bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2099: Assessing cancer drug response prediction from gene expression
Authors: Talwar James , Carter Hannah
Published: September 2020

Customizing treatments targeted to a patient specific disease landscape remains an open challenge in precision medicine. Gene expression data, generated through next generation sequencing technologies, has shown significant power for supervised machine learning approaches. Here, we evaluated neural network performance at predicting cancer cell-line specific drug sensitivity. Gene expression data for 17,737 genes across 1014 human cancer cell-lines with IC50 concentrations for 251 anti-cancer drugs were obtained from the Genomics of Drug Sensitivity in Cancer Project. Cell-lines were considered sensitive if IC50 concentration was below maximum drug concentration. For neural network input, gene expression values were scaled to a range of -0.5 to 0.5 through log transformation, z-scoring, subtracting the minimum and dividing by the range. A hyperparameter optimized neural network model consisting of two hidden layers of size 1024 and 512 respectively resulted in a test set accuracy ranging from 60.2% to 67.8% across drugs compared to an average baseline performance of 53.4%. Dimension reduction through clustering and Nearest Neighbor Networks did not result in improved performance. We found that classical machine learning classification methods including support vector machines showed comparable performance to our neural network approach. However, neural network cross-training on drugs sharing the same putative targets (e.g. AURKA) led to a 5.03% improvement in neural network prediction accuracy. Overall, our analysis shows that utilizing gene expression profiles independent of other -omics data for cancer drug response prediction through machine learning frameworks offers modest predictive capabilities. To increase performance, we suggest augmenting training size through shared pathway cross-training, optimizing feature encoding to maximize neural network predictive capabilities, and incorporating other -omics data.

Citation Format: James Talwar, Hannah Carter. Assessing cancer drug response prediction from gene expression [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2099.
Abstract 2115: An atlas of transposable element derived alternative splicing in cancer
Authors: Clayton Evan A. , Rishishwar Lavanya , Huang Tzu-Chuan , Gulati Saurabh , Ban Dongjo , McDonald John F. , Jordan I. King
Published: September 2020

Transposable element (TE) derived sequences comprise more than half of the human genome, and their presence has been documented to alter gene expression in a number of different ways, including the generation of alternatively spliced transcript isoforms. Alternative splicing has been associated with tumorigenesis for a number of different cancers. The objective of this study was to broadly characterize the role of human TEs in generating alternatively spliced transcript isoforms in cancer. To do so, we screened for the presence of TE-derived sequences co-located with alternative splice sites that are differentially utilized in normal versus cancer tissues. We analyzed a comprehensive set of alternative splice variants characterized for 614 matched normal-tumor tissue pairs across 13 cancer types, resulting in the discovery of 4,820 TE-generated alternative splice events distributed among 723 cancer-associated genes. SINEs (Alu) and LINEs (L1) were found to contribute the majority of TE-generated alternative splice sites in cancer genes. A number of cancer-associated genes - including MYH11, WHSC1, and CANT1 - were shown to have overexpressed TE-derived isoforms across a range of cancer types. TE-derived isoforms were also linked to cancer-specific fusion transcripts, suggesting a novel mechanism for the generation of transcriptome diversity via trans-splicing mediated by dispersed TE repeats.

Citation Format: Evan A. Clayton, Lavanya Rishishwar, Tzu-Chuan Huang, Saurabh Gulati, Dongjo Ban, John F. McDonald, I. King Jordan. An atlas of transposable element derived alternative splicing in cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2115.
Abstract 2118: Using electronic medical records to assemble a lung cancer cohort for prognosis study
Authors: Yuan Qianyu , Cai Tianrun , Hong Chuan , Cai Tianxi , Christiani David
Published: September 2020

Background: Electronic medical records (EMRs) provide a low-cost means of accessing longitudinal data on large populations with detailed information regarding diagnosis, clinical procedures, medications and tests. A lung cancer cohort assembled from EMR represents a powerful resource for studying prognosis.

Methods: EMRs are from the Massachusetts General Hospital and Brigham and Women's Hospital using Partners HealthCare System Research Patient Data Registry from 1988 to October 18, 2018. A previously validated phenotyping algorithm was developed to identify lung cancer patients based on a gold standard set of 200 patients. Demographics and clinical characteristics were extracted from both structured data and clinical notes utilizing natural language processing tools. The quality of EMR cohort was assessed by comparing to Boston Lung Cancer Study (BLCS) cohort using overlapped population. Specifically, we assessed: 1) absolute differences: the agreements of diagnosis dates, histological type and clinical stage; 2) relative differences: the effect sizes of variables on overall survival estimated from Cox regression models.

Results: The initial study population included 76,643 patients with a diagnostic code related to primary lung cancer. The phenotyping model identified 42,069 lung cancer patients with sensitivity of 75.2%, specificity of 90.0%, PPV of 94.4% and AUC of 0.927. A total of 5,053 patients overlapped in BLCS and EMR cohorts were used for quality assessment. The diagnosis dates from EMR agreed with diagnosis dates from BLCS cohort with median of 0 days. 10.9%, 7.5%, and 5.1% of the population had an absolute date discrepancy of more than 90 days, 180 days, and one year, respectively. The agreements of histological type and clinical stage were 90.1% and 82.8% respectively. Further analysis for overall survival showed high consistency in the two cohorts as Cox regression models controlled for age, sex, race, smoking status, histological type, stages and treatments yielded similar estimates.

Conclusion: We assembled a large lung cancer cohort from EMRs using phenotyping algorithm and extraction strategies combining structured and unstructured data. The quality of analytic data from EMRs were compared with the well curated epidemiology study to ensure their suitability for lung cancer prognosis research.

Citation Format: Qianyu Yuan, Tianrun Cai, Chuan Hong, Tianxi Cai, David Christiani. Using electronic medical records to assemble a lung cancer cohort for prognosis study [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2118.
Abstract 2124: Hotspots of sequence variability in gut microbial metagenomic datasets and their association with colorectal cancer
Authors: Martinez-Ramirez Rachell M. , Girod-Hoffman Miguel M. , Roche-Lima Abiel , Carrasquillo-Carrión Kelvin , Pérez-Santiago Josué , Baerga-Ortiz Abel
Published: September 2020

The gut microbiome has been found to impact host predisposition to disease. Previous research shows that certain species of microbes, encoding pro-inflammatory factors, increase the probability of developing dysplasia and colorectal cancer (CRC). Recently, through the oligotyping approach, we found genetic variants for an amplified region of usp, a genotoxic protein made by E. coli in the gut. These different variants were present in healthy, adenoma and CRC clinical stool samples. To our surprise, the same positions of genetic variability found experimentally were confirmed by BLAST analyses of shotgun metagenomic data from a case-control study conducted in France and Washington D.C. In this work, using the same metagenomics data, we searched for hotspots of genetic variability in the sequences for five genes with known pro-inflammatory and toxicity profiles: usp, tcpC, gelE, clbB, and clbN. More importantly, we extended our analyses to cover the entire length of these genes using a command line approach to BLAST+. The sequence reads for both clbB and clbN lacked coverage, rendering their analysis unquantifiable. The output data for both tcpC and gelE showed high levels of homology between the sequences of the healthy and CRC patients. However, we found twenty-nine hotspots in the usp gene, thirteen of which cause a modification in the primary structure of the protein. Among these thirteen positions, nine were different in cases and controls suggesting that these hotspots of variation are associated with CRC. All these results provide insight into both the link between variability and pathogenicity, and the viability of shotgun sequencing for such types of analyses.

Citation Format: Rachell M. Martinez-Ramirez, Miguel M. Girod-Hoffman, Abiel Roche-Lima, Kelvin Carrasquillo-Carrión, Josué Pérez-Santiago, Abel Baerga-Ortiz. Hotspots of sequence variability in gut microbial metagenomic datasets and their association with colorectal cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2124.
Abstract 2154: Immune pressure selects ANKRD52 mutations for cancer cells to escape T cell-mediated killing
Authors: Song Tianyu Y. , Zhao Haixin , Fan Hongjie , Long Min , Geng Chenlu , Xie Xiaoxiao , Liu Yang , Zhou Wenrong , Chen Ziyu , Huang Dawei , Peng Bo , Peng Zhengang , Cang Yong
Published: September 2020

Cancer arises after somatic mutations override cellular and immunological control of cell proliferation. Mutations in oncogenes and tumor suppressor genes endow cancer cells intrinsic growth advantage over neighboring cells. Mutations can also enable cancer cells to survive immune clearance during cancer progression, but systematic analysis of such mutations is lacking. We hypothesized that some genetic alterations carried in cancer cell lines might specifically affect the cell fitness to T cell-mediated killing. By deep sequencing of syngeneic xenograft tumors receiving different levels of immune pressure, we enriched 53 mutations in clonal populations against T cell immunity. To differentiate the driver from passenger mutations, we performed in vivo and T cell co-culture CRISPR screens with a guide RNA library targeting these candidate genes. We identified ANKRD52, a promoter of miRNA-mediated silencing, as required for PD-1-independent T cell cytotoxicity by activating the JAK-STAT signaling and antigen presentation in cancer cells. ANKRD52 mutations found in prevalent cancer patients failed to activate the interferon-γ pathway and these patients exhibit poor overall survival. We hereby provide an approach for interrogating cancer genetic heterogeneity to uncover evolutionarily conserved evasion mechanism from host immunity.

Citation Format: Tianyu Y. Song, Haixin Zhao, Hongjie Fan, Min Long, Chenlu Geng, Xiaoxiao Xie, Yang Liu, Wenrong Zhou, Ziyu Chen, Dawei Huang, Bo Peng, Zhengang Peng, Yong Cang. Immune pressure selects ANKRD52 mutations for cancer cells to escape T cell-mediated killing [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2154.
Abstract 2187: Kinetics and potency of T Cell-mediated cytolysis of glioblastoma
Authors: Chvatal Stacie A. , Logun Meghan T. , Hayes Heather B. , Millard Daniel C. , Karumbaiah Lohitash
Published: September 2020

Glioblastoma (GBM) is an aggressive form of brain cancer that has no effective treatments and a prognosis of only 12-15 months. Immune system effector T cells are a promising therapy due to their high specificity and innate cytotoxicity. The ability to assess the efficacy and potency of T cell therapies in vitro and with high throughput is vital for the further development of this promising therapy. Cellular impedance-based assays offer a sensitive, label-free, and nondestructive method to continuously monitor cancer cell proliferation and immune cell-mediated cytotoxicity in real-time and at high throughputs, revealing not only the potency but also the kinetics of T cell therapies. Here, we investigated the targeting potency of activated human T cells on human U87MG glioma cell monolayers across multiple cell densities.

U87MG cells were plated at 10k, 25k, and 50k cells per well on a PDL-coated CytoView-Z 96-well plate (n=12 wells per density), and their impedance was continuously monitored on the Maestro Z impedance platform. After 24 hours, activated patient-derived T Cells (ImmunoCult CD3/CD28 activation media) were added in a 10:1 effector:target ratio. Impedance and cytolysis were subsequently monitored for another 120 hours.

As expected, higher densities proliferated faster and reached a higher impedance level at 24 hours. The addition of activated human T cells resulted in a decrease of the impedance signal consistent with T cell-mediated lysis of the glioma cells. The highest density of T cells (500k) exhibited the fastest rate of U87 cytolysis, with a Kill Time 50 of 35 hours. All densities reached 100% cytolysis by 100 hours.

Overall, activated human T cells were highly effective for cytolysis of U87MG glioma cell monolayers of varying densities. The cellular impedance assay revealed high potency, with kinetics that varied across cell densities despite the same effector:target ratios.

Citation Format: Stacie A. Chvatal, Meghan T. Logun, Heather B. Hayes, Daniel C. Millard, Lohitash Karumbaiah. Kinetics and potency of T Cell-mediated cytolysis of glioblastoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2187.
Abstract 2207: Upfront metronomic chemotherapy synergizes with immunotherapy to optimize chemoimmunotherapy in squamous cell lung carcinoma
Authors: He Xi-Ran , Du Yang , Jin Yu-Shen , Bai Hua , Tian Jie , Wang Jie
Published: September 2020

Background and purpose: For squamous cell lung carcinoma (SQCLC), the survival benefits of combining chemotherapy (at the maximum tolerated dose, MTD) with concurrent immune checkpoint inhibitors (ICIs), also known as chemoimmunotherapy, have been confirmed in recent clinical trials. Nevertheless, the actual relationship between MTD chemotherapy and ICIs remains controversial, as most oncologists considered that MTD chemotherapeutic agents could cause immunosuppression. Hence, we attempted to optimize and assess different combinatorial patterns of chemoimmunotherapy in SQCLC.

Methods: We utilized the in vitro SQCLC cell lines, in vivo syngeneic immunocompetent mouse models, and patient samples to fully explore how to increase the ectopic lymphoid-like structures (ELSs) and the therapeutic targets for anti-programmed death 1 (PD-1) / anti PD-1 ligand (PD-L1) monoclonal antibodies (mAbs), as well as the underlying mechanisms, in order to render SQCLC to be more sensitive to ICIs and improve the efficacy of chemoimmunotherapy.

Results: Low-dose chemotherapeutic agents induced SQCLC cells to undergo immunogenic cell death (ICD) by activating the PI3K/Akt/NF-κB signaling pathway and thereby enhancing neoantigen exposure. Following, the high mobility group box-1 released by cells undergoing ICD promoted neoantigen uptake and presentation by activating dendritic cells (DCs) and consequently invoking specific T cell responses. In vivo, low-dose chemotherapeutic agents activated systemic immune responses and immunological memory, and enhanced antitumor ELSs compared with routine MTD chemotherapy. Moreover, the upfront metronomic (low-dose and frequent administration) chemotherapy extended the time window of the immunostimulatory effect and synergized better with the subsequent administration of anti-PD-1/PD-L1 mAbs. One possible mechanism of this synergy is increasing the activated type I macrophages, DCs, and cytotoxic CD8+ T cells, and maintaining the diversity and normal composition of intestinal gut microbiota. In contrast, when combined with ICIs, the effects of routine MTD chemotherapy appeared to be additive rather than synergistic.

Conclusion: The upfront metronomic chemotherapy better synergizes with immunotherapy over the routine MTD chemotherapy in SQCLC. This preclinical study provides a novel strategy to optimize chemoimmunotherapy, and it is worth being translated into the clinic in the future.

Citation Format: Xi-Ran He, Yang Du, Yu-Shen Jin, Hua Bai, Jie Tian, Jie Wang. Upfront metronomic chemotherapy synergizes with immunotherapy to optimize chemoimmunotherapy in squamous cell lung carcinoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2207.
Abstract 2228: PD1/CTLA4 humanized mice - A great model for pre-clinical toxicology and efficacy evaluation of macromolecular drugs
Authors: Ju Cunxiang , Zhang Mingkun , Mao Rui , Xiuying Ma , Tang Jin , Li Shuai , Wang Jingjing , Sun Hongyan , Zhao Jing , Gao Xiang
Published: September 2020

Immune checkpoint antibodies have conferred huge cancer immunotherapeutic effect (CITE). Besides, severe immunotherapy related adverse events (irAE) occurred in combination therapy such as anti-PD1 combines with anti-CTLA4 antibodies greatly limit the development of cancer therapy. Animal models which can recapitulate both clinical irAE and CITE will be benefit for developing safer immune-checkpoint-targeting reagents. However, no animal models were found can be used for preclinical safety evaluation of drugs up to now. Given this fact, PD1/CTLA4 double-humanized mice models were established in both BALB/c (BALB/c-hPD1/hCTLA4) and C57BL/6 (B6-hPD1/hCTLA4) background, which by replacing the mouse extracellular domain of CTLA4 and PD1 with human segments while retaining mouse intact intracellular part, respectively. Our data showed that strong CITE against anti-hCTLA4 treatment observed in models from both BALB/c and B6 background. Apparent inhibition of tumor growth also emerged on subcutaneously engrafted CT26 tumor in BALB/c-hPD1/hCTLA4 mice by anti-PD1/CTLA4 bispecific antibody treatment. Meanwhile, severe irAEs which have been observed in clinical patients, such as joint swelling, skin inflammation, heart damage and infiltration of inflammatory cells in different tissues and organs could be reproduced in BALB/c-hPD1/hCTLA4 mice. Consistent with previous reports, we could not observe similar irAEs under drugs treatment at the same dose in C57BL/6-hPD1/hCTLA4 mice. Our data indicated that adult BALB/c-hPD1/hCTLA4 mice, but not C57BL/6-hPD1/hCTLA4 mice, were more sensitive to irAEs. Taken together, adult PD1/CTLA4 humanized mice in BALB/c background can not only be used to screen humanized antibodies, but also have tremendous values for preclinical safety evaluation.

Citation Format: Cunxiang Ju, Mingkun Zhang, Rui Mao, Ma Xiuying, Jin Tang, Shuai Li, Jingjing Wang, Hongyan Sun, Jing Zhao, Xiang Gao. PD1/CTLA4 humanized mice - A great model for pre-clinical toxicology and efficacy evaluation of macromolecular drugs [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2228.
Abstract 2274: Development of bispecific antibodies using molecular imaging
Authors: Kamakura Daisuke , Yasunaga Masahiro , Asano Ryutaro , Matsumura Yasuhiro
Published: September 2020

(Background and purpose) A bispecific antibody (BsAb), as a next-generation therapeutic antibody, has two antigen binding sites in an antibody molecule. Many formats have been exploited for decades. Among them, we focused on T cell dependent BsAb (TDB), which can engage and redirect cytotoxic T cells against tumor cells and is expected to be effective in treating refractory cancer. However, although many studies revealed its potent antitumor effect in animal models, it has not been applied to solid tumors yet in clinics. In this context, we think that it is necessary to clarify pharmacokinetics (PK), pharmacodynamics (PD) and mechanism of action (MOA) of TDB, especially within tumor tissue. For this aim, we have decided to develop the molecular imaging-based systems for the evaluation of TDB in order to visualize antigen binding to two target antigens, BsAb delivery or immunological synapse formation.

(Materials a& Methods) We used hEx3 which is a humanized IgG-like antibody with bivalent Fv regions against each EGFR and CD3. We applied the TDB to colorectal cancer (CRC) cells with or without KRAS or BRAF mutation. In the first part, we visualized the BsAb binding to two antigens, EGFR on CRC cells and CD3 on T cells. Next, immunological synapse formation as a cutting-edge mechanism involving T cells-killing tumor cells, which is an important MOA of TDB, was visualized in combination with Granzyme staining. In the second part, we evaluated in vitro cytotoxicity and the in vivo antitumor effect of hEx3 in NOD-SCID mice bearing CRC xenografts with KRAS or BRAF mutation following human PBMC administration.

(Results) We found that CRC cells were damaged via Granzyme accumulation through immunological synapse. In the ELISA data, we also found that released gamma interferons can damage CRC cells. In vitro and In vivo studies showed that the hEx3 demonstrated a significant cytocidal effect and antitumor activity not only for KRAS wild but also mutant.

(Conclusion) we established a molecular imaging-based TDB evaluation system and visualized antigen-binding and immunological synapse formation as a MOA of TDB. Present data indicated that TDB can damage CRC cells in two distinct manners, namely immunological synapse-dependent and -independent manners using cytokines including a gamma interferon. TDB may thus be a promising next generation antibody therapy against CRC regardless KRAS status.

Citation Format: Daisuke Kamakura, Masahiro Yasunaga, Ryutaro Asano, Yasuhiro Matsumura. Development of bispecific antibodies using molecular imaging [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2274.
Abstract 2299: Sarcoma as second cancer in pediatric cancer survivors: Large population analysis
Authors: Makena Monish Ram , Nguyen Thinh H. , Yavvari Siddhartha , Kaur Maninder , Pham Teresia , Urias Eduardo , Panapitiya Narendra , Al-Rahawan Mohamad M.
Published: September 2020

Introduction: As the prognosis of a pediatric cancer continues to improve, the burden of long term therapy effects, including subsequent malignant neoplasm (SMN), in survivors is an increasing epidemiologic concern. The mortality rate from cancer in the pediatric population decreased from 6.5 per 100,000 in 1970 to 2.3 in 2015, indicating more chance of SMNs. Sarcoma as a SMN in pediatrics has important clinical significance and has been extensively reported globally. We quantified the percentage of sarcoma as second cancer and determined the primary cancer distribution for patients with sarcoma as second cancer.

Methods: The Surveillance, Epidemiology, and End Results (SEER) database, which includes 28% of the U.S population and data from 18 state cancer registries (SEER-18), was probed for the overall incidence of SMN in pediatric cancer survivors and the incidence of sarcoma as the SMN specifically.

Results: Our SEER database analysis found that out of 75,665 cases of primary pediatric malignancies, 1218 (1.61%) developed SMN. The second most common SMN was sarcoma, accounting for 14.37% of them in pediatric population. The breakdown of sarcoma into sub groups showed that osteosarcoma, fibrosarcoma, and rhabdomyosarcoma are the most common second sarcomas seen in pediatric cancer survivors. Finally, we looked at the distribution of primary cancer in pediatric cancer survivors who developed sarcoma as a SMN. We found that retinoblastoma, lymphoid leukemia, and Hodgkin lymphomas were the most common types of primary cancer. Similar results were reported among different racial groups around the world, which show a universal trend of sarcomas as second cancers in pediatric cancer survivors.

Conclusion: By analyzing the SEER database, we corroborated previous findings, suggesting that about 14% of SMN after a childhood cancer is encompassed by sarcoma. The exact etiology of cancer, be it primary predisposition or secondary to exposures, is uncertain. Radiation and chemotherapies used in patients with pediatric cancers can be carcinogenic. Our study highlights the need for development of novel non-DNA damaging or alternate antineoplastic therapies to avoid the long-term potential of development of SMN.

Citation Format: Monish Ram Makena, Thinh H. Nguyen, Siddhartha Yavvari, Maninder Kaur, Teresia Pham, Eduardo Urias, Narendra Panapitiya, Mohamad M. Al-Rahawan. Sarcoma as second cancer in pediatric cancer survivors: Large population analysis [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2299.
Abstract 2321: Validating breast cancer risk prediction models in the Korean Cancer Prevention Study-II Biobank
Authors: Jee Yon Ho , Gao Chi , Kim Jihye , Park Seho , Jee Sun Ha , Kraft Peter
Published: September 2020

Background: Informative and well-calibrated risk prediction models may be useful for precision breast-cancer screening. However, these models often have not been validated across diverse populations. Validation in East Asian populations is particularly lacking.

Objective: To evaluate the performance of breast cancer risk models developed in European-ancestry studies in a Korean population, both directly and after recalibration.

Methods: We compared discrimination and calibration of three multivariable risk models in a cohort of 77,457 women from the Korean Cancer Prevention Study-II. The first incorporated US breast-cancer incidence and mortality rates, US risk-factor distributions, and relative risk (RR) estimates from European-ancestry studies. The second recalibrated the first by using Korean incidence and mortality rates and Korean risk factor distributions, while retaining the European-ancestry RR estimates. Finally, we derived a Korea-specific model incorporating the RR estimates from Korean Cancer Prevention Study. The Individualized Coherent Absolute Risk Estimation (iCARE) software package was used to calculate 5 year predicted absolute risks of breast cancer and assess model performance.

Results: The US European-ancestry breast cancer risk model was well calibrated among Korean women <50 years (E/O=1.124 (0.989, 1.278)) but markedly overestimated the risk for those ≥50 years (E/O=2.472 (2.005, 3.049)). Recalibrating absolute risk estimates using Korean breast cancer rates and risk distributions markedly improved the calibration in women ≥50 (E/O=1.018 (0.825, 1.255)). The model incorporating Korean-based RRs had similar but not clearly improved performance relative to the recalibrated model; this may reflect at most modest differences in the RRs between European and Korean populations and the relatively small sample used to estimate RRs among Korean women.

Conclusions: The poor performance of the US European-ancestry breast cancer risk model among older Korean women highlights the importance of tailoring absolute risk models to specific populations. Recalibrating the model using Korean incidence and mortality rates and risk factor distributions greatly improved performance; we anticipate the performance could be further improved by incorporating multivariable risk-factor RRs from large Korea-based studies.

Citation Format: Yon Ho Jee, Chi Gao, Jihye Kim, Seho Park, Sun Ha Jee, Peter Kraft. Validating breast cancer risk prediction models in the Korean Cancer Prevention Study-II Biobank [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2321.
Abstract 2341: Predictive analysis of gynecologic cancer risk factors using decision tree analysis
Authors: Bahrani-Mostafavi Zahra , Huber Larissa B. , Sha Wei , Richardson Christine
Published: September 2020

Introduction: Gynecologic cancer (GYNC) accounts for 6.3% of all cancers and is the fourth leading cause of cancer death for women in the U.S. Autoimmune diseases (AD) are among the top ten leading causes of death among U.S. women age 65 and under. This high mortality rate among women with AD has been linked to cancer and other causes. Considering cancer and AD are the accumulative effect of genetics and lifestyle, and 90-95% of all cancers are linked to lifestyle and environmental factors, a study to investigate the association between patient-level predictors and GYNC among AD patients in the U.S. was imperative.

Methods: 2007-2013 data from Florida State Inpatient samples of the Healthcare Cost and Utilization Project were used. The study population (n=836,717) was restricted to women who had any AD. The outcome variable was diagnosis of GYNC. 36 categorical transformed variables including race/ethnicity, age, insurance type, income level, GYN procedures, and comorbidities were analyzed as predictive variables (PV). Bootstrap Forest (JMP pro13) were was used to create a 10,000-decision tree (DT) model to identify independent predictors of GYNC. Multiple outputs such as confusion matrix, column contribution, and ROC was created for predictive analytics.

Results: The analytical model used was confirmed by evaluating criteria such as AUC (0.82), sensitivity (0.68), specificity (0.82), false positive rate (0.18), wrongly predicted value (0.24), and overall accurate prediction (0.76) of the model. Using column contribution and single DT, the PV hysterectomy was the highest predictor of GYNC, followed by PV age;, and comorbidities such as diabetes, and obesity; along with race/ethnicity; and income level. Also, subpopulations of AD patients at risk for GYNC based on unique combinations of risk factors were established, including subpopulations such as women with AD, involved glandular disorders who had hysterectomy, and comorbidities such as diabetes and fluid and electrolyte disorders.

Discussion: Both GYNC and AD are major chronic diseases among women. Because of high prevalence of AD among women, more elucidation on the association between GYNC and AD is essential for GYNC management. The unique combinations of characteristics that describe subgroups of patients at risk for GYNC among AD patients can be used as a potential risk assessment, as well as an early detection and/ or prevention tools for GYNC.

Citation Format: Zahra Bahrani-Mostafavi, Larissa B. Huber, Wei Sha, Christine Richardson. Predictive analysis of gynecologic cancer risk factors using decision tree analysis [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2341.
Abstract 2365: Does a combination of type 2 diabetes mellitus and increased alcohol intake affect prospective total adenoma accumulation
Authors: Tobi Martin , Antaki Fadi , Judd Stephanie , Sochacki Paula , Rambus MaryAnn , Talwar Harvinder , Lawson Michael , Levi Edi , McVicker Benita
Published: September 2020

Introduction: Adenoma formation data in diabetics is inconclusive. Alcohol intake (AI), associated with colorectal neoplasia (CRN) has not been systematically studied in diabetes. We investigated effects of diabetes and AI in a prospective patient cohort at increased CRN risk.

Methods: Diabetes diagnoses based on patients' problem list, corroborated by HbA1c and glucose levels. Self-reported AI was quantified as more than occasional/social. Cumulative adenoma number were computed using available records. In a subset of patients, CRN-related Paneth cell marker p87 was used to semi-quantify immunohistochemically the colonic regions binding this label.

Results: 680 patients (348 diabetics 332 non-diabetic) were ascertained with 12.4-year median follow-up. Diabetics had more adenomas than non-diabetics (2.3±3.54 versus 1.81±2.91, p=0.05) and p87 levels were significantly higher in the descending colon (p<0.03) and rectum (p<0.008). Significant demographic differences of increased black ethnicity, lesser survival, increased BMI and increased smoking were appreciated in diabetics. In non-drinking patients, adenomas were also similarly increased in diabetics and demographics and p87 levels were as reported above without significant smoking differences. Comparing diabetics who drank actively with non-diabetics who did not, the diabetics had increased polyp accumulation (2.90±4.29 versus 1.62±2.45 p<0.012), increased proportion of black ethnicity, increased BMI and were younger. Rectal p87 was significantly increased (p<0.04) without smoking effects on polyp number.

Conclusion: Diabetics accumulate more adenomas than controls which is reflected in the increase of left-sided p87 expression. A combination of increased AI and diabetes particularly increases adenoma formation seemingly independent of factors such as age and smoking.

Citation Format: Martin Tobi, Fadi Antaki, Stephanie Judd, Paula Sochacki, MaryAnn Rambus, Harvinder Talwar, Michael Lawson, Edi Levi, Benita McVicker. Does a combination of type 2 diabetes mellitus and increased alcohol intake affect prospective total adenoma accumulation [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2365.
Abstract 2391: Centromeric chromatin alteration is associated with increase in alphoid array replication fork speed in ovarian cancer cell lines
Authors: Erliandri Indri , Redon Christophe , Kim Jung-Hyun , Fu Haiqing , Aladjem Mirit , Reinhold William , Larionov Vladimir
Published: September 2020

The centromere is well known as the center point of cell division, with aberrant centromeric function leading to mitotic dysfunction and chromosomal abnormalities. These abnormalities may in turn lead to diseases, including cancer and premature aging. Binding of CENPB to the CENPB box is orchestrated epigenetically, and has emerged as an important factor in the regulation of the centromeric-chromatin structural landscape. CENP-B depletion that resulted in euchromatization of the alphoid centromere array, also is associated with elevated centromeric DNA replication activity. Observation in two ovarian cancer cells from NCI-60 collection; OVCAR3 and SKOV3, identified as having low and high expression of CENPB RNA respectively, indicates the different level of centromeric DNA instability. Centromeric DNA damage fraction is more abundant and replication fork velocity is elevated in less CENPB expresser cells, indicates alphoid array alteration. We conclude that CENP-B is required for maintenance of centromeric chromatin structure and centromeric DNA integrity.

Citation Format: Indri Erliandri, Christophe Redon, Jung-Hyun Kim, Haiqing Fu, Mirit Aladjem, William Reinhold, Vladimir Larionov. Centromeric chromatin alteration is associated with increase in alphoid array replication fork speed in ovarian cancer cell lines [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2391.
Abstract 2440: The epigenetic influence of maternal diet on prevention of high-fat diet induced obesity and breast cancer in later life
Authors: Li Yuanyuan , Chen Min , Tollefsbol Trygve
Published: September 2020

Breast cancer is one of the most lethal diseases in women. Individual epigenetic profiles that are initially established in utero and postnatal environmental exposures contribute to later-life breast cancer incidence. Intervention on environmental factors such as diets during these sensitive periods provides excellent opportunities to re-program epigenetic profiles leading to cancer prevention. The bioactive dietary compound, genistein (GE) enriched in soybean products such as soymilk, soy protein and tofu, has been widely accepted as a potent anticancer reagent through regulation of epigenetic mechanisms. Our pilot study indicates that maternal dietary GE exposure effectively prevents later-life breast cancer development through epigenetic reprogramming in transgenic breast cancer mouse models. More importantly, we found that maternal GE significantly inhibited a postnatal overnutrition stimulus such as high-fat diet (HFD)-induced breast cancer promotion and metabolic disorders in mouse offspring. Diets with high saturated fat such as the Western diet and its related obesity are considered major risk factors for breast cancer. Importantly, we found that maternal dietary GE reversed HFD-induced lipid panel abnormalities, reduced obesity-related biomarkers and influences gut microbiome profiles through epigenetic regulations. Overnutrition-induced metabolic disorders such as overweight and obesity are a global epidemic that impair human life quality and increases risk of development of many human diseases including breast cancer. Elucidation of the key mechanisms and interactions between nutrition stress and breast cancer and exploration of a novel in utero preventive strategy through natural bioactive products will have global impact.

Citation Format: Yuanyuan Li, Min Chen, Trygve Tollefsbol. The epigenetic influence of maternal diet on prevention of high-fat diet induced obesity and breast cancer in later life [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2440.
Abstract 2449: A novel function of FTO in ovarian cancer stem cells through m6A RNA demethylation
Authors: Huang Hao , Wang Yinu , Kandpal Manoj , Zhao Guangyuan , Cardenas Horacio , Ji Yanrong , Tanner Edward , Chen Jianjun , Davuluri Ramana , Matei Daniela
Published: September 2020

Introduction: N6-Methyladenosine (m6A) is the most abundant internal modification in mammalian messenger RNAs (mRNAs). Although previous studies have showed that RNA methylation is reversible and plays important roles in various cellular processes, such as metabolism, stem cell development, and self-renewal, its functions in cancer remain elusive. The fat mass- and obesity-associated protein (FTO) is an m6A demethylase and was described as an oncogenic factor in leukemia and brain tumors. We hypothesized that RNA demethylation could be involved in the process of ovarian cancer initiation or progression.Methods: Here we measured FTO expression in ovarian tumors compared to fallopian tube epithelium (FTE) and in ovarian cancer stem cells (CSCs) compared to non-CSCs. To investigate its functions we used overexpression and siRNA-mediated knockdown. Colony, sphere formation and tumor initiation assays were carried out. RNA-Seq and MeRIP-Seq were used to investigate the mechanism by which FTO-mediated m6A modifications altered stemness in OC cells. Results: FTO was expressed at lower levels in ovarian tumors compared to FTE and in ovarian CSCs compared to non-CSCs (P<0.01). Overexpression of FTO inhibited the tumorigenic CSC population, its ability to form colonies and spheres, and to initiate tumors in vivo. This phenotype was not recapitulated by overexpression of mutant FTO, lacking enzymatic activity. Integrated RNA-sequencing and genome wide m6A mapping revealed significant transcriptomic changes associated with FTO overexpression and loss of m6A, involving pathways related to cell stem signaling, RNA transcription, DNA repair, and mRNA splicing. FTO augmented second messenger 3', 5'-cyclic adenosine monophosphate (cAMP) signaling and suppressed stemness features of ovarian cancer cells by reducing mRNA stability of two phosphodiesterase genes (PDE1C and PDE4B). Conclusions: Our results point to a new function of FTO in high grade serous ovarian cancer as a regulator of cAMP hydrolysis through post-transcriptional gene modifications.

Citation Format: Hao Huang, Yinu Wang, Manoj Kandpal, Guangyuan Zhao, Horacio Cardenas, Yanrong Ji, Edward Tanner, Jianjun Chen, Ramana Davuluri, Daniela Matei. A novel function of FTO in ovarian cancer stem cells through m6A RNA demethylation [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2449.
Abstract 2491: Targeted next generation sequencing identifies somatic variants in Egyptian breast cancer patients
Authors: Nassar Auhood , abouelhoda Mohamed , Bahnassy Abeer , El-Din Youssef Amira Salah , Lotfy Mai M. , Ahmed ola S. , Ismail Hoda , Zekri Abdel-Rahman N.
Published: September 2020

Breast cancer (BC) is the leading cause of cancer-related death in women worldwide and its incidence is progressively increasing in Egypt. Recent advances in next generation sequencing have been used to detect the acquired somatic mutations driving BC. However, there is insufficient knowledge of the acquired somatic mutations in Egyptian BC patients which limit our understanding of disease progression. Up to our knowledge, this is the first Egyptian cohort to sequence a multiple-gene panel of cancer related genes on BC patients.

409 cancer related genes were sequenced in 46 fresh breast tumors of Egyptian BC patients to identify somatic mutations and their frequencies, using the Ion Ampliseq Comprehensive Cancer Panel based on the Ion torrent DNA sequencing technology. The identified sequences were mapped to the human reference genome (hg19) and the detected genetic variants were annotated against different reference databases. The average depth of coverage is 668X and the average of the aligned reads which cover the target regions is 99.6%.

Our results showed that TP53 and PIK3CA were the most top two frequently mutated genes. We detected 15 different somatic mutations in TP53 and 8 different ones in PIK3CA, each in 27 samples (58.7%). Most of the detected somatic mutations in TP53 and PIK3CA are pathogenic and well established in known hotspot regions. According to Clinvar database; we found 19 pathogenic somatic mutations: 7 in p53, 5 in PIK3CA, and single variants of VHL, STK11, AKT1, KRAS, IDH2, PTEN and ERBB2. We also identified 5 variants with uncertain significance (4 in TP53 and 1 in CEBPA) and 4 variants with conflicting interpretations of pathogenicity (2 in TP53 and 1 in each of APC and JAK3). Moreover, 4 novel variants were identified in JAK2, MTOR, KIT and EPHB.

In this cohort, we shed the light on the most frequently detected somatic mutations in Egyptian BC patients which allows for more knowledge about BC progression.

Citation Format: Auhood Nassar, Mohamed abouelhoda, Abeer Bahnassy, Amira Salah El-Din Youssef, Mai M. Lotfy, ola S. Ahmed, Hoda Ismail, Abdel-Rahman N. Zekri. Targeted next generation sequencing identifies somatic variants in Egyptian breast cancer patients [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2491.
Abstract 2501: Delineating mutational lineages with single cell DNA sequencing using multi-patient specific panels
Authors: Leighton Jake , Hu Min , Davis Alexander , Sei Emi , Wang Yong , Navin Nicholas
Published: September 2020

Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer with high rates of metastasis. Although copy number aberrations (CNAs) and genome doubling have been extensively studied in relation to TNBC initiation, little is known regarding the timing and impact of point mutations during tumor initiation, outside of TP53. A major challenge in sequencing mutations in single cells is the significant cost of unbiased whole-exome analysis of many cells. To address this challenge, we developed an approach called multi-patient-panel (MPP) sequencing which involves first performing bulk deep-exome sequencing of many patient's tumors, after which hundreds of mutations are identified and pooled across patients to design a targeted panel for high-throughput single cell DNA sequencing. We applied MPP sequencing to profile 330 mutations across 23,000 single cells from 5 TNBC patients using a microdroplet system (Mission Bio). From this data we identified 1-4 major clonal subpopulations in each tumor which shared a common evolutionary lineage. Copy number data was inferred from the targeted panel coverage depth, which showed that CNAs were correlated with different subpopulations in the tumor. By integrating both the mutation and copy number data, we inferred phylogenetic lineages and identified the timing of mutations during primary tumor growth, which detected early truncal mutations (in addition to TP53) that were involved in the initiation of TNBC tumors. The MPP approach provides a powerful method to scale-up single cell DNA sequencing to tens of thousands of cells to detect mutations and infer cancer lineages and clonal substructure.

Citation Format: Jake Leighton, Min Hu, Alexander Davis, Emi Sei, Yong Wang, Nicholas Navin. Delineating mutational lineages with single cell DNA sequencing using multi-patient specific panels [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2501.