bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2301: Antiglycan antibodies as predictors of therapeutic outcome in cervical cancer patients
Authors: PUROHIT SHARAD , Tran Paul M. , Tran Lynn K. , Song Xuezheng , Ferris Ferris G. , Wallbillich John J. , Dun Boying , She Jin-Xiong
Published: August 2019

Cervical cancer is a significant cause of cancer related death among women, with the highest mortality rates in developing countries. We aim to identify serum biomarkers for predicting outcome of radio therapy alone or combination of radiotherapy and brachytherapy. We measured natural anti-glycan IgG antibodies in the serum of stage II (n=276) and III (n=292) cervical cancer patients treated with radiation alone or in combination with brachytherapy on a suspension glycan array containing 184 glycans. Overall and progression free survival was used to determine the treatment outcome by Kaplan-Meier and Cox proportional hazards ratio. Significant protective effects were observed for Blood Group H antigens (HR=0.642, p=0.0013), Lewis Antigens (0.72, 0.015; 0.654, 0.003), Galili antigens (0.671, p=0.004), and other glycans belonging to Isoglobo (0.671,0.004) and 3fucosyllactose series (0.687,0.004). The protective effects remained significant after adjusting for stage and treatment. Our data suggest that measurement of natural anti-glycan IgG antibodies in serum can predict outcome of therapy in cervical cancer patients.

Citation Format: SHARAD PUROHIT, Paul M. Tran, Lynn K. Tran, Xuezheng Song, Ferris G. Ferris, John J. Wallbillich, Boying Dun, Jin-Xiong She. Antiglycan antibodies as predictors of therapeutic outcome in cervical cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2301.
Abstract 2341: Indoleamine 2,3 dioxegenase 1 (IDO1) and T-cell infiltration in esophageal cancer
Authors: Rosenberg Ari J. , Wainwright Derek A. , Fought Angela J. , Zhai Lijie , Lauing Kristen , Villaflor Victoria M.
Published: August 2019

Background: Immune checkpoint blockade is emerging as an important immunotherapeutic strategy in esophageal cancer, yet response rates remain low. IDO1 is a rate-limiting immunosuppressive enzyme that may contribute to resistance to immune checkpoint blockade in human cancer, and may be an important immunotherapeutic target. The expression pattern of IDO1 across esophageal cancer histologies remains poorly understood. Here, we utilize immunohistochemistry to characterize the expression pattern and relevance of IDO1 in esophageal cancer.

Methods: Tumor microarray containing samples of surgically resected esophageal carcinoma and normal esophageal tissue were stained for IDO1 and CD3ϵ (marker of T-cell infiltration). Demographic and staging data were collected. Light microscopic immunoscoring analysis was performed. Correlations were analyzed using Fisher’s exact test.

Results: 192 samples were assessed (180 esophageal carcinoma, 12 normal esophageal tissue.) Median age was 60 years (range 34-78). 69.3% of patients were male. Of the 180 esophageal carcinoma samples, 150 (83.3%) squamous cell carcinoma, 16 (8.9%) adenocarcinoma, 13 (7.2%) small cell carcinoma, 7 (3.9%) undifferentiated carcinoma, 2 (1.1%) carcinoid, 2 (1.1%) adenosquamous carcinoma, and 2 (1.1%) adenoid cystic carcinoma. IDO1 was positive in 81 samples (45.0%) overall with 52.0% in squamous cell carcinoma and 46.7% in adenocarcinoma. Positive IDO1 was associated with higher stage and nodal positivity (P=0.04). T-cell infiltration in esophageal carcinoma specimens was present in 133 samples (73.9%). IDO1 positivity correlated with increased T-cell infiltration (P<0.01).

Conclusions: Here our study suggests that expression of IDO1 is positive in almost half of esophageal tumors, and is associated with T-cell infiltration. Additionally, positive IDO1 was associated with higher likelihood of nodal involvement and more advanced stage. These data suggest that IDO1 may play a role in adaptive immune resistance in T-cell inflamed tumors, and that incorporating IDO1 inhibition into an immunotherapeutic strategy in esophageal cancer may enhance T-cell mediated anti-tumor effect.

Citation Format: Ari J. Rosenberg, Derek A. Wainwright, Angela J. Fought, Lijie Zhai, Kristen Lauing, Victoria M. Villaflor. Indoleamine 2,3 dioxegenase 1 (IDO1) and T-cell infiltration in esophageal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2341.
Abstract 238: Therapeutic activity of the non-internalizing antibody drug conjugate 1959-sss/DM3 targeting galectin3-binding protein in human neuroblastoma
Authors: Capone Emily , Ponziani Sara , Giansanti Francesco , Gentile Roberta , Vittorio Giulia Di , Laurenzi Vincenzo De , Sallese Michele , Bibbò Sandra , Sala Arturo , Ippoliti Rodolfo , Sauniere Jean Frederic , Iacobelli Stefano , Sala Gianluca
Published: August 2019

Neuroblastoma is a solid tumour affecting the peripheral nervous system accounting for ∼13% of all pediatric cancer mortality. Despite immunotherapy with the GD2 antibody has improved the clinical outcome of a fraction of patients with metastatic neuroblastoma, the majority of patients with relapsing, high risk disease cannot be successfully treated. Recently, it has been shown that non-internalizing, linker-less antibody drug conjugates (ADCs) targeting the tumor extracellular environment can exert a potent therapeutic activity against different tumors.

We identified LGALS3BP (aka Mac-2 BP or 90K) as an important target for non-internalizing ADC development, as the protein is largely secreted by the majority of human tumors, while being virtually undetectable in normal adult tissues.

In this study, we show that a variant of the humanized 1959 antibody, targeting human LGALS3BP, coupled to the maytansinoid drugs DM3 by means of disulfide linker, bound human neuroblastoma cell lines harboring or not N-myc amplification, although with different affinity. Importantly, normal human fibroblasts were not decorated by the antibody. The ADC potently inhibited metastatic lesions in the liver and lungs of NSG mice injected intravenously with the neuroblastoma cell line SKNAS. Our findings offer a preclinical proof-of-concept for the development of a non-internalizing ADC endowed with potent therapeutic activity for neuroblastoma treatment through an innovative mechanism of action.

Citation Format: Emily Capone, Sara Ponziani, Francesco Giansanti, Roberta Gentile, Giulia Di Vittorio, Vincenzo De Laurenzi, Michele Sallese, Sandra Bibbò, Arturo Sala, Rodolfo Ippoliti, Jean Frederic Sauniere, Stefano Iacobelli, Gianluca Sala. Therapeutic activity of the non-internalizing antibody drug conjugate 1959-sss/DM3 targeting galectin3-binding protein in human neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 238.
Abstract 2399: LAG-3/PD-L1 mAb2 can overcome PD-L1-mediated compensatory upregulation of LAG-3 induced by single-agent checkpoint blockade
Authors: Faroudi Mustapha , Kraman Matthew , Fosh Natalie , Reader Claire , Gliddon Daniel , Seal Claire , Lucas Christa , Koers Alexander , Wydro Mateusz , Morrow Michelle , Brewis Neil
Published: August 2019

FS118, currently tested in Phase I clinical trial in patients with advanced malignancies (NCT03440437), is a first-in-class bispecific antagonistic antibody (known as mAb2) targeting LAG-3 (Lymphocyte-Activation Gene 3) and PD-L1 (Programmed Death-Ligand 1), two immune checkpoint molecules that promote tumour escape from immune surveillance. Resistance to anti-PD-1 treatment is associated with upregulation of other checkpoint inhibitor receptors such as LAG-3. Dual targeting in immune checkpoint blockade (ICB) using bispecific monoclonal antibodies could potentially overcome this resistance, further increase the clinical benefit of ICB therapy and prevent relapse or resistance after immunotherapy. In a syngeneic model we used a surrogate mAb2 of FS118 (blocking both mPD-L1 and mLAG-3 binding to their receptors) to determine the effect of dual checkpoint blockade on tumour growth and to elucidate the modulation of the underlying immune mechanisms following treatment with the mAb2. Dual blockade of LAG-3 and PD-L1 with the surrogate mAb2 in the MC38 tumour-bearing mice model resulted in an increased anti-tumour activity comparable to a combination of the single agents targeting LAG-3 and PD-L1. Moreover, the mAb2 and single agent combination resulted in distinct modulations of LAG-3 and PD-L1 cell surface expression within the spleen and tumour microenvironment (TME). While both the mAb2 and combination therapy significantly reduced the number of free PD-L1 binding sites on CD4+ and CD8+ T cells in spleen and TME, total LAG-3 cell surface expression increased following treatment with the combination, whereas it reduced with mAb2 treatment. In addition, analysis of serum samples collected at various timepoints confirmed evidence of drug target engagement with increasing levels of both soluble LAG-3 (sLAG-3) and soluble PD-L1 (sPD-L1) in the mAb2 treated animals. Modulation of sPD-L1 levels in the serum of treated animals was also observed in cynomolgus monkeys treated with FS118. These data provide a strong rationale for investigating both cell surface and soluble LAG-3 and PD-L1 levels as potential pharmacodynamic biomarkers in further clinical development.

Citation Format: Mustapha Faroudi, Matthew Kraman, Natalie Fosh, Claire Reader, Daniel Gliddon, Claire Seal, Christa Lucas, Alexander Koers, Mateusz Wydro, Michelle Morrow, Neil Brewis. LAG-3/PD-L1 mAb2 can overcome PD-L1-mediated compensatory upregulation of LAG-3 induced by single-agent checkpoint blockade [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2399.
Abstract 24: Novel STAT3 & HDAC inhibitors that selectively target triple-negative breast cancer cell
Authors: Wu Bocheng
Published: August 2019

Signal transducer and activator of transcription 3 (STAT3) is an oncogenetic transcriptional factor which can modulate cancer cells apoptosis. Stimulation of cancer cells by cytokines such as IL-6, INF-a, etc., can induce phosphorylation of STAT3, resulting in the translocation of p-STAT3 into the nucleus where it facilitates the expression of anti-apoptosis genes. This p-STAT3 anti-apoptotic activity is one drug resistance mechanism developed by cancer cells against chemotherapies including histone deacetylase inhibitors (HDACi). Pyrimethamine has been reported to inhibit STAT3 phosphorylation, mRNA transcriptional level, and STAT3-dependent cell viabilities. In this presentation, we disclosed novel pyrimethamine-based bifunctional STAT3-HDAC inhibitors as potential therapeutic agents for p-STAT3-dependent cancers. We will describe the design, synthesis and biological activities of STAT3-HDAC inhibitors. We will show that these bifunctional agents inhibit HDAC deacetylase activity and STAT3 phosphorylation. A subset of these compounds is more cytotoxic to MDA-MB-231, a triple-negative breast cancer cell line that is highly dependent on STAT3.

Citation Format: Bocheng Wu. Novel STAT3 & HDAC inhibitors that selectively target triple-negative breast cancer cell [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 24.
Abstract 240: Therapeutic targeting of protein kinase ck2 in mycn-driven neuroblastoma
Authors: Lian Haiwei , Shen Ning , Zhou Yun , Li Dun , Feng Hui
Published: August 2019

Amplification of the MYCN oncogene occurs in about 30-40% of advanced neuroblastoma cases and is the most reliable predictor of poor prognosis. Protein kinase CK2 (casein kinase II) is a highly conserved serine/threonine kinase that can be effectively inhibited by small molecules. In fact, CX-4945, a potent, specific, ATP-competitive CK2 inhibitor, is currently tested in clinical trials to treat multiple cancers. However, the role of CK2 in MYCN-driven neuroblastoma remains unknown. To determine the relevance of CK2 in MYCN-driven neuroblastoma pathogenesis, we analyzed published microarray data and compared the expression of the CK2 subunits in primary neuroblastoma patients samples. We found that both CK2α and CK2α’ are upregulated in neuroblastoma patients samples with MYCN amplification, compared to the ones without MYCN amplification. To determine the effect of CK2 inhibition on neuroblastoma cells, we treated a panel of human neuroblastoma cell lines with the CK2 inhibitor CX-4945 and short hairpin RNA specifically targeting CK2α. CK2 inhibitor CX-4945 suppressed human neuroblastoma cell growth, mainly through inducing apoptosis, especially in the MYCN-amplified cells. More over, CK2α knockdown also induced cell apoptosis. In-vitro assay indicated that CK2 inhibition through either genetic or pharmacological approaches effectively reduced cell growth of human neuroblastoma cells primarily through induction of apoptosis. 14 days in-vivo treatment, CX-4945 significantly decreased tumor growth in mouse xenografts by subcutaneously implanting human KELLY neuroblastoma cells, but didn’t affect their body weight. These studies characterize the role of CK2 in neuroblastoma development, and provide valuable information about the relevance of CK2 as a target in MYCN-driven neuroblastoma.

Note: This abstract was not presented at the meeting.

Citation Format: Haiwei Lian, Ning Shen, Yun Zhou, Dun Li, Hui Feng. Therapeutic targeting of protein kinase ck2 in mycn-driven neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 240.
Abstract 2409: Predictive accuracy of Cox proportional hazards cure models with application in cancer studies
Authors: Han Xiaoxia , Zhang Yilong , Shao Yongzhao
Published: August 2019

With recent development in cancer screening, diagnosis and treatment, many early-stage cancer patients will never experience recurrence, metastasis or death due to their primary cancer, whom can be considered as clinically cured. In the era of precision medicine, it is of interest to develop predictive models for cure status as well as for survival among uncured patients. The area under the ROC curve (AUC) is commonly used for assessing discriminative accuracy for dichotomous outcome (cured/uncured). Yet the conventional AUC cannot be directly used here due to unobserved cured status. In this study, we extend the conventional AUC to Cox proportional hazards (PH) cure models for evaluating prognostic utility in the presence of latent cured patients. We develop consistent and asymptotically normal estimates with explicit formulas for sensitivity, specificity and AUC. Furthermore, we reviewed the prognostic accuracy estimators for survival time among uncured patients for Cox PH cure models. Numerical studies show that our proposed estimators perform well for finite sample size. A melanoma data is used to illustrate the utility of our proposed prognostic metrics. We also have developed an R package called evacure to efficiently compute these estimates and their confidence intervals.

Citation Format: Xiaoxia Han, Yilong Zhang, Yongzhao Shao. Predictive accuracy of Cox proportional hazards cure models with application in cancer studies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2409.
Abstract 2412: Development of a gene signature to predict positive or negative sentinel nodes as a prognostic marker in melanoma
Authors: Majeske Audrey J. , Geddes Timothy J. , Keidan Richard , Wilson George D.
Published: August 2019

In recent years, sentinel lymph node (SLN) biopsy has been adopted as a less invasive technique to assess the prognostic outcome of melanoma, whereby draining the key lymph nodes for presence of a tumor decreases unnecessary lymph node dissections and reduces the risk of developing lymphedema. However, this technique only has therapeutic value in patients with SLN-positive tumor nodes, which only represents about half of the population diagnosed with melanoma. In a pilot study, we assessed the predictive efficacy of using a commercialized multi-biomarker next-generation sequencing (NGS) assay (Illumina® Comprehensive Cancer Panel) containing selected genes which have been shown to have a prognostic impact in melanoma progression, to determine whether these can identify primary tumors which do not require SLN biopsy. We used laser capture microdissection to capture pathologist-identified areas of tumor from four groups of samples 1) skin lesions from SLN-positive patients, 2) skin lesions from SLN-negative patients, 3) node samples from SLN-positive patients and node samples from SLN-negative patients; some cases of skin lesions and nodes were matched for the same patient. Sequencing identified 14 genes containing variants in >70% of the positive node samples, which were absent in samples with negative nodes. This included EGFR, PDGFR, ATM, PIK3CA, TP53 and ERBB4. Of note, variants in ERBB4 is of interest as it has been shown in the past to be a potential molecular target in the treatment of melanoma. We are currently validating these preliminary findings in a larger cohort of patients (n=31) and will report on the NGS findings of this study and the efficacy of using genetic biomarkers in skin biopsy samples as a potential prognostic marker for early stage melanoma patients who may not require SLN biopsy.

Citation Format: Audrey J. Majeske, Timothy J. Geddes, Richard Keidan, George D. Wilson. Development of a gene signature to predict positive or negative sentinel nodes as a prognostic marker in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2412.
Abstract 2420: The development of novel detection system for circulating tumor DNA using DNA chip system
Authors: Nakamura Noriaki , Okamura Hiroshi , Yamano Hirofumi , Ito Hiromichi , Zembutsu Hitoshi
Published: August 2019

Gene panels covering hundreds of mutation hotspots for detection of cell-free DNA (cfDNA) have been developed for the establishment of clinically practical circulating tumor (ctDNA) detection system. Although amplicon-based or capture-based genomic profiling of genes commonly mutated in cancer using next-generation sequencing (NGS) system have been developed, they are not sufficiently sensitive nor accurate to be used for clinical diagnosis in hospital. As a result of preliminary study using 87 advanced pancreatic cancer (stage lll/lV), we observed that one or more KRAS mutation(s) could be detected in 60.9% of patients with advanced pancreatic cancer by using the amplicon-based deep sequencing system. To develop more sensitive and accurate ctDNA detection system, we optimized conditions of our DNA chip system. We firstly used 100 synthetic DNA samples, whose KRAS mutant allele frequencies were from 0.1% to 10.0%, and investigated the quantitativity of our DNA chip system. We amplified target regions by PCR to obtain 2,000 copies of synthesized DNA. The PCR product was hybridized with the probe on the DNA chip. The fluorescence ratio (mutant allele fluorescence intensity / total fluorescence intensity) of 100 synthetic DNA samples were clearly distinguished to that of negative control by using the DNA chip system. We defined an appropriate cut-off values of small quantities (0.1%) of mutations. Furthermore, to confirm the accuracy and reliability of this method, we verified our DNA chip system using 15 plasma cfDNA samples from patients with mutant KRAS (0.1~10.0%) and 15 samples from patients without mutant KRAS as negative control. 10 ng of ctDNA which extracted from blood sample is used in PCR. We observed that detected mutant status by DNA chip was completely concordant (100%) with those by amplicon-based deep sequencing system. Our data confirmed that mutant allele in cfDNA can be sensitively and accurately detected by DNA chip system. These results suggest that the ctDNA detection system developed in this study could be a novel diagnostic tool for tumor burden, and could realize the ultra-early detection of refractory tumors including pancreatic cancer.

Citation Format: Noriaki Nakamura, Hiroshi Okamura, Hirofumi Yamano, Hiromichi Ito, Hitoshi Zembutsu. The development of novel detection system for circulating tumor DNA using DNA chip system [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2420.
Abstract 243: Differential effects of combination treatment of biochanin A and statins on glioblastoma multiforme cell proliferation and cell metabolism
Authors: Desai Vilas S. , Buchhalter Eric , Cabanzo Max , Tiwari Arushi , Kaushal Gagan , Lai James C. , Bhushan Alok
Published: August 2019

Glioblastoma Multiforme (GBM) is a deadly brain cancer and represents the most common central nervous system (CNS) tumors in adults. Although GBM does not metastasize, its aggressive growth and invasive nature are responsible for poor patient prognosis. The current standard therapy for newly diagnosed GBM patients involves surgical resection, followed by radiation and chemotherapy with Temozolomide. However, its rapid rate of infiltration into normal brain tissue ultimately renders the therapy ineffective. Epidemiological studies on dietary isoflavones (e.g., genistein, biochanin A) have shown their anti-cancer potential in different cancers. Though primarily used in management of hyperlipidemia and cardiovascular diseases, statins are known to exert anti-proliferative effects. We therefore hypothesized that a combination treatment of biochanin A & statins (e.g., Atorvastatin, Lovastatin, Simvastatin, Fluvastatin and Pravastatin) exerts enhanced anticancer effects on GBM U-87 MG and T98 G cells. Our studies showed statins induced differential effects on viability of GBM cells in combination with biochanin A, with U-87 MG being more susceptible than T98 G cells. The combination treatment of biochanin A and atorvastatin also decreased invasion in U-87 MG cells. Additionally, cell metabolism studies using seahorse XFp analyzer showed a switch in their metabolic phenotype with an increase in mitochondrial respiration and a decrease in glycolytic activity with the combination treatment. We also performed metabolite extraction on GBM cells for a global unbiased profiling of metabolites using a single extraction procedure and dual separation analysis by LCMS. A differential analysis of alternative GBM treatment indicated statistically significant changes in carbohydrate and amino acid metabolism as well as alterations to various degradation pathway intermediates. Together, the combination treatment-induced effects on GBM cell lines are differential and our results may have potential implications in developing combination therapies with biochanin A in vivo and support the design of new and better therapies for the treatment of a lethal cancer like GBM.

Citation Format: Vilas S. Desai, Eric Buchhalter, Max Cabanzo, Arushi Tiwari, Gagan Kaushal, James C. Lai, Alok Bhushan. Differential effects of combination treatment of biochanin A and statins on glioblastoma multiforme cell proliferation and cell metabolism [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 243.
Abstract 2443: Predicting the impact of somatic mutations on chromatin conformation using deep learning
Authors: Trieu Tuan , Khurana Ekta
Published: August 2019

DNA in eukaryotes is packed into hierarchical layers of loops resulting in the 3D structure of the genome. 3D genome organization plays vital roles in many biological processes of the cell such as gene regulation, cell division and stem cell differentiation and its disruption can lead to gene dysregulation and diseases, including cancer. We developed a deep learning model to predict the impact of single nucleotide variants, indels and structural variants on 3D chromatin loop structures of the genome. We first built a deep convolutional neural network to learn DNA sequence patterns of boundaries of 3D chromatin loops. The learned patterns of boundaries are then used to train another neural network to learn if two boundaries are likely boundaries of a chromatin loop given their DNA sequences. The model produces a probability indicating the likelihood of the two boundaries to form a chromatin loop (loop probability). It is trained with DNA sequence only, and therefore, it can detect effects of DNA variants on 3D chromatin loops as changes in loop probabilities. We trained our model with 80% of 3D chromatin loop from the cell line GM12878. Our model to predict boundaries of loops can distinguish DNA sequences of boundaries from random sequences with AUC of 0.96 on a balanced test-set from the cell line GM12878 and also performs well on data from the K562 cells with AUC of 0.93. Our result shows that variants in lymphoblastoid cells GM12878 do not change loop probabilities as much as variants in leukemia cells K562 do, consistent with the greater disruptive role of tumorigenic variants in the cancer cells. We next applied our model on whole-genome sequences of 240 malignant lymphoma patients to identify loop-disrupting variants that may act as drivers of cancer. We find that genes in predicted altered loops show more differential expression in tumor samples compared to genes in unchanged loops. Our method can be applied on large cohorts of patients with whole-genome sequences to analyze the chromatin conformation changes caused by somatic variants.

Citation Format: Tuan Trieu, Ekta Khurana. Predicting the impact of somatic mutations on chromatin conformation using deep learning [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2443.
Abstract 2453: A new deconvolution algorithm for accurate assessing immune and stromal cell populations in mouse transcriptomic data
Authors: Lu Xiaoyu , Tu Szu-wei , Chang Wennan , Huo Yan , Wang Pengcheng , Zhang Yu , Zhang Chi , Cao Sha
Published: August 2019

Multiple deconvolution methods have been developed for investigating the heterogeneous immune and stromal (I/S) cell types in human cancer tissue by deciphering their relative abundances using transcriptomic data. However, there is a lack of a user-friendly software for mouse transcriptomic data deconvolution. Key challenges for developing such a tool include: (1) limited training data sets for available for deriving signature genes of I/S cell types in sporadic mouse data; (2) mouse models of diverse geno-/pheno-types may have varied expressions of I/S cell marker genes; (3) the transcriptomic data may be collected from mouse with certain levels of immuno-deficiency; and (4) the transcriptomic data may come from highly diverse experimental platforms. To solve these challenges, we (i) developed a novel non-parametric analysis method to derive potential I/S cell signature genes from a large collection of mouse data sets; (ii) implemented a low rank sub matrix identification method with a non-negative matrix factorization (NMF) based deconvolution method; and (iii) enabled the flexibility that certain I/S cell types may be absent if their respective cell markers do not form a significant low rank structure. The new method is applied to mouse prostate cancer data sets to infer the level of anti-cancer immune cell populations. Genes expressed by cancer cells that are negatively associated with the anti-cancer immune cells are further inferred, and compared with the results derived in human data. A user-friendly R package of the deconvolution method is released through GitHub.

Citation Format: Xiaoyu Lu, Szu-wei Tu, Wennan Chang, Yan Huo, Pengcheng Wang, Yu Zhang, Chi Zhang, Sha Cao. A new deconvolution algorithm for accurate assessing immune and stromal cell populations in mouse transcriptomic data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2453.
Abstract 2454: Cancer RNA:DNA interactome analysis and prediction
Authors: Kuznetsov Vladimir A.
Published: August 2019

Transcriptional R-loops are three-stranded RNA:DNA hybrid structures essential for many normal and pathobiological processes. Previously, we have proposed and validated a quantitative R-loop forming structure (RLFS) model, QmRLFS, and predicted about 660,000 RLFSs in the human genome; most of them are localized in total within 75% of the coding and non-coding genes and gene-flanking regions, transcribed enhancer and pseudogene regions. RLFSs are also commonly co-localized as the singleton or clusters at regulatory sites and disease-associated genomic loci. Recently, it was computationally predicted and experimentally shown that RNA:DNA hybrid/R-loop interactome may play critical roles in mutagenesis, chromosome breaks, genome instability and cancer development. Herein, we conducted a comprehensive comparative analysis between the RLFSs, their clusters, publically available DRIP-seq and DRIPc-seq, and our own experimental datasets. QmRLFS demonstrated high accuracy (82-92%) and unbiased performance with resolution on the nucleotide, gene and genome scales. A preferential co-localization of the RLFSs with promoters, U1 splice sites, gene ends, enhancers and non-B DNA structures, such as G-quadruplexes, provides evidences for the mechanic links between RLFSs and dynamical DNA tertiary structures, transcription initiation and critical regulatory genome signals. We introduced and characterized a class of 25000 paired reverse-forward RLFS clusters highly enriched with non-B DNA structures, which co-localized in the transcribed promoters of sense-antisense gene pairs and enhancer’s flanks. In the cancer genomes, we found the RLFSs that form RNA:DNA hybrids/R-loops and could preferentially link open promoters and transcriptionally active enhancer regions. This suggests new mechanisms for in trans RNA:DNA hybrid-mediated 3D-chromatin loop formation. Finally, we found the RLFS clusters supported by cancer cell RNA:DNA hybrids/R-loop data, which were overlapped with hyper-mutated clusters, kataegis expression signatures. Overall, our study provides a rationale for the prediction, discovery, and characterization of the RLFSs as novel functional structures for an emerging quantitative biology and pathobiology of RNA-DNA interactomes.

Citation Format: Vladimir A. Kuznetsov. Cancer RNA:DNA interactome analysis and prediction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2454.
Abstract 2466: Designing an intuitive visualization of BRCAness scores for clinicians
Authors: Allegakoen Hannah R. , Goldman Mary , Caughey Bennett , Consunji Martin , Benz Christopher C. , Haussler David , Zhu Jingchun , Collisson Eric A.
Published: August 2019

Objective: Genomic interrogation of tumors has changed the way we care for cancer patients. Monogenic, single mutation tests clearly and accurately define patient populations whose tumors will or will not likely respond to specific therapies. Next generation sequencing has enabled diagnostics derived from broader footprints, such as signatures of mutational processes. Currently, no universal guidelines exist on translating complex predictive signatures into the clinic, and their interpretability is a barrier to uptake by clinicians. Visually displaying genomic signatures may help clinicians interpret them. We designed a user-directed approach to developing understandable displays of an individual’s BRCAness signature through testing at clinical cancer conferences.

Materials and Methods: We adopted a two-stage approach to optimizing user-testing methods. First, 44 attendees at the 2018 Gastrointestinal Cancer Symposium participated in a tablet-based test of a visualization of a patient’s BRCAness signature. We refined our testing methods and continued tabled-based testing of 51 attendees at the 2018 American Society of Clinical Oncology. Participants viewed slides explaining the signature and visualization. They were asked to interpret a patient’s BRCAness signature when provided information both as text and as a visualization. Participants received one of three similar versions of the visualization.

Results: Participants interpreted patients’ BRCAness signatures faster when given a visual. When shown a visual indicating BRCAness scores of germline BRCA mutated tumors, participants interpreted the information fastest without sacrificing accuracy or confidence in their answer. Participants’ interpretation of an individual’s BRCAness signature was associated with their self-reported likelihood to recruit the individual to a clinical trial.

Conclusion: Visualizing distributions of BRCAness signatures with germline BRCA mutations displayed helped participants respond faster without sacrificing accuracy or confidence in their answer. Testing attendees at cancer conferences presents a potential platform to include clinicians and researchers in the development of genomics visualization tools.

Citation Format: Hannah R. Allegakoen, Mary Goldman, Bennett Caughey, Martin Consunji, Christopher C. Benz, David Haussler, Jingchun Zhu, Eric A. Collisson. Designing an intuitive visualization of BRCAness scores for clinicians [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2466.
Abstract 2469: The COSMIC Cancer Gene Census - a comprehensive study of all mutated cancer-driving genes
Authors: Sondka Zbyslaw , Speedy Helen E. , Bamford Sally , Cole Charlotte G. , Ward Sari A. , Forbes Simon A.
Published: August 2019

The COSMIC Cancer Gene Census (https://cancer.sanger.ac.uk/census) is a catalogue of genes that drive all forms of human cancer. Since 2004, a consistent curation approach to the scientific literature has grown this resource into a comprehensive description of 723 genes, detailing how each gene contributes to disease causation The entire Cancer Gene Census has been fully re-evaluated, and each gene has been classified as Oncogene, Tumour Suppressor and/or Fusion gene - depending on their somatic mutation profile and functional role in carcinogenesis. Genes included in the CGC are characterised by the presence of somatic or germline mutations, which change the activity or expression of the protein product in a way that promotes one or multiple hallmarks of cancer. The minimum level of evidence required for CGC inclusion are at least 2 publications from independent research groups showing increased mutation frequency in at least one type of cancer; and 2 or more published experimental evidence of functional involvement of a gene in promoting the hallmarks of cancer. The functional description of how each mutated gene causes cancer is now underway, with approximately half the Census now described in both functional and mechanistic terms. These characteristics clearly show that many genes can participate in oncogenesis in multiple ways that are highly dependent on the type of genetic alteration and tissue in which the gene is expressed, as well as disease stage. Alongside this evidence-based characterisation of genes we know drive cancer, a “second tier” of genes is now encompassed in the Census, to describe genes implicated in oncology, but with less robust published evidence. These genes, often revealed by combining whole-tumour-genome sequencing studies are increasing rapidly in number and often underpin exciting new targets in oncology. Inclusion of these in the Census completes its ability to describe the contribution of inherited and acquired genetics to human oncology. With substantial research ongoing, the Census is updated with additional content every three months, included with every new release of the COSMIC database (https://cancer.sanger.ac.uk/).

Citation Format: Zbyslaw Sondka, Helen E. Speedy, Sally Bamford, Charlotte G. Cole, Sari A. Ward, Simon A. Forbes. The COSMIC Cancer Gene Census - a comprehensive study of all mutated cancer-driving genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2469.
Abstract 2477: CopyCat: estimating genomic copy number profiles from high-throughput single cell RNA seq data
Authors: Gao Ruli , Navin Nicholas
Published: August 2019

CopyCat is a computational approach for estimate genomic-copy number profiles from high-throughput single cell RNAseq data that is generated by technologies, such as Drop-Seq, 10X genomics or Nanowells. CopyCat involves first normalizing and transforming unique molecular index (UMI) count data matrices to calculate single cell copy number states from low-coverage datasets using gene-bin windows across the human genome, and does not require a reference normal cell control. The resulting binned data is normalized and used for segmentation to reduce noise from individual genes that can contribute to gene dosage effects along chromosomes. We show that this methods is highly effective at distinguishing diploid and aneuploid cells in human tumors or cancer cell lines, and can efficiently detect major (>10mb) chromosomal amplifications and deletions compared to copy number data generated by DNA sequencing of match samples. We further show that this method can resolve some clonal substructure within individual tumors, when subpopulations are distinguished by large chromosomal events. Our method outputs segmented copy number profiles and predicted classifications of normal (diploid) and tumor (aneuploid) cell states for individual single cells. It is implemented in R and is available on Github.

Citation Format: Ruli Gao, Nicholas Navin. CopyCat: estimating genomic copy number profiles from high-throughput single cell RNA seq data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2477.
Abstract 2484: An online tool to validate predictive biomarkers of therapy response using transcriptomic data of 3,651 ovarian cancer patients
Authors: Györffy Balazs , Fekete Janos , Osz Agnes , Pete Imre , Szasz Marcell
Published: August 2019

Systemic therapy of ovarian cancer can include chemotherapy and targeted therapy. Prognostic biomarkers are capable to predict survival and predictive biomarkers are capable to predict therapy response. To date, multiple online tools were established to identify prognostic biomarkers, but no platform is yet available for predictive biomarkers. In this study, we describe the first release of an online available tool capable to validate gene expression based predictive biomarkers using transcriptomic data of a large set of ovarian cancer patients.

Published gene expression data of 35 independent datasets was integrated with treatment data into a unified database. The classification is based on either author-reported pathological complete response (n=1,022) or relapse-free survival status at six months (n=1,347) or relapse-free survival status at twelve months (n=1,282). Treatment data includes chemotherapy (platin, taxol, docetaxel, paclitaxel, gemcitabine, topotecan) and targeted therapy (avastin). The transcriptomic database includes 54,675 probe sets corresponding to 20,089 distinctive genes. Finally, we performed a sample collection at the National Institute of Oncology (NIO cohort), and used these patient samples to validate the top six genes in ovarian cancer patients. Gene expression and therapy response were compared using receiver operating characteristics and Mann-Whitney tests.

In the validation of the tool we focused on paclitaxel-resistance associated genes. We selected the top genes after running the analysis across all samples and validated these by PCR in the NIO cohort of patients (n=80). The best performing paclitaxel-resistance biomarker candidates were ARAF (AUC=0.743, p=4.1E-09), PPCS (AUC=0.733, p=4.2E-07), GNL2 (AUC=0.718, p=2.7E-08), TFE3 (AUC=0.718, p=4.8E-06), PDXK (AUC=0.717, p=1.1E-05) and TOP1 (AUC=0.716, p=4.6E-05).

The analysis pipeline enables to validate and rank predictive biomarker nominees. By analyzing the candidate genes in a large set of independent patients, we can select the most reliable candidate and abolish those which are most likely to fail in a clinical setting. The registration-free interface of the online analysis platform is accessible at www.rocplot.org/ovar.

Citation Format: Balazs Györffy, Janos Fekete, Agnes Osz, Imre Pete, Marcell Szasz. An online tool to validate predictive biomarkers of therapy response using transcriptomic data of 3,651 ovarian cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2484.
Abstract 2493: Disulfide bond disproportionation agents activates the death receptor 5 pathway to kill highly resistant breast cancer
Authors: Wang Mengxiong
Published: August 2019

There are significant unmet medical needs among patients who have HER2+ breast cancers that have acquired resistance to targeted agents, and patients with Triple-Negative Breast Cancers (TNBCs) that lack therapeutic targets. Novel treatment strategies are needed to target these cancers. Disulfide bond Disproportionation Agents (DDAs) represent a new chemical class of anticancer drugs and show prominent anti-cancer activities both in vitro and in animal model. Blockade of breast tumor growth by DDAs is associated with downregulation of EGFR/HER2/HER3 in parallel, induction of AKT dephosphorylation, and activation of ER stress. However, it is not known how DDAs trigger cancer cell death without affecting non-transformed cells. This study aims to investigate the death pathways involved in the anti-cancer activities of DDAs, and to develop strategies that target drug resistant breast cancer and cancer metastasis. This study demonstrates that DDAs induce breast cancer cell death by activating the Death Receptor 5 (DR5) pathway. DDAs are the first compounds identified that upregulate DR5 via both transcriptional and post-transcriptional mechanisms and uniquely cause DR5 accumulation and oligomerization by altering DR5 disulfide bond pattern. This study also shows that the combination of DDAs and Tumor Necrosis Family-Related Apoptosis-Inducing Ligand (TRAIL), a natural ligand of DR5, significantly overcomes TRAIL resistance that has been encountered in clinical trials with this ligand. Furthermore, DDAs and TRAIL synergistically kill Lapatinib-resistant breast cancer and cancer metastatic cells, and that this anti-cancer effect is amplified by the overexpression of EGFR/HER2/MYC. Together, this study highlights a promising novel pharmacological approach against drug resistant cancer and cancer metastasis.

Citation Format: Mengxiong Wang. Disulfide bond disproportionation agents activates the death receptor 5 pathway to kill highly resistant breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2493.
Abstract 2496: Dynamic BH3 profiling identifies active combinations with conventional chemotherapy in non-small cell lung cancer
Authors: Potter Danielle S. , Letai Anthony G.
Published: August 2019

Mitochondrial apoptotic priming (referred to as priming) determines a cell’s ‘readiness’ for cell death and is regulated by the B-cell lymphoma 2 (BCL-2) family of proteins. It has been shown in multiple disease settings such as acute lymphoblastic leukemia, acute myeloid leukemia, multiple myeloma and ovarian cancer, that chemosensitivity correlates with priming. Patients with highly primed tumors exhibited superior clinical response to chemotherapy. In contrast, chemoresistant cancers and normal tissues were poorly primed. Priming is relative and can be measured using BH3 profiling. BH3 profiling is a functional assay which uses BH3 peptides derived from the BH3 domain of pro-apoptotic BH3-only BCL-2 family members to provoke a response from viable mitochondria. To identify drugs that enhance priming, tumor cells can be incubated with drugs prior to BH3 profiling, a method called dynamic BH3 profiling (DBP). DBP is a functional approach to precision medicine and measures early changes in death signaling after drug perturbation. An increase in priming after short term drug treatment (8-24 hours) has been shown to result in cell death days later. Moreover, it has been shown to predict in vivo response to therapy. Therefore, DBP can predict efficacious therapies within 24 hours.We hypothesized that drugs that enhance priming would render cancers more sensitive to conventional chemotherapy. To determine whether drugs that increase priming enhanced sensitivity to docetaxel and etoposide in non-small cell lung cancer (NSCLC), we first identified agents that enhanced priming via DBP. We found that targeted agents that increased priming of NSCLC tumor cells resulted in increased chemosensitivity in vitro. To assess whether targeted agents that increase priming might enhance the efficacy of cytotoxic agents in vivo, we carried out an efficacy study in PC9 xenograft mouse model. The BH3 mimetic navitoclax, which inhibits BCL-xL, BCL-w and BCL-2, consistently primed NSCLC tumors in vitro and in vivo. The BH3 mimetic venetoclax, which inhibits BCL-2, did not. In vivo navitoclax reduced tumor burden whilst mice were treated but as soon as therapy was stopped tumors recovered comparable to vehicle treated mice. Etoposide as a single agent had no effect on tumors. However, combining navitoclax with etoposide significantly reduced tumor burden after treatment was stopped, increasing mouse survival. Adding venetoclax to etoposide had no effect on tumor burden. These data suggest that targeted agents that increase priming, increased chemosensitivity resulting in reduction of tumor burden in vivo.

Citation Format: Danielle S. Potter, Anthony G. Letai. Dynamic BH3 profiling identifies active combinations with conventional chemotherapy in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2496.