR defects are the underlying cause of Lynch syndrome, a familial cancer predisposition syndrome that increases susceptibility to multiple cancers, specifically colorectal cancer. MMR defects are also commonly found in sporadic colorectal cancers. Model systems such as Saccharomyces cerevisiae, Escherichia coli, and human cell lines have been used to study the MMR proteins and pathways. The basics of the MMR mechanism are fairly well understood; however, proteins associated with MMR are still being identified, and the roles of these proteins are largely unknown. We have identified the yeast protein Rad5 as an interactor with the yeast MMR proteins Msh2 and Mlh1. Rad5 is a helicase and an E3 ubiquitin ligase which is involved in post-replicative repair and damage tolerance. However, to date, Rad5 has no known role in MMR. We have determined that these interactions are conserved through evolution to human Rad5 homologs, HLTF and SHPRH. The Rad5 interactions with Mlh1 and Msh2 appear to be split between the human homologs with human Msh2 interacting with HLTF and human Mlh1 interacting with SHPRH. We have found that loss of SHPRH induces resistance to MMR-mediated apoptosis. Current experiments are in progress to determine the binding sites between these proteins. We are also investigating what functional impact the Rad5 homologs have on mutation rate and MMR-induced apoptosis and how the interactions affect the roles of MMR. Together this will allow for a deeper understanding of how accessory proteins may influence canonical and non-canonical MMR. Since MMR status is currently used to determine patient treatment, understanding how commonly mutated accessory factors interact is critical.

Citation Format: Anna Kristin Miller, Guogen Mao, Christine Rahal, Christopher Putnam, Eva Goellner. HLTF and SHPRH in mismatch repair and cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 799.
Abstract 854: The role of protocadherin, FAT2 in breast cancer
Authors: Roache Thomas , Sumera Megan , Laird Zalaila , Datta Amrita
Published: June 2022

Protocadherins are cell adhesion molecules that belong to the cadherin superfamily. They are novel cadherin like proteins predominantly associated with early development and morphogenesis, cell growth and patterning, cell-cell adhesion, cell motility (including cell invasion and migration). The Fat-protocadherins are derived from an ancestral Drosophila FAT like cadherin and are evolutionarily conserved. They have been primarily implicated in neuronal cell development and cancer. Several studies have implicated protocadherin dysfunction in cancer. Loss of protocadherin expression, chromosome deletion and epigenetic silencing have been implicated in kidney, prostate, colorectal and breast cancer. More recently they have been implicated in gastric tumors and gliomas. Based on these findings, protocadherins are thought to be tumor suppressors and in general seem to regulate cancer cell proliferation, migration and/or apoptosis. However, multiple exceptions have also been observed and individual protocadherin functions seem to be context-dependent, as some can be considered either tumor suppressors or proto-oncogenes according to the type of cancer being examined. The mechanistics of the roles of the protocadherins in neuronal development have been well dissected but most oncological studies have focused on their characterization as potential biomarkers while the molecular signaling pathways through which the protocadherins regulate growth, invasion and metastasis are still poorly understood. For example recent research has shown that FAT1 is repressed in oral cancer owing to homozygous deletion or epigenetic silencing and is preferentially downregulated in invasive breast cancer. On the other hand, FAT1 is upregulated in leukemia and prognosis of preB-ALL patients with FAT1 upregulation is poor. Therefore FAT1 is tumor suppressive or oncogenic in a context-dependent manner, while FAT4 is tumor suppressive. FAT2 is highly expressed in breast cancer and lung squamous cell carcinoma and the elevated expression of FAT2 is correlated with poor patient outcome.Our preliminary research analysis of the TCGA data from the Genomic Data Commons Portal shows that protocadherins FAT4 and FAT1 are among the top dysregulated genes in cancer. We have also determined that FAT2 has higher Copy Number Variation (CNV) gain events than loss events. Given that there is a well-known concordance between CNV and differential gene expression we believe that FAT2 has a paradoxical oncogenic role in breast cancer.

Citation Format: Thomas Roache, Megan Sumera, Zalaila Laird, Amrita Datta. The role of protocadherin, FAT2 in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 854.
Abstract 88: ATAD3A enhances head and neck cancer malignancy via mitochondrial ERK1/2 signaling
Authors: Lang Liwei , Loveless Reid , Qin Zhaohui , Qiu Peng , Shay Chloe , Teng Yong
Published: June 2022

Targeting mitochondria as a cancer therapeutic strategy has attracted more and more attention in the recent years. ATAD3A is identified as a nuclear-encoded mitochondrial enzyme that regulates mitochondrial dynamics, cholesterol metabolism, and signal transduction. However, its impact and underlying regulatory mechanisms in cancers remain to be determined. We report here that ATAD3A is highly expressed in head and neck squamous cell carcinoma (HNSCC), where it plays a critical role in favoring tumor progression. Loss of ATAD3A expression dramatically incudes tumor regression in orthotopic tongue tumor-bearing mice, whereas gain of ATAD3A expression produces the opposite effects. Mechanistically, ATAD3A binds to ERK1/2 at HNSCC cell mitochondria in the presence of VDAC1, and this interaction is essential for the activation of mitochondrial ERK1/2 signaling. Most importantly, the ATAD3A-ERK1/2 signaling axis enhances HNSCC development in a Ras-independent manner and, thus, tumor suppression is more effectively achieved when ATAD3A and Ras signaling pathways are co-inhibited. These novel findings highlight the importance of activation of ATAD3A-ERK1/2 axis in cancer progression and suggest that combined targeting of ATAD3A and Ras signaling could potentiate anticancer activity for HNSCC treatment.

Citation Format: Liwei Lang, Reid Loveless, Zhaohui Qin, Peng Qiu, Chloe Shay, Yong Teng. ATAD3A enhances head and neck cancer malignancy via mitochondrial ERK1/2 signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 88.
Abstract 889: NF-κB-mediated mitophagy contributes to the maintenance of cancer stem cells in ovarian cancer
Authors: Li Na , Pal Tejinder , Cai Shurui , Banerjee Ananya , Bai Xuetao , Lavudi Kousalya , Wang Qi-En
Published: June 2022

Tumors contain phenotypically and functionally heterogeneous cancer cells. Among them, a minority of cell subpopulation, termed cancer stem cells (CSCs), which possess the self-renewal capacity and are able to generate the heterogeneous lineage of cancer cells, has been believed to be responsible for the initiation and progression of the tumor. However, it is still unclear how the stemness properties of CSCs are maintained in the tumor. Mitophagy is a process by which damaged mitochondria are cleared via autophagy. The significance of mitophagy in the maintenance of CSC has been investigated in multiple CSC types. Our recent study shows that ovarian CSCs also exhibit enhanced mitophagy, which is mainly attributed to elevated expression of mitophagy receptors BNIP3 and BNIP3L. Downregulation of BNIP3 or BNIP3L significantly diminished mitophagy in ovarian CSCs and compromised their self-renewal capability. Mechanistic investigation further revealed that enhanced NF-κB signaling contributes to the increased expression of BNIP3 and BNIP3L. Inhibition of NF-κB signaling pathway via p65 knockdown or specific inhibitors is able to reduce mitophagy in ovarian CSCs. In summary, our data suggest that selective inhibition of NF-κB is able to deplete CSCs by interfering with mitochondria quality control in these cells and has potential to prevent tumor relapse and metastasis.

Citation Format: Na Li, Tejinder Pal, Shurui Cai, Ananya Banerjee, Xuetao Bai, Kousalya Lavudi, Qi-En Wang. NF-κB-mediated mitophagy contributes to the maintenance of cancer stem cells in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 889.
Abstract 93: Soluble mesothelin acts as a signaling molecule
Authors: Ewa Theressa , Avula Leela , Joseph Sarah , Rudloff Michael , Sevilla Samantha , Koparde Vishal , Zhang Xianyu , Alewine Christine
Published: June 2022

Mesothelin (MSLN) is a cell surface glycoprotein that is expressed by most pancreatic ductal adenocarcinoma (PDAC) and is used as a target for anti-cancer therapy. MSLN expression appears to make pancreatic cancer more aggressive. Previously, we found that MSLN KO PDAC cells grow in culture and as subcutaneous tumors similarly to wild-type (WT) cells but form intraperitoneal metastases poorly. MSLN pre-cursor (pre-MSLN) is a 71-kD glycosylphosphatidylinositol (GPI)-anchored protein that is cleaved intracellularly to make the 31-kD secreted protein Megakaryocyte Potentiating Factor (MPF), and a 40-kD mature MSLN (mMSLN) that retains membrane attachment. The mMSLN can be shed from the cell surface by the action of specific proteases, resulting in release of soluble MSLN (sMSLN) to both the tumor microenvironment and serum. The goal of this study is to see if sMSLN promotes cancer cell aggressiveness. We transduced MSLN KO pancreas cancer cells to express: 1) a mutant, secreted-only pre-MSLN (includes WT MPF) with a C-terminal truncation (MSLNΔ599) that prevents GPI-linkage of MSLN to the membrane, and 2) truncated pre-MSLN consisting of MPF only. Results show that complementation of KO cells with MPF or MSLNΔ599 does not rescue the MSLN KO phenotype, while MSLNΔ599 bearing a Y318A point mutation that disrupts the binding of MSLN to MUC16/CA125 does restore growth of peritoneal metastasis. We performed RNA-deep sequencing on MSLN KO cells exposed to WT or Y318A sMSLN from conditioned medium. We identified 2000 genes that were differentially expressed across the treatment groups. Exposure to sMSLN resulted in changes in expression of cell adhesion and sterol biosynthetic synthesis pathway genes. Individual genes that were top hits were also identified and are under investigation. Exposure to sMSLN changes the transcriptomic program of pancreas cancer cells and may promote peritoneal colonization.

Citation Format: Theressa Ewa, Leela Avula, Sarah Joseph, Michael Rudloff, Samantha Sevilla, Vishal Koparde, Xianyu Zhang, Christine Alewine. Soluble mesothelin acts as a signaling molecule [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 93.
Abstract 933: Macrophage-derived C/EBPb promotes breast tumorigenesis
Authors: Dow Alexa M. , Rojo Michelle D. , Treadwell Scout M. , Machado Heather L.
Published: June 2022

Breast cancer growth and progression relies on complex interactions between tumor cells and surrounding stromal cells, including immune cells. Infiltrating immune cells, including macrophages, have been shown to promote tumor progression and metastasis, and efforts have aimed at the tumor microenvironment as a therapeutic strategy. Although tumor-promoting roles of macrophages are well-established, the specific macrophage factors and transcription factor-mediated regulatory programs that drive breast cancer progression are less understood. Using a p53-/- syngeneic model of premalignant progression to invasive cancer, we identified distinct subpopulations of macrophages that resemble both normal tissue resident macrophages and tumor-associated macrophages. Interestingly, most of these macrophage subsets highly express C/EBPβ, suggesting a global function of C/EBPβ in macrophages. C/EBPβ is a transcription factor that is overexpressed in breast cancer tissues and is important for monocyte differentiation and myeloid-derived suppressor cell function. To address the function of macrophage C/EBPβ during tumorigenesis, Cebpb-floxed mice were bred to iCsf1r-Cre mice to generate mice (CebpbΔM) where Cebpb is selectively deleted in macrophages (CSF1R-expressing myeloid cells). Genetic ablation of macrophage C/EBPβ in premalignant lesions results in a significant decrease in progression to invasive cancer. In established claudin-low tumors, deletion of macrophage C/EBPβ results in decreased tumor latency and the re-expression of cytokeratin 8+E-cadherin+ cells, reminiscent of luminal-like tumors. This phenoytpe was recapitulated in an ex vivo 3D co-culture model, where uniformly round structures that lack mesenchymal projections form in the presence of CebpbΔM BMDMs. These data suggest that macrophage C/EBPβ may help maintain a mesenchymal phenotype in claudin-low tumors. Ongoing studies are aimed at identifying the Cebpb-induced gene networks in macrophages that mediate tumor progression. These studies will have critical implications for whether inhibition of C/EBPβ-regulated genes may revert claudin-low tumors to a luminal-like phenotype, rendering tumors responsive to current therapies. This work is supported by NIH R01CA212518 (H.L.M.).

Citation Format: Alexa M. Dow, Michelle D. Rojo, Scout M. Treadwell, Heather L. Machado. Macrophage-derived C/EBPb promotes breast tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 933.
Abstract 949: Novel stilbene compounds inhibit triple-negative breast cancer invasive potential
Authors: Rhodes Lyndsay V. , Julmeus Kaelyn
Published: June 2022

Triple-negative breast cancer (TNBC) is a highly aggressive breast subtype of breast cancer that lacks targeted therapies. We have previously identified several novel stilbene compounds that effectively decreased viability of TNBC. Stilbenes are natural defense compounds produced by plants and have been popularized in recent years due to general observed health benefits. Resveratrol, the most widely studied stilbene, has been revealed to possess significant antioxidant and anti-cancer effects. Many stilbenes are classified as phytoestrogens, but unlike estrogens, stilbenes do not appear to negatively impact normal breast tissue or reproductive organ health. Thus, these compounds represent new alternatives for cancer therapeutic development. The focus of this research was to identify stilbene compounds with anti-migration and/or anti-invasive properties in TNBC cells and to determine the mechanism of these inhibitory effects. Two TNBC cell lines, MDA-MB-157 and BT-549, were treated with stilbene compounds at sub-lethal doses and assessed for effects on migration and invasion using transwell assays. Cell morphology changes were evaluated with results suggestive of reversal of epithelial-to-mesenchymal transition (EMT), a key contributor in the metastatic process and a common characteristic of many TNBC cells. Gene expression analysis confirmed stilbene-induced changes of EMT-related genes. These data indicate that stilbenes, like resveratrol and related analogues, reduce cell motility and invasion through regulation of EMT gene expression in TNBC cells. Development of synthetic analogs of natural compounds remains a viable drug development opportunity for new therapeutics.

Citation Format: Lyndsay V. Rhodes, Kaelyn Julmeus. Novel stilbene compounds inhibit triple-negative breast cancer invasive potential [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 949.
Abstract CT569: Combination of reovirus (pelareorep) and granulocyte-macrophage colony-stimulating factor (GM-CSF) alongside standard chemoradiotherapy and adjuvant chemotherapy (temozolomide) for patients with glioblastoma multiforme (GBM): Long term follow up results of the ReoGlio phase Ib trial
Authors: Short Susan C. , Kendall Jessica , Chalmers Anthony , McBain Catherine , Melcher Alan , Samson Adel , Phillip Rachel , Brown Sarah
Published: June 2022

Background: Oncolytic viruses are of increasing interest as an immunologic approach to treating glioma. We previously reported safety data from a phase Ib, open-label study of intravenous pelareorep with GM-CSF alongside standard chemoradiotherapy in newly diagnosed glioblastoma and confirmed that the combination is tolerable. Following agreement from the relevant ethics authorities we have now completed long term follow up data on all patients treated in the study to investigate whether there is a signal of impact on survival. METHODS: 15 patients with newly diagnosed GBM were treated with GM-CSF 50μg subcutaneously on days 1-3 and pelareorep on days 4-5 in weeks 1 and 4 of chemoradiotherapy, and subsequently in week 1 of each adjuvant temozolomide course: 7 patients received 1x1010TCID50 (dose level 1); 8 received 3x1010TCID50 (dose level 2). The primary objective was to determine the maximum tolerated dose of pelareorep and GM-CSF with standard chemoradiotherapy. Following end of study patients were followed up as per institutional practice. Ethical approval was granted to collect survival data in all patients who survived beyond study closure up to June 2021.

Results: We showed that using intravenous pelareorep with GM-CSF alongside standard chemoradiotherapy in patients with GBM was tolerable with 87% of patients completing treatment as planned. Survival data analysis showed that median OS was 12.6 months for patients in dose level 1 and 16.1 months in dose level 2, giving median OS for all patients 13.1 months. It was notable however that a small number of patients survived beyond 24 months. The 24-month survival estimate for all patients was 33%, 16.7% for dose level 1 and 50% for dose level 2. One patient in dose level 2 remains alive at 42 months.

Conclusion: We previously reported that intravenous delivery of pelareorep with standard chemoradiotherapy is tolerable in newly diagnosed GBM. Although based on small numbers, these long-term follow up data suggest that this may be an active combination in a subset of GBM patients and further randomized studies are warranted.

Citation Format: Susan C. Short, Jessica Kendall, Anthony Chalmers, Catherine McBain, Alan Melcher, Adel Samson, Rachel Phillip, Sarah Brown. Combination of reovirus (pelareorep) and granulocyte-macrophage colony-stimulating factor (GM-CSF) alongside standard chemoradiotherapy and adjuvant chemotherapy (temozolomide) for patients with glioblastoma multiforme (GBM): Long term follow up results of the ReoGlio phase Ib trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr CT569.