bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2501: Functional properties and regulation of the catechol-O-methyltransferase gene in prostate cancer
Authors: Tanaka Yuichiro , Hashimoto Yutaka , Shiina Marisa , Shahryari Varahram , Kulkarni Priyanka , Yamamura Soichiro , Majid Shahana , Tabatabai Z Laura , Dahiya Rajvir
Published: July 2021

The catechol-O-methylase (COMT) gene has been shown to play a protective role in the cell by reducing catechol-compounds that can cause genetic mutations and enhance the carcinogenesis process. In this study, we determined the functional effects and regulation of COMT in prostate cancer. Both The Cancer Genome Atlas (TCGA) and immunohistochemical analysis of clinical specimens demonstrated a reduction of COMT expression in prostate cancer. Also, western analyses of prostate cancer cell lines show COMT levels to be minimal in DuPro and DU145 and thus, these cells were used for further analyses. Re-expression of COMT led to suppressed migration ability (wound healing assay) and enhanced apoptosis (flow cytometric analyses), and when challenged with 4-hydroxyestradiol, a marked reduction of cell proliferation (MTT assay) was observed. Xenograft growth in athymic mice also resulted in inhibition due to COMT. As a mechanism, western analyses show cleaved CASP3 and BID were increased whereas XIAP and cIAP2 were reduced due to COMT. As COMT expression is low in prostate cancer, its regulation was determined. Databases identified several miRNAs capable of binding COMT and of these, miR-195 was observed to be increased in prostate cancer according to TCGA. Real-time PCR validated upregulation of miR-195 in clinical prostate cancer specimens as well as DuPro and DU145 and interestingly, luciferase reporter showed miR-195 capable of binding COMT. These results demonstrate COMT to play a protective role by activating the apoptosis pathway and for miR-195 to regulate its expression. COMT may thus be a potential biomarker or a therapeutic target for prostate cancer.

Citation Format: Yuichiro Tanaka, Yutaka Hashimoto, Marisa Shiina, Varahram Shahryari, Priyanka Kulkarni, Soichiro Yamamura, Shahana Majid, Z Laura Tabatabai, Rajvir Dahiya. Functional properties and regulation of the catechol-O-methyltransferase gene in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2501.
Abstract 2502: Co-existing P53 and ARID1A mutations promote metastatic endometrial tumorigenesis
Authors: Reske Jake J. , Wilson Mike R. , Holladay Jeanne , Risinger John I. , Chandler Ronald L.
Published: July 2021

P53 and ARID1A are frequently mutated across cancer but rarely in the same tumor. Uterine endometrial cancer displays the highest P53-ARID1A mutual exclusivity rate. The genetic basis underlying P53-ARID1A mutual exclusivity and the relationship between molecular programs imposed by either mutation have not been elucidated in vivo mouse models. Here, genetically engineered mice were used to discern both unique and overlapping roles of P53 and ARID1A in the endometrium. Endometrial epithelial hyperplasia is driven by P53 loss with oncogenic PIK3CAH1047R in the endometrial epithelium. Sorted hyperplastic endometrial epithelial cells were transcriptome profiled and compared to control cells and ARID1A-PIK3CA mutant endometrium. Both P53 and ARID1A mutations lead to activation of inflammatory pathways but differ on other gene expression programs, such as epithelial-to-mesenchymal transition. Gene expression patterns observed in the genetic mouse models are reflective of human tumors with respective genetic alterations. ARID1A co-regulates P53 transcriptional gene targets, and the P53 pathway is activated in ARID1A mutant endometrial tumors. Finally, TP53 and ARID1A mutations co-occur more frequently in metastatic lesions, and co-existing TP53-ARID1A mutations are viable in the endometrium and lead to invasive endometrial cancer. These data suggest P53 and ARID1A mutations stimulate shared and distinct tumorigenic programs in the endometrium and promote metastasis when existing simultaneously. We propose that ARID1A loss in P53 mutant endometrial cancer promotes metastasis.

Citation Format: Jake J. Reske, Mike R. Wilson, Jeanne Holladay, John I. Risinger, Ronald L. Chandler. Co-existing P53 and ARID1A mutations promote metastatic endometrial tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2502.
Abstract 2519: Targeting glucose metabolism in HER2+breast cancer
Authors: Chang Simone , Chesney Jason , Trent John O. , Telang Sucheta
Published: July 2021

Primary and metastatic breast cancers are driven by oncogenic mutations to rely on glucose metabolism to support their rapid proliferation. Of these genetic changes, the increased activity of the human epidermal growth factor receptor 2 (HER2/ErbB2) is observed in a third of all breast tumors. HER2 has been shown to activate downstream effectors (e.g. Ras, HIF-1α) that stimulate glycolysis - in part by activation of the 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase family of enzymes (PFKFB1-4). The PFKFBs produce fructose-2,6-bisphosphate (F26BP) which activates a key rate-limiting glycolytic enzyme, 6-phosphofructo-1-kinase (PFK1).

In preliminary studies, we found that the PFKFB4 family member was highly expressed in a series of patient-derived HER2+ breast tumors relative to normal breast with markedly higher expression in their matched metastatic lymph nodes. We next determined that silencing PFKFB4 markedly reduced F26BP, glycolysis and cell survival in HER2+ breast cancer cells and inhibited tumor growth in vivo. Through virtual screening, we have discovered a first-in-class small molecule inhibitor of PFKFB4, termed 5MPN, that selectively inhibits PFKFB4 activity with a resultant decrease in F26BP, glycolysis and cancer cell growth. 5MPN also caused a significant decrease in the invasion and migration of HER2+ breast cancer cells in vitro, importantly at concentrations well below levels that affect cell viability and marked suppression in the growth of established tumors, without systemic toxicity.

In additional studies, we have found that the related PFKFB3 isoform is also expressed in HER+ breast tumors. Our previous work found that the PFKFB4 enzyme localizes to the cytoplasm (where PFK1 and the glycolytic pathway function) indicating a possible dominant role for PFKFB4 in glycolytic regulation. PFKFB3 however largely localized to the nucleus where it serves an important function in proliferation via activation of cyclin-dependent kinases. Based on the different roles played by these enzymes in cancer cells, we next evaluated the effects of simultaneous administration of 5MPN ± a clinical candidate PFKFB3 inhibitor on survival and proliferation in HER2+ breast cancer and found that the combination synergistically and significantly decreased viability and growth in several examined HER2+ breast cancer cell lines. Our data indicate that targeting PFKFB4 may be a viable therapeutic option against breast cancer and strongly support the further exploration of co-targeting PFKFB4 and PFKFB3 as a potential therapeutic strategy for the successful treatment of HER2+ breast cancer.

Citation Format: Simone Chang, Jason Chesney, John O. Trent, Sucheta Telang. Targeting glucose metabolism in HER2+breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2519.
Abstract 252: Navigating networks of oncology biomarkers mined from the scientific literature: A new open research tool
Authors: Wager Kim , Chari Dheepa , Ho Steffan , Rees Tomas J. , Schijvenaars Robert J.
Published: July 2021

Introduction: Oncology biomarkers have a pivotal role in diagnosis, prognosis, assessment of disease progression and the prediction of treatment efficacy. There are > 5000 known biomarkers; some are well characterised, while others are emerging as biomarkers of potential interest. Biomarker panels, incorporating combinations of biomarkers, are increasingly used to enhance the power and precision of testing.

Objective: We sought to identify key emerging biomarkers and biomarker relationships by applying analytical techniques to the corpus of recent scientific publications using an artificial intelligence (AI)-driven platform.

Methods: Biomarker targets were obtained from the Early Detection Research Network. Recent (<5 years old) publications mentioning biomarkers in six cancer types (bladder, breast, colorectal, lung, prostate and renal) were identified using Dimensions (a linked research knowledge system); emerging biomarkers were identified by number and growth in publications. For selected biomarkers, full text proximity searching was used to identify biomarker co-occurrence, which was visualized and characterized using network analysis and co-occurrence heatmaps per cancer type. Relationships between biomarkers were also assessed in an indication-agnostic dataset. Key biomarkers were identified by a measure of their network importance.

Results: A total of 720 biomarkers were analyzed, and 41 clusters identified across the cancer types. Data visualizations are available at https://reports.dimensions.ai/mined-oncology-biomarkers/

Conclusion: Using large-scale analytics of published literature, biomarkers across six cancer types were successfully characterized in terms of their emergence in the published literature and the context in which they are described. This novel AI-driven approach could help identify biomarkers and biomarker panels for exploration in a clinical setting.

Example clusters - growth rate is compound annual growth rate (CAGR)Cancer typeBiomarkers (n)Publications (n)Cluster key biomarkersCluster publication growth rate (%)Bladder49168CAV1/CXCL8/THBS153.1Breast2651593AREG/CXCL10/CXCL832.6Colorectal193921CAV1/CDCP1/MTHFR31.6Lung2231061SFTPC/C9/GPI41.4Prostate166717FABP5/FLNA/CAV131.6Renal44185CXCL10/CXCL8/CSNK2A149.5

Citation Format: Kim Wager, Dheepa Chari, Steffan Ho, Tomas J. Rees, Robert J. Schijvenaars. Navigating networks of oncology biomarkers mined from the scientific literature: A new open research tool [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 252.
Abstract 2545: A novel tool for the accurate and affordable early diagnosis of pancreatic cancer via machine learning and bioinformatics
Authors: Goel Siya , Honorio Jean
Published: July 2021

Pancreatic cancer (PC) is the fourth leading cause of cancer death in the United States due to its five-year survival rate of 8.9%. Late diagnosis, affiliated with the asymptomatic nature in early stages and the location of the cancer with respect to the pancreas, makes current widely-accepted screening methods unavailable. Prior studies have achieved low (70-75%) diagnostic accuracy, possibly because 80.1% of PC cases are associated with diabetes, leading to misdiagnosis. To address the problems of frequent late diagnosis and misdiagnosis, an accessible, accurate, and affordable diagnostic tool was developed by analyzing the expression of nineteen genes in PC and diabetes. First, machine learning algorithms were trained on four groups of subjects, depending on the occurrence of PC and Diabetes. The models were analyzed with 400 PC subjects at varying stages to ensure validity. Naive Bayes, Neural Network, and K-Nearest Neighbors models achieved the highest testing accuracy of around 92.6%. Second, a novel user interface, PanCan Diagnosis, was designed to test an individual's occurrence of PC where the average likelihood of PC was displayed. Third, the biological implication of the nineteen genes was investigated using bioinformatics tools. It was found that these genes were significantly involved in regulating the cytoplasm, cytoskeleton and nuclear receptor activity in the pancreas, specifically in acinar and ductal cells. This novel tool is the first in the literature that achieves a PC diagnostic accuracy of above 90%, potentially increasing the five-year survival rate to 36%.

Citation Format: Siya Goel, Jean Honorio. A novel tool for the accurate and affordable early diagnosis of pancreatic cancer via machine learning and bioinformatics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2545.
Abstract 2551: The development of cancer digital videos to increase participation in marginalized communities
Authors: Valera Pamela , Alzate-Duque Luis , Acuna Nicholas
Published: July 2021

Social media, in the form of digital videos, targeted people with limited health literacy, as well as disadvantaged or marginalized groups, may help reduce cancer health disparities and improve health outcomes in these populations. In this article, we document the process of adapting the content from the Cancer 101 curriculum to create animated scripts about the cancer care continuum that is clear, straightforward, and in plain language. The development of the Cancer 101 digital videos required a multidisciplinary collaboration from - public health, medicine, technology, and expertise in correctional health, smoking cessation, web development, video producers, and individuals directly impacted by cancer disparities. The Cancer 101 videos were showcased at a community health fair where the videos were viewed by attendants waiting to be seen by a medical provider. While waiting for their cancer screening, thirteen individuals were selected and invited to watch all eleven videos totaling less than 60-minutes of viewing time. Overall, participants agreed that they would recommend the videos to friends/family and that they plan to watch other video modules to learn more information about cancer. Additionally, participants enjoyed the graphics and audio of the videos presented. Furthermore, participants noted that Cancer 101 digital videos described cancer in plain language, leading to a better understanding of the disease. Future research is needed to implement Cancer 101 digital videos in healthcare clinics to increase cancer information and improve cancer screening rates in marginalized communities.

Citation Format: Pamela Valera, Luis Alzate-Duque, Nicholas Acuna. The development of cancer digital videos to increase participation in marginalized communities [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2551.
Abstract 2562: EGCG targeting of adipogenesis reveals a STAT3-mediated paracrine oncogenic control of triple-negative breast cancer cell invasive phenotype
Authors: Suarez Narjara Gonzalez , Torres Sahily Rodriguez , Annabi Borhane
Published: July 2021

Background: Obese subjects have an increased risk of developing triple-negative breast cancer (TNBC), in part associated with the chronic low-grade inflammation state. On the other hand, epidemiological data indicates that increased consumption of polyphenol-rich fruits and vegetables plays a key role in reducing incidence of some cancers.

Objectives: Here, we tested whether green tea-derived epigallocatechin-3-gallate (EGCG) could alter adipogenesis involved in the maturation of pre-adipocytes, and how this impacts the paracrine regulation of the mature adipocytes secretome on the TNBC invasive phenotype.

Methods: Differentiation was performed and conditioned media (CM) from preadipocytes and mature adipocytes harvested. Human TNBC-derived MDA-MB-231 real-time cell migration was performed using the exCELLigence system. Differential gene arrays and RT-qPCR were used to assess gene expression levels. Western blotting was used to assess protein expression levels. In vitro vasculogenic mimicry (VM) was assessed with Matrigel.

Results: EGCG was found to inhibit the induction of numerous key adipogenic biomarkers, including lipoprotein lipase, adiponectin, leptin, fatty acid synthase, and fatty acid binding protein 4. Increased MDA-MB-231 chemotaxis and VM were found in response to mature adipocytes secretome, and this was correlated with the induction of the STAT3 signaling pathway. This invasive phenotype was prevented by EGCG, JAK/STAT inhibitors Tofacitinib and AG490, as well as upon STAT3 gene silencing.

Conclusion: Adipocytes secretome plays a key role in the paracrine regulation of TNBC cells invasive phenotype. Dietary catechin-mediated interventions may, in part through the inhibition of adipogenesis and modulation of adipocytes secretome, prevent the onset of an obesogenic environment that favors TNBC development.

Citation Format: Narjara Gonzalez Suarez, Sahily Rodriguez Torres, Borhane Annabi. EGCG targeting of adipogenesis reveals a STAT3-mediated paracrine oncogenic control of triple-negative breast cancer cell invasive phenotype [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2562.
Abstract 2574: Collagen density and obesity promote mammary gland inflammation
Authors: Williams Abbey E. , Williams Abbey E. , Hoffman Erica , Warren Julia , Ponik Suzanne , Arendt Lisa M.
Published: July 2021

Recent epidemiological studies suggest that the risk factors of breast density and obesity together increase breast cancer risk in premenopausal women, and these women have a worsened prognosis following breast cancer diagnosis. Although the underlying causes of increased risk associated with dense breasts and obesity have individually been explored, little is known about how these underlying risk factors interact together to enhance breast cancer risk. To model breast density, we used heterozygous Col1a1tmjae mice, that have a mutation that limits collagen degradation, leading to increased mammary collagen deposition. Heterozygous (het) mice or wild type (wt) litter mates were fed either a control diet (CD) or a high fat diet (HFD) to induce obesity. We quantified F4/80-positive macrophages within mammary glands using immunohistochemistry. We observed significantly increased numbers of macrophages in mammary glands of CD/het, HFD/wt and HFD/het mice compared to CD/wt mice. We observed significantly enhanced picrosirius red stained collagen surrounding mammary ducts from CD/het, HFD/wt, and HFD/het mice compared to those from CD/wt mice. Notably, HFD/het mice had significantly more collagen surrounding ducts than in mammary glands from CD/het mice. These results may suggest that obesity enhances collagen deposition and macrophage-driven inflammation within dense breast tissue in the mammary glands of non-tumor-bearing mice.

Citation Format: Abbey E. Williams, Abbey E. Williams, Erica Hoffman, Julia Warren, Suzanne Ponik, Lisa M. Arendt. Collagen density and obesity promote mammary gland inflammation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2574.
Abstract 2587: Investigating the impact of chemotherapy on gut microbiota and microbiota-derived metabolites and their link to inflammation and cardiometabolic disorders in children with cancer
Authors: Benmoussa Abderrahim , Levasseur Laurence , Coté-Sergerie Shuxia , Bélanger Véronique , Levy Emile , Laverdière Caroline , Stintzi Alain , Sinnett Daniel , Marcil Valérie
Published: July 2021

Children treated for acute lymphoblastic leukemia (ALL) often suffer serious side-effects, including vomiting, diarrhea, severe infections, and cardiometabolic disorders. We hypothesized that deregulation of the intestinal microbiota, and its metabolites, is related to these side effects, and promotes inflammation and cardiometabolic disorders in this population. To explore this new avenue, we are recruiting 38 children with ALL treated at Sainte-Justine UHC in Montreal. At each treatment cycle, we compile clinical, treatment, and diet data, cardiometabolic status (weight, height, blood lipids, glucose, insulin, blood pressure), and collect blood and stool samples. We use high throughput sequencing to analyze the intestinal microbiota. Bacterial metabolites (SCFA, acyl-carnitines, p-cresol and TMAO) in stool and plasma are measured by GS-MS and HPLC-MS/MS. Biomarkers of inflammation (CRP, leptin, TNF-α, IL-6) and oxidative stress (ox-LDL, MDA, 8-OHdG) are evaluated in plasma or red blood cells by ELISA/Bioplex. On admission, 83% of patients had at least one cardiometabolic risk factor (59% high CRP, 83% pre/hypertriglyceridemia, 51% hypertension, 32.5% overweight/obesity, 27.9% hyperglycaemia) and 49% had a family history. After 31 days of treatment, some of these disorders were stabilized while others persisted or worsened (+7% obesity/overweight, -34% hypertriglyceridemia, -4.5% hypertension, +16% high CRP, -16.6% hyperglycaemia) and were associated with changes in short-chain acyl-carnitines (x1.3 - x3.4) and TMAO (x18.3). The links between these disorders, their temporal variation and inflammation, treatments, and side effects are being investigated. This project will serve as a basis for mechanistic and interventional studies to prevent inflammation and cardiometabolic disorders in children with cancer.

Citation Format: Abderrahim Benmoussa, Laurence Levasseur, Shuxia Coté-Sergerie, Véronique Bélanger, Emile Levy, Caroline Laverdière, Alain Stintzi, Daniel Sinnett, Valérie Marcil. Investigating the impact of chemotherapy on gut microbiota and microbiota-derived metabolites and their link to inflammation and cardiometabolic disorders in children with cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2587.
Abstract 2592: Boosting immune surveillance by low-dose PI3K inhibitor facilitates early intervention of breast cancer
Authors: Zhang Yuan , Wang Jinyang , Xiao Yi , Yuan Xiangliang , Li Ping , Duan Yimin , Seewaldt Victoria L. , Yu Dihua
Published: July 2021

Prevention of estrogen receptor–negative (ER-) breast cancer is an unmet challenge, although tamoxifen and aromatase inhibitors can successfully decrease the incidence of ER-positive (ER+) breast cancer. PI3K pathway activation has been detected in tamoxifen-resistant ER- breast lesions of patients. Here, we further ratified that the PI3K pathway is significantly activated in premalignant ER- breast lesions compared with paired normal tissues of patients, which prompted our assessment of targeting PI3K on inhibition of ER- mammary tumor initiation and progression. Both genetic knockdown of PIK3CA or intervention with low-doses of a PI3K inhibitor (GDC-0941) prevented the dysplasia phenotype of semi-transformed human ER- mammary epithelial cells in 3-dimensional culture in vitro. Importantly, low-dose GDC-0941 treatment significantly delayed mammary tumor initiation in the MMTV-neu mouse model without exhibiting discernable adverse effects. Interestingly, increased CD8+/GZMB+ T-cells were detected in mammary tissue after GDC-0941 treatment, suggesting enhanced immune surveillance. Mechanistically, elevated expression of potent T-cell chemo-attractants, including CCL5 and CXCL10, were detected both in vitro and in vivo after GDC-0941 treatment. Furthermore, inhibition of PI3K significantly increased T-cell recruitment in a CCL5/CXCL10–dependent manner. In human ER- breast cancer, PI3K activation is correlated with significantly reduced CCL5, CXCL10 and CD8A expression, suggesting that the decreased CD8+ T-cell recruitment and escape of immune surveillance may contribute to ER- breast cancer development. In summary, our study indicates that low-dose PI3K inhibitor treatment may intervene early stage ER- breast cancer development by enhancing immune surveillance via CCL5/CXCL10.

Citation Format: Yuan Zhang, Jinyang Wang, Yi Xiao, Xiangliang Yuan, Ping Li, Yimin Duan, Victoria L. Seewaldt, Dihua Yu. Boosting immune surveillance by low-dose PI3K inhibitor facilitates early intervention of breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2592.
Abstract 2599: Does tumor volume effect the spectroscopic classification of brain cancer patients
Authors: Theakstone Ashton G. , Brennan Paul M. , Baker Matthew J.
Published: July 2021

This study focuses on investigating the link between brain tumor volume and the spectroscopic classification between patients with known gliomas and healthy controls. Discrimination of brain cancer vs. non-cancer patients using serum-based ATR-FTIR diagnostics was first developed by Hands et al. achieving sensitivity and specificity values of 92.8% and 91.5% respectively. Cameron et al. then went on to stratifying between specific brain tumor types and was successful in providing a sensitivity of 90.1% and a specificity of 86.3%. Expanding on these studies, it is vital to determine if the size of a tumor has a direct effect on the sensitivity and specificity and whether or not it was only the larger tumors that were being identified as cancerous. A cohort of 90 patients whose tumor volumes were calculated using their MRI images (either T1-weighted contrast enhanced, T2-weighted or FLAIR images), including patients with high-grade glioblastoma multiforme (GBM), and low-grade gliomas such as anaplastic astrocytoma, astrocytoma, oligoastrocytoma and oligodendroglioma, were used for investigation. Utilizing ATR-FTIR spectroscopy coupled with machine learning algorithms these tumor patients were stratified against 87 healthy controls and were classified as either cancer or non-cancer. From these initial findings' sensitivities, specificities and balanced accuracies were greater than 88% and cancer patients with tumor volumes as small as 0.2 cubic cm were correctly identified, demonstrating that classifications are not affected by tumor volume. Both small and low-grade gliomas were identified which shows great promise for this technique to be used as a screening tool or in diagnostics for early detection of brain tumors.

Citation Format: Ashton G. Theakstone, Paul M. Brennan, Matthew J. Baker. Does tumor volume effect the spectroscopic classification of brain cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2599.
Abstract 2604: Urinary microRNAs as biomarkers for early detection of urothelial cancer
Authors: Takayama Kazuya , Yamazaki Kohei , Yamaguchi Hiroki , Tsuda Keishu , Yasui Takao , Ichikawa Yuki
Published: July 2021

microRNAs modulate gene expression in various cancer types, and their profiles differ in healthy and cancer groups of people and they represent a warning sign for various cancer scenarios. Identification of tumor-specific microRNAs presents a powerful opportunity to potentially reduce cancer mortality through early detection. In order to achieve early detection through population screening, noninvasive approaches are needed to complement and improve upon current strategies for urothelial cancer (UC) screening. Since all microRNAs in the blood cannot be transferred from donor to recipient cells during single blood circulation, kidney filtration could pass some untransferred microRNAs from blood to urine, therefore urinary microRNAs might be used as biomarkers for the diagnosis of cancer. We investigated whether urine levels of microRNA can differentiate patients with UC from healthy individuals. Here, we successfully identified UC-related microRNA ensembles in urine through a combination of microfluidic microRNA extraction device and machine learning-based analysis.

We analyzed 93 urine samples from 27 UC patients and 66 healthy individuals (controls). An initial set of 74 microRNAs was selected by microarray microRNA profiling assay as biomarker candidates. Quantitative reverse-transcription PCR was used for further analysis to validate the expression of microRNAs.

We selected a group of 6 microRNAs for validation; (miR-6089, miR-4488, miR-4784, miR-26a-5p, miR-148a-3p, and miR-143-3p) were confirmed to be significantly different in UC and controls. We adopted a logistic regression model and successfully developed a classifier based on these 6 microRNAs, which showed remarkably high sensitivity (94%) and specificity (85%).

In summary, patients with UC have significantly different patterns of microRNA expression from healthy individuals. We identified a signature of 6 microRNAs as predictors that can differentiate patients with UC from those who are healthy. These microRNAs could be potentially developed as biomarkers for UC.

Citation Format: Kazuya Takayama, Kohei Yamazaki, Hiroki Yamaguchi, Keishu Tsuda, Takao Yasui, Yuki Ichikawa. Urinary microRNAs as biomarkers for early detection of urothelial cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2604.
Abstract 2606: A nCounter-Based mRNA signature in plasma associates with localized non-small cell lung cancer
Authors: Capitán Ana Giménez , Bracht Jillian , Potie Nicolas , González-Cao María , Viteri Santiago , Martínez-Bueno Alejandro , Cabrera-Gálvez Carlos , Rubinstein Pablo , Mayo-de-las-Casas Clara , Valarezo Joselyn , Huang Chung-Ying , Pedraz Carlos , Boykind Richard , Warren Sarah , Rosell Rafael , Molina-Vilaa Miguel Ángel , Aguilar-Hernández Andrés
Published: July 2021

Background: 80% of non-small cell lung cancer (NSCLC) cases are diagnosed at stages IIIB-IV and have a dismal prognosis with a median life expectancy that does not exceed 2 years. In contrast, patients diagnosed at early and locally advanced stages (I-IIIA) can undergo surgery and have the potential to be totally cured. Imaging technologies often detect lung nodules of unknown significance that pose a diagnostic challenge; some patients with benign nodules are submitted to unnecessary surgical interventions while others with small tumors are just kept in observation, risking a significant delay for treatment. A diagnostic test that could differentiate between benign and malignant masses would be of great help in this setting.

Methods: Circulating-free RNA (cfRNA) was isolated from the plasma of healthy individuals (N=21), early(I-II) stage (N=22) and stage IIIA (N=12) NSCLC patients, using an automatic extraction method(Qiasymphony, Qiagen). Purified cfRNA was quantified using Qubit, retrotranscribed and pre-amplified (14cycles) using the Low RNA Input Amplification kit (NanoString Technologies). Gene expression analysis was performed on the nCounter platform using the PanCancer IO360TM (NanoString Technologies), which can detect 770 transcripts related to tumor biology, micro-environment and the immune system.

Results: Gene expression analysis revealed differential patterns for some cf-mRNAs from localized stage NSCLC patients versus healthy controls. A bioinformatics recursive feature elimination algorithm selected a 16-gene mRNA signature that was able to distinguish between localized NSCLC and control samples with an area under the ROC curve of 0.91 to 0.95. Furthermore, the signature scores derived from the algorithm were significantly different between the two cohorts.

Conclusions: We have found an 16-gene signature that can differentiate between cfRNA of localized stages NSCLC patients and control individuals. Our results warrant validation studies in larger cohorts.

Citation Format: Ana Giménez Capitán, Jillian Bracht, Nicolas Potie, María González-Cao, Santiago Viteri, Alejandro Martínez-Bueno, Carlos Cabrera-Gálvez, Pablo Rubinstein, Clara Mayo-de-las-Casas, Joselyn Valarezo, Chung-Ying Huang, Carlos Pedraz, Richard Boykind, Sarah Warren, Rafael Rosell, Miguel Ángel Molina-Vilaa, Andrés Aguilar-Hernández. A nCounter-Based mRNA signature in plasma associates with localized non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2606.
Abstract 2611: Transcription factor-nucleosome dynamics inferred from plasma cfDNA delineates tumor and tumor-microenvironment phenotype
Authors: Rao Satyanarayan , Han Amy , Zukowski Alexis , Kopin Etana , Kabos Peter , Ramachandran Srinivas
Published: July 2021

Our current understanding of solid tumors and their progression primarily relies on in vitro models, cell lines, patient-derived xenografts, and scarce data from invasive tissue biopsies from patients. The ability to monitor changes in chromatin structure and transcription factor binding in tumor cells using a minimally invasive approach in humans has the potential to revolutionize our understanding of disease progression and treatment resistance. In this study, we use the example of estrogen receptor (ER) positive breast cancer, the most common disease subtype, and define the ER axis from plasma cell-free DNA (cfDNA). While lymphoid/myeloid cell turnover represents the dominant source of cfDNA in the bloodstream, a detectable fraction of DNA from tumor tissue-of-origin can be found in patients with solid cancers. cfDNA is the product of the action of endogenous nucleases on chromatin; and retains the map of epigenomes from cells of origin. Our method therefore non-invasively captures TF-nucleosome dynamics in tumor tissue-of-origin using plasma cfDNA. First, we show that we can reliably identify the active binding of hematopoietic pioneer factor PU.1 and CTCF from cfDNA of healthy humans and cancer patients. Then to define cfDNA binding of disease specific TF ER, we used ER+ patient-derived xenograft (PDX) models allowing for a clear separation of tumor signal from hematopoietic background. This allowed us to establish the sensitivity and specificity of our approach. We also identified the subset of CUT&RUN-defined ER binding sites that feature the strongest binding in vivo from both lymphocyte background as well as cancer cells. Furthermore, we can define the active binding sites of pioneer factor FOXA1, which facilitates ER binding by opening the chromatin. Based on the TF protection levels from cfDNA we were able to define tumor as well as hematopoietic-specific TF binding sites that can serve as potential hotspots to monitor ER+ disease state at around 1% tumor fraction. These data demonstrate our ability to simultaneously monitor TF and nucleosome dynamics at disease sites just from plasma that can enable real-time monitoring of disease phenotype in a minimally invasive manner.

Citation Format: Satyanarayan Rao, Amy Han, Alexis Zukowski, Etana Kopin, Peter Kabos, Srinivas Ramachandran. Transcription factor-nucleosome dynamics inferred from plasma cfDNA delineates tumor and tumor-microenvironment phenotype [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2611.
Abstract 2640: Characterization and targeted therapy using patient tumor-derived 3-D spheroids in a metastatic castrate resistant prostate cancer model
Authors: Kase Adam M. , Tan Winston , Copland John A.
Published: July 2021

Targeted therapy in prostate cancer is in its early stages and has a promising future since many genomic alterations in metastatic castrate resistant prostate cancer (mCRPC) do not have FDA approved agents for this indication. Three-dimensional culture has been shown to recapitulate patient response to therapy. We characterized a unique patient tumor-derived, GUR017M, 3D culture spheroid model and tested novel therapies based on its genomic profile. This tumor was obtained from a patient with mCRPC who progressed on enzalutamide, abiraterone, cabazitaxel, and had exposure to docetaxel, however discontinued due to toxicity. In order to characterize and test novel therapies for mCRPC, a 3-D spheroid drug assay was utilized and was able to recapitulate the GUR017M response to previous therapies (resistance to docetaxel and enzalutamide). Using a 3-D spheroid drug assay, single agents were investigated based on the GUR017M genomic profile which included cyclin D1, LYN, and FGF3/4/19 amplifications along with HRAS Q61R mutation, and TP53 splice site 672+2T>G. Single agents (abemaciclib, bafetinib, erdafitinib, tipifarnib, MK2206, APR-246) all caused dose dependent inhibition up to 100% inhibition. This rare prostate cancer model, GUR017M allows us to test novel single agents and combination strategies in 3-D culture. This patient tumor has also proven to be a successful PDTX model which allows for confirmatory testing in animal models in order to move forward with clinical trial proposals.

Citation Format: Adam M. Kase, Winston Tan, John A. Copland. Characterization and targeted therapy using patient tumor-derived 3-D spheroids in a metastatic castrate resistant prostate cancer model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2640.
Abstract 2642: Using 3-Dimensional in vitro models to unravel the complexity of the metastatic microenvironment in high-grade serous ovarian cancer
Authors: Malacrida Beatrice , Delaine-Smith Robin , Nichols Sam , Maniati Eleni , Jones Roanne L. , Knight Martin M. , Pearce Oliver M. , Balkwill Frances R.
Published: July 2021

Studying the complexity of the tumor microenvironment (TME) still represents a challenge in research. The intricate communication within the stroma - fibroblast, immune cells, endothelial cells and the extracellular matrix (ECM) - and the malignant cell compartment sustains every stage of cancer progression and resistance to cancer therapies, but it is difficult to model this using human cells. Using a multi-level deconstruction of human metastases as a template and validation, we developed multicellular models of high-grade serous ovarian cancer (HGSOC) with increased complexity. The different models - tri-, tetra- and penta-cultures - consist of different combinations of primary adipocytes, fibroblasts, mesothelial cells, HGSOC cells and myeloid cells that mimic the structure and the composition of a human omental metastatic tissue. In HGSOC biopsies, we previously identified a prognostic matrisome signature and a number of pathways correlating ECM deposition and disease progression. This knowledge combined with the versatile nature of our platforms has allowed us to identify the contributions of each cell type in supporting tumor progression and ECM remodeling. For instance, 14-day tri-culture of malignant cells, adipocytes and fibroblasts was sufficient to replicate the deposition of specific ECM proteins and the prognostic matrisome signature seen in human omental metastases. Moreover, we found that TGFβR and Hedgehog signaling pathways act together on the fibroblasts to stimulate ECM production. In addition, in the tetra-culture model, we identified platelets as promoters of early metastatic invasion by activating mesothelial cells. As the immune system plays an important role in HGSOC tumor microenvironment, we have now added myeloid cells to form a more complex penta-culture in which we can analyze the behavior and impact of myeloid cells. In conclusion, the multicellular models presented here could be a new resource to study new and established cancer therapies and provide a useful tool to better understand the molecular mechanisms that drive cancer progression.

Citation Format: Beatrice Malacrida, Robin Delaine-Smith, Sam Nichols, Eleni Maniati, Roanne L. Jones, Martin M. Knight, Oliver M. Pearce, Frances R. Balkwill. Using 3-Dimensional in vitro models to unravel the complexity of the metastatic microenvironment in high-grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2642.
Abstract 2643: Human and mouse reconstructed plate-based 3-dimensional culture assays that mimic the tumor microenvironment
Authors: Steffey Michael E. , Qu Ying , Karalewitz Andrew , Urs Sumithra , Kirshner Julia , Wise Scott
Published: July 2021

In order to predict efficacy and toxicity of compounds advancing in the oncology drug discovery pipeline, and to minimize requirements for multiple animal studies, the development of in vitro assays that recapitulate in vivo conditions is increasingly important. While high throughput screening favors 2D assays, both for cost and relative speed in culturing and plating, they do not recapitulate the tumor architecture and the microenvironment that is more comparable to in vivo models. We now report this has been accomplished using zPREDICTA's organ-specific three-dimensional (3D) culture models which support long-term culture of carcinoma cells. Physiologic extracellular matrix (ECM) components are critical in maintaining the physical and spatial microenvironment as well as tumor phenotypes in reconstructed bone marrow (r-Bone) and mouse breast (r-mBreast) models. The r-Bone ECM allows for co-culture of tumor cells with mesenchymal stem cells, fibroblasts, lymphoid, myeloid, and CAR-T cells. The data here describes clear differences in the in vitro pharmacology of several standard of care agents in 2D, in adherent or suspension cultures, compared to the recapitulated 3D tumor microenvironment of the human hematopoietic compartment or the mouse breast ductal epithelium. For example, we find that cisplatin has a 10-30 fold higher IC50 in 4 different murine cell lines (MMTV-PyMT, 4T1, EMT6, and E0771) when cultured in the r-mBreast model than when those cells are adhered to the polystyrene in a 2D culture. Cytotoxicity assays such as CellTiter-Glo® can also be performed in a high throughput format in both 96 and 384-well 3D assay formats and we demonstrate equivalent bortezomib IC50 values in RPMI 8226 cell r-Bone cultures in both plate types. Additionally, cells can be isolated from the matrix after test agent exposure and analyzed by an appropriate downstream application, such as flow cytometry, where we show anti-CD19 CAR-T cell killing of CD19+ NALM6 cells in r-Bone cultures. These 3D models represent new early opportunities to screen test agents in a platform that is designed to more closely mimic in vivo tissue microenvironments and serve as a more relevant tool for multi drug screening and as a prerequisite to animal studies.

Citation Format: Michael E. Steffey, Ying Qu, Andrew Karalewitz, Sumithra Urs, Julia Kirshner, Scott Wise. Human and mouse reconstructed plate-based 3-dimensional culture assays that mimic the tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2643.
Abstract 2648: A dual functional agent inhibits the angiogenesis and DNA synthesis resulting in the growth suppression of consensus molecular subtypes 1 and 4 in colorectal cancer xenografts
Authors: Rao Vaikar Navakanth , Kuppuswamy Ramajayam , Lai Kuo Chu , Su Tsann-Long , Lee Te-Chang
Published: July 2021

Purpose: We have synthesized a series of bifunctional molecules, which are able to induce DNA interstrand crosslinks and inhibit angiogenesis as potent anticancer agents [1] and leads to develop new hybrids molecules. To analyze one of the novel bifunctional agent BO-2762 activity in consensus molecular subtype (CMS) classified as colorectal cancer (CRC) which are classified into four subtypes [ CMS1, MSI-immune; CMS2, epithelial and canonical; CMS3, epithelial and metabolic; and CMS4, mesenchymal] in in vitro and in vivo models.

Experimental Design: We analyzed the anticancer effect of BO-2762 in CMS primary colorectal cancer cells which are reported in previous studies [2] and their respective xenografts (CMS-1: LoVo; CMS-2: LS1034; CMS-3: HT-29 and CMS-4: SW620). CMS provided a new platform to analyze BO-2762 functionalized subtype-specific sensitivity in CRC.

Results: BO-2762 has a distinct bifunctional activity by DNA crosslinking in CRC cells and inhibiting angiogenesis in endothelial cells at IC50 of nanomolar to micromolar ranges. Angiogenesis inhibition was likely due to the suppression of VEGFR-2 phosphorylation in EA.hy 926 cells. Additionally, BO-2762 could inhibit cell migration, invasion, and induce apoptotic cell death in CRC. In our observation, no subtype-sensitivity has observed in in vitro conditions as reported in previous studies [3]. Using xenograft models, 20 mg/kg BO-2762 suppressed remarkably LoVo (CMS-1), and SW620 (CMS-4) subtypes, moderately in LS1034 (CMS-2) which was administrated via i.v. injection. However, HT29 cells classified as metabolic dysregulated, which is the CMS-3 subtype, have shown resistance to BO-2762.

Conclusion: BO-2762 functions as an angiogenesis inhibitor by inhibiting the phosphorylation of VEGFR2 and inhibits the DNA synthesis by cross-linking the DNA. Consequently, BO-2762 was shown to profoundly suppress the growth of CRC xenografts of CMS-1 and 4 subtypes but not that of CMS-2 and 3. Accordingly, BO-2762 has great potential for further development as a specific anti-CRC agent against CMS-1 and 4 subtypes and lead the further investigation on how to overcome the resistance of metabolic dysregulated CMS-3 subtype as a fundamental question that warrants our investigation.

References: 1. J Med Chem, 2019. 62(5): p. 2404-2418. 2. Clin Cancer Res, 2018. 24(4): p. 794-806. 3. Neoplasia, 2020. 22(9): p. 365-375

Citation Format: Vaikar Navakanth Rao, Ramajayam Kuppuswamy, Kuo Chu Lai, Tsann-Long Su, Te-Chang Lee. A dual functional agent inhibits the angiogenesis and DNA synthesis resulting in the growth suppression of consensus molecular subtypes 1 and 4 in colorectal cancer xenografts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2648.