bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract LB-146: The impact of pancreatic cancer resection on long-term survival in the era of effective systemic treatment
Authors: Lawrence Yaacov R. , Shtern Alina , Margalit Ofer , Golan Talia , Symon Zvi
Published: September 2020

Background: Surgical resection is the only curative modality in pancreatic cancer, yet the vast majority of patients undergoing surgery succumb of their disease. No large randomized studies have been performed to assess the survival impact of the procedure. We hypothesized that in the era of effective systemic treatments the survival advantage of surgical resection would be lessened.

Methods: A meta-analysis of published phase II and phase III clinical trials in pancreatic cancer in both the post resection adjuvant setting and the locally advanced / metastatic setting. Trials were included based upon a systemic literature search. Eligibility criteria included: at least 50 patients per arm, detailed overall survival rates reported. Exclusion criteria: patients from trial arms for which there were not complementary data sets with / without surgical resection, trials testing non-pharmacological modalities or neoadjuvant approaches. Data was stratified based upon the systemic agents used, and analysed using an indirect aggregate approach. Primary endpoint was 3 year overall survival (OS_3yr), comparing patients treated with systemic treatment alone vs. surgery followed by adjuvant systemic treatment.

Results: 74 treatment arms from 56 prospective trials published between 1990 and 2018 were included in the analysis. Overall a total of 11,898 patients were included, of whom 3,600 underwent resection. Median follow-up was 29.8 months for studies were stated. OS_3yr was for systemic treatment alone was 0%, 0%, 0.5%, 2.5%, 0.16%, 1.2%, 3.8% for No chemo, 5FU, Gemcitabine, S-1, Gemcitabine + xeloda, Gemcitabine + S-1, and Folfirinox respectively, and 19.9%, 24.9%, 32.9%, 58.8%, 42.5%, 52%, and 62.5% for the same agents delivered in the adjuvant setting; the advantage in OS_3yr provided by resection was 19.9%, 24.9%, 32.4%, 56.3%, 42.3%, 50.8%, and 58.8% for these agents, respectively. The advantage in OS_3yr provided by resection correlated closely with reported response rates for each systemic agent, r=0.96 p<0.001.

Conclusions: Within the limitations of this analysis, it appears that our hypothesis was incorrect, and that the opposite is true. The introduction of effective systemic therapies has greatly increased the impact of pancreatic surgery on long-term survival in pancreatic cancer. Furthermore, it appears that for pancreatic cancer, systemic agents are more active in the adjuvant than the metastatic setting. Consequently, every effort should be made to bring patients to curative resection.

Citation Format: Yaacov R. Lawrence, Alina Shtern, Ofer Margalit, Talia Golan, Zvi Symon. The impact of pancreatic cancer resection on long-term survival in the era of effective systemic treatment [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 LB-146.
Abstract LB-157: Obesity at early adulthood increases subsequent risk of gastric cancer in high incidence nation: Results from the Health Examinees-Gem (HEXA-G) study
Authors: Lee Hwi-Won , Shin Woo-Kyoung , Yang Jae Jeong , Song Minkyo , Shin Aesun , Lee Jong-koo , Kang Daehee
Published: September 2020

Background: The global trend of obesity, or the “obesity epidemic,” is not confined to adults. The increasing rates of obesity at young age signifies potential burden to our society as a whole, and requires prompt attention. Although emerging evidence has indicated a possible link of obesity in early life to subsequent cancer risks, the association with gastric cancer remains largely unknown, especially among the populations with high incidence rates of gastric cancer. Objective: Using data from the Health Examinees (HEXA) study of Korea, this study aimed to investigate the association of obesity at younger age (ages 18-20 and 35) with the later risk of gastric cancer in a population with high incidence rate of gastric cancer. Method: Included were 114,155 cancer-free subjects who participated in the large-scale prospective cohort study of the Health Examinees-Gem (HEXA-G) study during 2004-2013. Multivariate Cox proportional hazards models were used to estimate hazard ratios (HR) and 95% confidence intervals (CI) for gastric cancer risk associated with body mass index (BMI) at age 18-20 and 35. To consider substantial differences in incidence rates between men and women, the overall associations were further evaluated, separately by sex. Results: During a median follow-up period of 6.2 years, 851 gastric cancer cases (476 men and 375 women) were identified. When compared to normal BMI (18.5 - 23.0kg/m2), obesity (BMI ≥30kg/m2) at age 35 was significantly associated with increased risk of gastric cancer later in life: HR (95% CI) = 2.60 (1.57-4.33) for total participants, 2.11 (1.03-4.34) for men, and 3.82 (1.86-7.86) for women. No significant associations were found for obesity at late adolescence in both men and women. Conclusion: Our findings suggest that obesity in early adulthood may be associated with increased risk of gastric cancer. Preventing obesity in early life may help reduce the health burden of gastric cancer in later life.

Citation Format: Hwi-Won Lee, Woo-Kyoung Shin, Jae Jeong Yang, Minkyo Song, Aesun Shin, Jong-koo Lee, Daehee Kang. Obesity at early adulthood increases subsequent risk of gastric cancer in high incidence nation: Results from the Health Examinees-Gem (HEXA-G) 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 LB-157.
Abstract LB-177: BET and CDK9 protein inhibitors: Novel epigenetic therapy to synergistically kill human melanoma cells
Authors: Emran Abdullah Al , Tseng Hsin-Yi , Gunatilake Dilini , Cook Stuart , Tiffen Jessamy , Gallagher Stuart , Hersey Peter
Published: September 2020

Background: Dysregulation of epigenetic modifiers is a frequent event in melanoma and underlies many aspects of melanoma biology including resistance to targeted and immunotherapies. Here we report that dual targeting of BET and CDK9 proteins have synergistic effect in melanoma cells in vitro and in vivo. Methods: Cell viability was measured by Cell titre glow and colony forming assays. Annexin V/PI staining was performed to assess apoptosis. Apoptotic, anti-apoptotic, pro-survival signalling proteins were probed by immunoblotting. Genome wide expression analysis were performed by RNA-seq analysis of sensitive cell lines. Live-dead staining and apoptosis were performed in 3D spheroid models. In vivo studies were carried out on the YUMM1.1 mouse model in C57BL/6 syngeneic mice. Results: We report that BET and CDK9 inhibitor iBET151 and CDKI73 synergistically killed melanoma cells independent of their genetic background compared to single inhibitors. Combination index (CI) was calculated by calcusyn software also showed strong synergism (<0.3). However, these drugs did not kill human dermal fibroblast suggestive of a cancer cell specific effect. There was a time dependent increase in cell death that was associated with downregulation of anti-apoptotic proteins BCL2 and MCL1 and the oncogene c-MYC. These findings in 2D models were corroborated in 3D spheroid models. Gene Set Enrichment Analysis (GSEA) revealed that HALLMARK G2M CHECKPOINT, HALLMARK E2F TARGETS, HALLMARK MYC TARGETS were negatively enriched in the combination treatment (Normalized enrichment score =<-2.5). The in-vivo studies on the anti-PD1 resistant mouse melanoma cell line YUMM 1.1. showed that iBET151 and CDKI73 combination had marked effects on tumour growth compared to vehicle control and the individual drugs (p<0.05). Conclusion: Our findings have revealed that this novel combination of two epigenetic inhibitors targets multiple downstream genes associated with cell cycle, oncogenesis and, apoptotic pathways which augments cell death compared to effects of the single drugs. Overall, the findings warrant further investigation of key targets involved in the responses and the extent to which effects of CDK9 inhibition is due to effects on chromatin modelling. The combination would appear promising to consider for future clinical trial in melanoma patients not responding to current therapies.

Citation Format: Abdullah Al Emran, Hsin-Yi Tseng, Dilini Gunatilake, Stuart Cook, Jessamy Tiffen, Stuart Gallagher, Peter Hersey. BET and CDK9 protein inhibitors: Novel epigenetic therapy to synergistically kill human melanoma cells [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 LB-177.
Abstract LB-178: Identification of DNA 5hmC decision signature biomarkers for azacitidine prior to hi-dose cytarabine and mitoxantrone chemotherapy in patients with high-risk AML
Authors: HAN Dali , Zhang Wei
Published: September 2020

DNA 5hmC biomarkers to predict the outcomes to the of azacitidine prior to hi-dose cytarabine and mitoxantrone chemotherapy for patients with high-risk AML. Azacitidine (AZA), a DNA methyltransferase inhibitor and epigenetic modulator, has been combined with chemotherapy to treat high-risk AML patients for better clinical outcomes. However, the complete remission (CR) rate and prognosis remains unsatisfactory. Here, we proposed that the use of AZA for high-risk AML patients helped to sensitize leukemia cells to chemotherapy. We analyzed 45 high-risk AML patients who had received AZA treatment followed by High-dose cytarabine and mitoxantrone (AZA-HiDAC-Mito) therapy. We performed RNA-Seq and DNA 5hmC-Seq on available RNA/DNA samples. By comparing differential expressed genes between patients responded to therapy (CR or CRi, responder) and those did not (non-responder), we found that patients with better response had lower expression on ephrin receptor gene and AR pathway related genes. Using XGBoost machine learning model, we developed an 11-gene-5hmC signature to predict treatment outcomes, and it achieved 87.76% sensitivity and 87.10% specificity (AUC=0.911). The signature was also capable of distinguishing which patients would have better response to HiDAC-Mito only treatment, indicating that the signature had a potential to serve as a general predictor for intensive chemotherapy. Our findings show that DNA 5hmC patterns could be used as the prognostic biomarker for AZA-HiDAC-Mito therapy, which could guide further biomarker-based clinical trials.

Citation Format: Dali HAN, Wei Zhang. Identification of DNA 5hmC decision signature biomarkers for azacitidine prior to hi-dose cytarabine and mitoxantrone chemotherapy in patients with high-risk AML [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 LB-178.
Abstract LB-182: Combination of sulforaphane and 5-aza-2′-deoxycytidine slows the growth and upregulates the chemoattractant CCL5 in metastatic melanoma
Authors: Chiang Tung-Chin , Koss Brian , Storey Aaron J. , Zabaleta Jovanny , Choudhury Samrat Roy , Shields Bradley D. , Draper Elizabeth C. , Su L Joseph , Tackett Alan J.
Published: September 2020

UV exposure-induced oxidative stress is implicated as a driving mechanism for melanoma. Increased oxidative stress results in DNA damage and epigenetic dysregulation. We previously found that a low dose of the antioxidant sulforaphane (SFN) in combination with the epigenetic drug 5 –aza –2 ′–deoxycytidine (DAC) slowed cell growth in melanoma at a greater rate than DAC alone. Here, we report a multi –omics analysis with combination and single drug treatment. We observed a significant increase in global protein abundance with an altered level of expression in the combination treatment as compared to individual treatment. Proteins associated with methylation patterns and with reactive oxidative species were found dysregulated in combination treatment. A comparison analysis of proteomic and transcriptomic data with Ingenuity Pathway Analysis showed common canonical pathways involved in phosphorylation (ERK/MAPK signaling) and immune response with combination treatment. The global DNA methylation pattern was analyzed to explore the impact of combination and single drug treatment on methylation status. Interestingly, we observed an increase in the levels of a critical immuno-regulator cytokine, C –C motif ligand 5 (CCL5), which functions as a chemoattractant for natural killer (NK) cells. Animal studies showed the level of CCL5in blood and tumor was increased with DAC and SFN combination treatment compared to that of control, which coincided with tumor reduction. Our data demonstrate the impact of SFN on the effectiveness of the FDA –approved drug DAC to reduce metastatic melanoma tumors.

Citation Format: Tung-Chin Chiang, Brian Koss, Aaron J. Storey, Jovanny Zabaleta, Samrat Roy Choudhury, Bradley D. Shields, Elizabeth C. Draper, L Joseph Su, Alan J. Tackett. Combination of sulforaphane and 5-aza-2′-deoxycytidine slows the growth and upregulates the chemoattractant CCL5 in metastatic melanoma [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 LB-182.
Abstract LB-230: Nanotherapy targeting metastatic factor RHAMMB-positive pancreatic neuroendocrine tumors
Authors: Lee Seung Koo , Chen Xiang , Du Yi-Chieh Nancy , Tung Ching-Hsuan
Published: September 2020

Pancreatic neuroendocrine tumors (PNETs) represent one-third of gastroenteropancreatic neuroendocrine tumors and are the second malignancy of the pancreas. The 5-year survival rate of metastatic PNETs is only about 15%. We have recently demonstrated that receptor for hyaluronic acid-mediated motility isoform B (RHAMMB) is upregulated in PNETs and promotes metastasis of PNETs. We have also reported that Bcl-xL accelerates the formation of PNETs with invasive properties. Here, we propose a RHAMM-targeted combination therapy (RCT), as a novel treatment for PNETs. RCT is designed to accomplish a synergistic apoptotic/anticancer effect, by aiming RHAMMB, a receptor for hyaluronic acid (HA), and codelivering Bcl-xL siRNA with mitochondria-fusing peptide to kill PNET cells. Yet, it is a substantial challenge to codeliver multiple drugs to RHAMM-expressing tumors. To simultaneously transport these unconventional therapeutics for a synergistic effect, a siRNA for Bcl-xL and a mitochondria-fusing peptide are layered onto a nanocore by charge-charge interaction, followed by a layer of HA for targeting RHAMMB. We showed that the prepared RCT is efficiently internalized by RHAMMB-positive cells, but not by RHAMMB-negative cells. We have found that the encapsulated Bcl-xL siRNA and the mitochondria-fusing peptide are released inside cells to silence Bcl-xL gene expression and induce apoptosis by fusing the mitochondrial membrane. A synergistic cell killing effect was achieved in vitro (> 83% cell death). In a preclinical mouse model, we demonstrated that systemically-injected RCT significantly reduced tumor burden (> 65% reduction) and sustained the blood glucose levels of mice bearing RHAMMB-positive PNETs. Together, the developed RCT can serve as a promising drug delivery system for RHAMMB-overexpressed cancer treatments.

Citation Format: Seung Koo Lee, Xiang Chen, Yi-Chieh Nancy Du, Ching-Hsuan Tung. Nanotherapy targeting metastatic factor RHAMMB-positive pancreatic neuroendocrine tumors [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 LB-230.
Abstract LB-249: PiRADL: An advanced deep learning tool for piRNA detection and its application in cancer biomarker identification
Authors: Chen Shaoqiu , Deng Youping
Published: September 2020

PIWI-interacting RNAs (piRNAs) are a large class of non-coding RNAs expressed in animal cells. Although many programs involved in identifying piRNAs from small RNA sequencing datasets, the boundaries are still hard to overcome. Here we developed a new tool called piRADL, by using deep learning to identify piRNA sequences. We transform the sequences into the 3D Numpy arrays(16X32X256), then the conventional neural network classifier was applied to train on the datasets from four different species (rat, human Caenorhabditis elegans, and Drosophila melanogaster). In the validation dataset, the piRADL shows better performance in comparison with other programs in accuracy, precision, sensitivity, and specificity. It is user-friendly, the user only needs to submit the sequences to the software. Based on this tool, we have found some interesting PiRNA prognosis biomarkers to predict colorectal, lung and breast cancer patient survival.

Citation Format: Shaoqiu Chen, Youping Deng. PiRADL: An advanced deep learning tool for piRNA detection and its application in cancer biomarker identification [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 LB-249.
Abstract LB-251: Investigation of few-shot deep learning techniques on a small, high dimensional head and neck carcinoma dataset for prediction of cancer recurrence
Authors: Ondrey Frank G. , Schutte Dalton
Published: September 2020

Introduction: Artificial Intelligence (AI) techniques may be useful in predictive oncology. We examined the feasibility of applying open source Few-shot learning to genomics data for the purpose of predicting head and neck cancer recurrences. We compared basic feed forward neural networks (vanilla networks) to a special architecture designed for few-shot learning called a Siamese network. Methods: Affymetrix U133A gene chip data (D=22,215, 41 tumor/13 normal) of patients with non-recurrent (46.34%) and recurrent (53.66%) head and neck carcinomas (nRHNC and RHNC, respectively) was analyzed. Shallow (one-layer) and deep (three-layer) variants were examined for both vanilla and Siamese networks to predict RHNC using the PyTorch framework. Four models were built using PyTorch: one shallow vanilla (SV) network with a single layer of 100 neurons, based on the top performing model from the authors' previous work, one deep vanilla (DV) network with layers of 256, 64, and 8 neurons, one shallow Siamese (SS) network with a single layer of 100 neurons, and one deep Siamese (DS) network with layers of 256, 64, and 8 neurons. Each model was initialized, trained, and evaluated 11 times. Kaiming initialization and Stochastic Gradient Descent with Nesterov Momentum (0.5) was employed with typical assumptions. Results: The model with the highest mean F1 score, AUC, and sensitivity was the SV network (0.7001, 0.6667, and 0.6800 respectively) the model with the highest sensitivity was DV (0.7217). When comparing the mean metrics for the following pairs: SV/DV, SS/DS, SV/SS, and DV/DS, the only difference of means that were found to be statistically significant was the SV/SS pairing for F1, AUC, and specificity. Conclusion: The simplest model, with the least representational capacity, performed best but not in a statistically significant manner in nearly all cases. Interestingly, the DS model performed better than the SS model AUC and specificity while the SV model performed better than its deep counterpart in those metrics. In this initial analysis, we conclude that it is feasible to apply PyTorch AI to Affymetrix gene chips to obtain meaningful data about head and neck cancer recurrences.

Citation Format: Frank G. Ondrey, Dalton Schutte. Investigation of few-shot deep learning techniques on a small, high dimensional head and neck carcinoma dataset for prediction of cancer recurrence [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 LB-251.
Abstract LB-267: Detection of lung cancer by metabolomics of exhaled breath and machine learning
Authors: Qiu Mantang , Li Hang , Meng Shushi , Li Qingyun , Zhou Zuli , Wang Jun
Published: September 2020

Background: Exhaled breath-based test is an attractive option for cancer detection due to it is non-invasive and feasible nature. Here, we reported an effective approach to detect early-stage lung cancer (LC) by integration of metabolomics of exhaled breath and machine learning.

Methods: Healthy controls (HC) were adults who received low-dose CT for annual physical examination with no calcified pulmonary nodules and without history of cancer within 5 years. Treatment-naïve LC patients without history of cancer were enrolled. Exhaled breath samples of LC patients were collected before surgery. Exhaled breath samples were collected and stored in Tedla bags and detected by a high-pressure photon ionization time-of-flight mass spectrometry (HPPI-TOFMS). A CO2 sensor was applied during exhaled breath collection to ensure only “alveolar air” was collected. Detection model construction and feature selection were performed by support vector machine (SVM).

Results: Firstly, an exploratory cohort of 119 HC and 118 LC was set up. Exhaled breath samples were directly detected by HPPI-TOFMS and 32500 features were extracted from each sample. 22 features were selected and subjected to SVM to construct detection model in the exploratory cohort, which was randomly divided into training (n=159) and test (n=78) set. This model achieved a sensitivity of 89.74%, specificity of 92.31%, and accuracy of 89.74% in the test set, suggesting exhaled breath is accurate for LC detection. Secondly, a quantitative detection method was established by introducing mixed internal standard gas at 15 mL/min controlled by a mass flow meter, by which individual violate organic compound could be quantified. Then, a prospective cohort of 53 LC and 129 HC was set up and detected by the quantitative method. For mass spectrometry data with inner standard gas, 21 features were selected by SVM. Similarly, the prospective cohort was randomly divided into training (n=122) and test (n=60) set. The 21 features-based quantified model was trained and tested in the prospective cohort and achieved a sensitivity of 88.24%, specificity of 100%, and accuracy of 96.67% in the test dataset.

Conclusions: Exhaled breath with machine learning is a highly accurate approach for early-stage LC detection and inner standard gas could improve detection performance.

Citation Format: Mantang Qiu, Hang Li, Shushi Meng, Qingyun Li, Zuli Zhou, Jun Wang. Detection of lung cancer by metabolomics of exhaled breath and machine learning [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 LB-267.
Abstract LB-295: Discovery of potent selective oral ACSS2 inhibitors for the treatment of acetate avid tumors
Authors: Goutopoulos Andreas , Erez Omri , Nakache Philippe , Alchanati Iris , Hay-Koren Avital , Paz Dikla , Kovalerchik Dimitri , Oppenheimer Hannah , Gottlieb Eyal , Botti Simone , Mor Inbal , Pastukh Nina
Published: September 2020

Under the low oxygen and lipid-depleted conditions, often encountered in the tumor microenvironment, acetate is used as nutrient by cancer cells for the biosynthesis of fatty acids. ACSS2, the enzyme responsible for acetate capture within the cell and its conversion into Acetyl-CoA, is upregulated under metabolically stressed conditions and its silencing is shown to inhibit tumor growth in xenografts. Two independent HTS campaigns identified the same small molecule ACSS2 inhibitor series that exhibited uncompetitive binding behavior in respect to ATP. A co-crystal structure of human ACSS2 in complex with a congener of the series revealed that it binds in the acetate pocket and forms favorable interactions with ATP, which is bound adjacently. These compounds were over 1000-fold times selective for ACSS2 over the mitochondrial ACSS1 and other Acyl-CoA synthetases. Medicinal chemistry optimization of this series resulted in advanced compounds with sub-nanomolar biochemical potency and single digit nanomolar cellular EC50s in inhibiting de novo fatty acid synthesis from labeled acetate and excellent pharmacokinetic properties. In vivo, in mice, these compounds inhibited labeling of fatty acids in various tissues after administration of labelled acetate or ethanol. They exhibited in vivo anti-tumor efficacy after oral administration in xenograft models that are acetate avid, whereas had no effect in tumors that show low acetate uptake. MTB-9655, one of the compounds from this series with optimally balanced properties, is currently entering IND-enabling studies to allow its testing in cancer patients.

Citation Format: Andreas Goutopoulos, Omri Erez, Philippe Nakache, Iris Alchanati, Avital Hay-Koren, Dikla Paz, Dimitri Kovalerchik, Hannah Oppenheimer, Eyal Gottlieb, Simone Botti, Inbal Mor, Nina Pastukh. Discovery of potent selective oral ACSS2 inhibitors for the treatment of acetate avid tumors [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 LB-295.
Abstract LB-309: Comprehensive genomic insights into dynamic mechanism underlying the development of non-malignant human liver disease into hepatocellular carcinoma
Authors: Zhang Xiangyu , Cao Ran , Zhou Kaiqian , Wang Xinyu , Zhou Cheng , Chen Feiyu , Bao Hua , Wu Xue , Shao Yang W. , Fan Jia , Zhou Jian , Wang Zheng
Published: September 2020

Aim: Hepatocellular carcinoma (HCC) is a dynamically developing disease. However, the molecular and evolutionary mechanism underlying the development of human non-malignant liver disease into HCC remains largely unknown. Methods: We performed whole-genome sequencing studies on 3 different types of samples (e.g. liver cirrhosis (LC), dysplastic liver nodules (DN), and hepatocellular carcinoma (HCC)) which were collected simultaneously from each of 8 liver cancer patients. Bioinformatics analysis was performed on somatic mutations, mutational signatures, copy number alterations, structure variants, telomere length, and phylogenetic trees. Results: Surprisingly, few passenger mutations were shared across LC, DN and HCC samples within each patient. Compared with the non-malignant LC and DN samples, HCC was characterized by significantly greater number of somatic mutations (particularly oncogenic mutations), copy number alterations, genomic rearrangements, as well as shorter telomeres. HCC exhibited much similar mutational signatures as dysplastic nodules but different from background cirrhotic liver. Several mutational signatures (e.g. COSMIC signatures 16, 22, 24) were substantially more active in tumor and DN samples than LC, while some mutational signatures (e.g. signatures 5, 8) were universal and equally active in both non-malignant hepatocytes and HCC. Most somatic copy number alterations (SCNAs) were only observed in HCC and no overlap across different samples was found. In contrast to universal subclonal SCNAs, minimal subclonal diversification of mutations was identified in HCC, implying the majority of mutations are acquired at the earliest stages. Conclusions: HCC can be characterized by punctuated evolution of mutations in short bursts followed by subclonal diversification driven by SCNAs. Despite little overlap of mutations, the mutational context indicates a common mutagenesis mechanism underlying HCC and DN, which is different from LC.

Citation Format: Xiangyu Zhang, Ran Cao, Kaiqian Zhou, Xinyu Wang, Cheng Zhou, Feiyu Chen, Hua Bao, Xue Wu, Yang W. Shao, Jia Fan, Jian Zhou, Zheng Wang. Comprehensive genomic insights into dynamic mechanism underlying the development of non-malignant human liver disease into hepatocellular 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 LB-309.
Abstract LB-314: Development of reference material guaranteed copy number of DNA for liquid biopsy
Authors: Osaki Yusuke , Sato Yoshiharu , Ishii Miho , Yonekawa Yuki , Matoba Ryo
Published: September 2020

cfDNA (cell free DNA) analysis using liquid biopsy plays an important role in cancer research. In particular NGS (next-generation sequencer)-based assay has attracted wide interests, because it can not only screen many cancer genes but also can detect ultra-low-concentration mutations at the same time. However, there is no reference material to evaluate correctly its performance. Currently, most researchers use diluted human genomic DNA that is commercially available as reference, but adjusting its concentration is difficult because of the Poisson distribution. Herein, we have developed a method to dispense cells with counting a cell one by one using inkjet technology (Manabu Seo, et. Al., 2019, Anal. Chem.). By lysing cells after dispensing, the defined copy number of DNA is prepared with a single molecule level. In this study, we assessed the feasibility of our reference material prepared by inkjet as a control for rare mutation detection (e.g. minimal sampling bias and high reproducibility). Spike-in control samples with exact allele frequencies with 0.07%, 0.53%, 0.64%, and 1.0%, were prepared by accurately dispensing with inkjet the cells that contain a sequence of exons 18, 19, 20, and 21 of EGFR. The EGFR sequence has G719A, E746_A750del, T790M, C797S, L858R, and L861Q mutations. For comparison, a few samples were also prepared by manual dilution process. The EGFR mutations were analyzed by the method of high-sensitivity procedure using NGS (Yoji Kukita, et. Al., 2013, PLoS ONE.). Result of the inkjet method had less variation than the manual dilution method, and high repeatability was obtained. Especially in E746_A750del (0.53%) the inkjet samples were tested three times (n = 24 each), and their CVs (coefficient of variation) were 17%, 17%, and 12%. In contrast, the manual sample's one was 33%. In addition, linearity of T790M and L858R were R2 = 0.98 and R2 = 0.96, respectively. The reference material produced by inkjet method can be provided under the same conditions at each facility and make it possible to improve the reliability of liquid biopsy. Therefore, the reference material could be appropriate standard for external quality control for EGFR mutant detection of liquid biopsy.

Citation Format: Yusuke Osaki, Yoshiharu Sato, Miho Ishii, Yuki Yonekawa, Ryo Matoba. Development of reference material guaranteed copy number of DNA for liquid biopsy [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 LB-314.
Abstract LB-326: The role of HER3 in HER2-amplified cancers other than breast cancers
Authors: Majumder Avisek , Steri Veronica , Salangsang Fernando , Moasser Mark
Published: September 2020

Introduction: Although recent studies showed that HER3 plays a key role in the pathophysiology of HER2-amplified breast cancers, its role in other cancers driven by HER2 amplification remains unknown. This study aimed to define the importance of HER3 signaling in other types of HER2-amplified cancer. Method: The expression and signaling activity of HER2, HER3, and downstream pathway proteins were studied in cell panels representing HER2-amplified cancers of the breast, bladder, colon and rectal, stomach, esophagus, lung, tongue, and endometrium along with controls lacking HER2 amplification. The time-dependent compensatory upregulation of HER3 in response to HER2 inhibitor therapy was assayed by western blotting and the apoptotic effects of HER2 inhibition were assayed by flow cytometry. The functional significance of HER3 in promoting tumorigenic growth in xenograft assays was determined in selected HER2-amplified cancer cell types by shRNA knockdown. Results: Many HER2-amplified cancers of the breast (HCC1569, HCC1954, HCC1419, UACC732, SUM190), bladder (CLS-439), stomach (N87, OE19), esophagus (TE4, KYSE410), lung (Calu3), and endometrium (USPC-ARC1, USPC-ARC2) showed HER3 activation, whereas HER2-nonamplified cancers of the same organs did not. With some exceptions, all HER2-amplified cancer cells undergo apoptosis when HER2 signaling is inhibited by lapatinib. Lapatinib induced apoptosis correlated with HER3 activation. Tumor growth was reduced upon HER3 knockdown in HER2-amplified cancers other than breast cancers, particularly cancers with constitutive HER3 phosphorylation. Significance: These results suggest that HER3 plays a functionally significant role in HER2 amplified cancers other than breast cancers, and may underlie resistance to HER2-targeting in these cancers. Combined HER2-HER3 targeting may be of value across the spectrum of different types of cancers.

Citation Format: Avisek Majumder, Veronica Steri, Fernando Salangsang, Mark Moasser. The role of HER3 in HER2-amplified cancers other than breast cancers [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 LB-326.
Abstract LB-335: Loss of function of the BRCA1-PALB2-BRCA2 axis accelerates p53-associated tumorigenesis
Authors: Huo Yanying , Mahdi Amar , Selenica Pier , Reis-Filho Jorge S S. , Weigelt Britta , Xia Bing
Published: September 2020

The BRCA1-PALB2-BRCA2 axis plays essential roles in the DNA damage response, thereby suppressing genome instability and cancer development. It is widely held that p53 loss promotes BRCA/PALB2-associated tumorigenesis. Here, through parallel conditional knockout of Brca1, Palb2 and Brca2 along with one allele of Trp53 in mice, and by studying mice with a mutation that disengages the PALB2-BRCA1 interaction in different Trp53 backgrounds, we present evidence that support an alternative view, that is, functional loss of the BRCA1-PALB2-BRCA2 axis accelerates p53-associated tumorigenesis. Our results also demonstrate a functional equivalence of BRCA1, PALB2 and BRCA2 in their basic tumor suppressive activity, an epistasis between PALB2 and BRCA2 in tumor suppression, and likely complementary roles of BRCA1 and the PALB2/BRCA2 complex in maintaining cell fitness. These findings may significantly advance the current understanding of the genetic mechanisms that underlie the development of BRCA/PALB2- and p53-associated cancers.

Citation Format: Yanying Huo, Amar Mahdi, Pier Selenica, Jorge S S. Reis-Filho, Britta Weigelt, Bing Xia. Loss of function of the BRCA1-PALB2-BRCA2 axis accelerates p53-associated tumorigenesis [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 LB-335.
Abstract LB-343: A Leu(CAG)-tRNA derived small RNA regulates ribosomal protein S28 after translation initiation in both human and mouse liver cancers
Authors: Kim Hak Kyun , Xu Jianpeng , Chu Kirk , Park Hyesuk , jang Hagoon , Li Pan , Valdmanis Paul , Zhang Qiangpeng , Kay Mark
Published: September 2020

Transfer-RNA-derived small RNA (tsRNA) is implicated in regulating many cellular processes and is dysregulated in various diseases. We recently revealed that the 3′ end of the LeuCAG tRNA-derived small RNA (LeuCAG3′tsRNA) binds to two target sites in human RPS28 mRNA coding region and 3′ UTR, and unwinds their double-stranded secondary structure, which enhances RPS28 translation and subsequently regulates ribosome biogenesis. Inhibition of this tsRNA suppressed the growth of hepatocellular carcinoma in vivo, making it a bona-fide target for cancer therapeutics1. However, the functional conservation between species and the detailed mechanism by which the tsRNA regulates mRNA translation need to be determined in more detailed. Here, we showed that the target site in RPS28 coding region in human is highly conserved in many vertebrate species. While the 3′ UTR target site forms a double-stranded secondary structure with the translation initiation site (TIS) in human RPS28 mRNA, the functional 3′ UTR target site is not present in the species distantly related to human. We revealed that a conserved target site in the mouse Rps28 coding region was sufficient for tsRNA-regulated enhanced translation of the mRNA and cancer cell viability in mouse cell line. Moreover, we demonstrated that the tsRNA regulates mRNA translation after initiation in both human and mouse. Our results have implications for providing additional insights into the biological role of LeuCAG3'tsRNA in post-transcriptional gene regulation and cancer cell viability.1. Kim, HK, et al. (2017). A transfer-RNA-derived small RNA regulates ribosome biogenesis. Nature: 1-21doi:10.1038/nature25005.

Citation Format: Hak Kyun Kim, Jianpeng Xu, Kirk Chu, Hyesuk Park, Hagoon jang, Pan Li, Paul Valdmanis, Qiangpeng Zhang, Mark Kay. A Leu(CAG)-tRNA derived small RNA regulates ribosomal protein S28 after translation initiation in both human and mouse liver cancers [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 LB-343.
Abstract LB-356: Deep immune profiling of de novo and recurrent glioblastoma
Authors: Alanio Cécile , Binder Zev A. , O'Rourke Donald M. , Wherry E. John
Published: September 2020

To understand potential immune system alterations in glioblastoma patients and provide a foundation for immunotherapy, we profiled intra tumoral leucocytes from newly diagnosed de novo patients as well as patients with recurrent tumor using high dimensional CyTOF. All recurrent patients underwent standard-of-care therapy, including surgical resection, concurrent temozolomide and radiotherapy, and adjuvant temozolomide. We used two immune profiling panels: a broad profiling panel that includes 45 phenotypic markers that together permit the identification and enumeration of the main innate and adaptive immune cell subsets in humans, and a deep profiling panel that includes 45 features focused on T cell phenotype and biology. We report in both de novo and recurrent tumors a predominant infiltration by CD11b+CD14+ monocytes (43.6±13%. of CD45+ cells). These monocytes displayed an immunomodulatory M2 profile (CD163+HLA-DR-/+CD80-CD86-/+). The adaptive compartment was sparse and dominated by alpha beta T cells, although some mucosal associated invariant T cells and gamma delta T cells were also present. T cells were both conventional T cells and regulatory T cells. The latter tended to be more abundant in the de novo as compared to recurrent tumors (22.8±17.9% of CD4+ T cells in de novo vs 12.9±12.5% in recurrent tumors, P=0.09). Conventional T cells were mostly CD27-CD45RA- effectors, with high expression of PD1 (69.9±17.6% of CD8+ T cells). Using high dimensional approaches, we confirmed that this high expression of PD1 reflects T cell exhaustion, as defined by co-expression of other inhibitory receptors such as Tim3, CTLA-4 and LAG-3. Exhausted T cells typically co-expressed PD1 and CD39 in the de novo tumors, and this pattern was less often observed in recurrent tumors (63.4±22.84% of CD8+ T cells in de novo vs 46.3±14.5% in recurrent tumors, P=0.03). Together, our results highlight the potential issue of a substandard T cell compartment at the time of GBM diagnosis. We are now investigating the mechanisms underlying these observations, as well as their impact on T cell immunity of the patients, as well as current immunotherapy strategies. Our studies should provide a foundation for improving therapy in glioblastoma patients.

Citation Format: Cécile Alanio, Zev A. Binder, Donald M. O'Rourke, E. John Wherry. Deep immune profiling of de novo and recurrent 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 LB-356.
Abstract LB-399: Late interferon-gamma blockade improves antitumor efficacy of anti-CTLA-4 and anti-PD-1 combination treatment
Authors: Mok Stephen , Chin Renee , Allison James P.
Published: September 2020

The FDA has approved the use of immune checkpoint blockade antibodies targeting cytotoxic T-lymphocyte antigen-4 (CTLA-4) and programmed cell death-1 (PD-1) for cancer. Patients with metastatic melanoma that receive anti-CTLA-4 have a 22% 10-year overall survival rate, while those treated with anti-PD-1 have a 34% 5-year overall survival rate. The combination treatment of both mediates a 64% overall survival rate. Current literature suggests interferon signaling mediates the expression of inhibitory receptors such as programmed death-ligand 1 (PD-L1) in tumor microenvironment that may affect the responseivness to immunotherapy. However, the role of interferon signaling network throughout the timecourse of treatment remains unclear. In the B16F10 melanoma model, we first show that activated T-cells in combination treated mice produce more interferon-gamma (IFN-gamma) than naïve controls. Then, we have injected mice with anti-IFN-gamma antibody when 1) mice are first treated with combination CTLA-4/PD-1 blockade (early time point) and 2) the combination treatment is finished (late time point). We demonstrated that blocking IFN-gamma at the early time point compromises the antitumor efficacy of the combination treatment. In contrast, the antitumor efficacy of the combination treatment is improved and the expression of inducible co-stimulator (ICOS) on CD8 T-cells is increased if IFN-gamma is blocked at the late time point. Additionally, we found that the expression of PD-L1 in the tumor microenvironment is significantly reduced by IFN-gamma blockade at the late time point. Thus, we treated mice with anti-PD-L1 blocking antibody at the late time point and its antitumor tumor efficacy is similar to the mice treated with anti-IFN-gamma. It suggests that the improved antitumor efficacy of IFN-gamma blockade at the late time point in combination-treated mice is PD-L1 dependent. Collectively, we show that IFN-gamma has a complex and differential role throughout the time course of immunotherapy treatments, and this work suggests a potential combination treatment strategy with checkpoint blockade and late IFN-gamma blockade.

Citation Format: Stephen Mok, Renee Chin, James P. Allison. Late interferon-gamma blockade improves antitumor efficacy of anti-CTLA-4 and anti-PD-1 combination treatment [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 LB-399.
Abstract NG01: MADR: Rapid generation of somatic mosaics to model cancer in mice and human organoids
Authors: Kim Gi Bum , Pacheco David Rincon Fernandez , Saxon David , Yang Amy , Sabat Sara , Dutra-Clarke Marina , Levy Rachelle , Watkins Ashley , Park Hannah , Akhtar Aslam Abbasi , Linesch Paul W. , Kobritz Naomi , Shandra Swasty S. , Grausam Katie , Ayala-Sarmiento Alberto , Molina Jessica , Sedivakova Kristyna , Gareau Daniel S. , Filbin Mariella G. , Bannykh Serguei , Tang Jie , Suva Mario L. , Chen Bin , Danielpour Moise , Breunig Joshua J.
Published: September 2020

In situ transgenesis methods such as virus and electroporation can create somatic transgenic mice quickly, but they lack the exquisite control over copy number, zygosity, and locus specificity. We have recently established mosaic analysis by dual recombinase-mediated cassette exchange (MADR), which permits stable labeling of mutant cells expressing transgenic elements from precisely-defined chromosomal loci. MADR provides a toolkit of elements for combinatorial labeling, inducible/reversible transgene manipulation, VCre recombinase expression, and genetic manipulation of human cells. Further, we have demonstrated the versatility of MADR by creating glioma models with mixed, reporter-identified zygosity or with “personalized” driver mutations from pediatric glioma. For example, introducing H3f3a mutation variants with MADR regulates the spatiotemporal profile of glioma, and single-cell RNA and ATAC sequencing analysis demonstrates a recapitulation of developmental hierarchy seen in K27M-mutant human glioma. Moreover, we have generated novel models of supratentorial ependymoma using patient-derived oncofusion transgenes. These models display a high degree of fidelity and we now compare these models on a single-cell level with our previous models and human tumor cell transcriptomes. In addition, we now demonstrate the ability to generalize the MADR technology to other non-CNS tissues using local plasmid delivery. Finally, we have engineered human cells to allow for MADR transgenesis and somatic transgenic organoids. These combined approaches will enable researchers to discovery disease mechanisms and test therapeutics in more physiologically relevant cancer models.MADR is extensible to thousands of existing mouse lines and can be adapted to human cells, providing a flexible platform to democratize the generation of somatic transgenic disease models.

Citation Format: Gi Bum Kim, David Rincon Fernandez Pacheco, David Saxon, Amy Yang, Sara Sabat, Marina Dutra-Clarke, Rachelle Levy, Ashley Watkins, Hannah Park, Aslam Abbasi Akhtar, Paul W. Linesch, Naomi Kobritz, Swasty S. Shandra, Katie Grausam, Alberto Ayala-Sarmiento, Jessica Molina, Kristyna Sedivakova, Daniel S. Gareau, Mariella G. Filbin, Serguei Bannykh, Jie Tang, Mario L. Suva, Bin Chen, Moise Danielpour, Joshua J. Breunig. MADR: Rapid generation of somatic mosaics to model cancer in mice and human organoids [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 NG01.