bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2167: Efficacy assessment of BTK inhibitor ibrutinib in de novo and viral-induced B cell lymphoma
Authors: Wang Jessie Jingjing , Zheng Meiling , Huang Xuesong , Song Yanrui , Qian Wubin , Zhang Likun , Cai Jie , Guo Sheng , Li Henry Qixiang , Ouyang Davy Xuesong
Published: August 2018

Bruton's tyrosine kinase (BTK) is crucial for B cell maturation. Its activation has also been considered as a major oncogenic driver for various B cell-derived lymphoid cancers. A BTK inhibitor, Ibrutinib, has been approved for mantle cell lymphoma, chronic lymphocytic leukemia, and Waldenström's macroglobulinemia, a form of non-Hodgkin's lymphoma (NHL). Ibrutinib has also shown encouraging efficacies in defuse large B cell lymphoma (DLBCL), specifically in activated B cell-like (ABC) subtype, but not in germinal center B cell-like (GCB) subtype. We have established a series of patient derived xenograft (PDX) models, recapitulating diverse genotypes of de novo DLBCL patients, including two MYD88L265P/CD79BY197N double mutants (LY2298, LY2264), one MYD88L265P single mutant (LY0257), and a variety of wild-types (LY2214, LY3604, and LY6934, etc.). This cohort of PDX models serve as perfect preclinical tools to investigate Ibrutinib responses in different genotypes. Our studies demonstrated a moderate to robust efficacies of Ibrutinib in the MYD88/CD79B double mutants, suggesting that CD79B mutation is the predictive biomarker for chronic activation of B cell receptor (BCR) signaling, as well as generally good responses to BTK inhibitor. Interestingly, the MYD88 single mutant model LY0257, where the disease is likely driven by constitutive activation of MYD88 signaling, also showed response to Ibrutinib when dosed in drinking water. In the wild type PDXs, two of seven models tested so far are either partially responsive or sensitive to Ibrutinib, while the others are resistant to the treatment. It seems that Ibrutinib response does not always require CD79B mutation, and BCR pathway addiction may occur by other means in DLBCL, even when MYD88 signaling is constitutively active. Notably, all 5 wild type DLBCL PDXs that are non-responsive to Ibrutinib are EBV positive verified by RNAseq. These EBV-transformed B lymphoma PDX models, which share the similar histopathology as de novo DLBCL, but have distinct molecular pathology signatures and different pathogenesis. In efficacy studies, none of the transformed B lymphoma PDXs showed response to Ibrutinib. Taken together, our DLBCL and EBV-induced lymphoma PDX models provide a valuable preclinical platform for evaluating BTK inhibitors, as well as future drug discovery efforts on other targets in the BCR and MYD88 pathways, such as PI3K, SYK, and IRAK4.

Citation Format: Jessie Jingjing Wang, Meiling Zheng, Xuesong Huang, Yanrui Song, Wubin Qian, Likun Zhang, Jie Cai, Sheng Guo, Henry Qixiang Li, Davy Xuesong Ouyang. Efficacy assessment of BTK inhibitor ibrutinib in de novo and viral-induced B cell lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2167.
Abstract 2170: Single mouse preclinical trial: A tool for translational research
Authors: Mignard C , boisferon M Hillairet de , Bichat F , France D , Duchamp O
Published: August 2018

Roughly, 85% of preclinical agents entering oncology clinical trials fail to demonstrate sufficient safety or efficacy to gain regulatory approval. Hence, there is a need for experimental systems which better mimic the inter-patient response heterogeneity observed in the clinic. Patient-derived tumor xenograft (PDX) mouse models have emerged as a relevant oncology research tool to study tumor evolution, drug response, biomarkers, resistance phenomenon and adjusting chemotherapeutic approaches for individual patients. We will here expose the effectiveness of the single mouse preclinical trial paradigm for evaluating drug response, as mono or combo therapy using our well-characterized PDX collection. Based on the “1 PDX tumor/1 mouse/1 treatment” experimental design, a cohort of colorectal, breast, pancreas, lungs PDX models (minimum 20 of each) was used to explore response to Standard Of Care (SOC) and combo therapy used in clinic. We compared single-animal response data with treatment group data taken from historical experiments. We demonstrated that about >80% of the individual response matched the treatment group data, supporting the idea of using one single animal to predict the drug response. The response of each PDX to treatment was correlated to their histological and genetic profiles. This approach represents a new experimental design to address the tumor biology of cancer patients, and investigate targeted therapies in relevant mouse models, which could improve our ability to predict clinical trial responses, stratify patients for clinical trial, identify drug resistance mechanism, responsive sub-populations as well as biomarker. By combining genomic profiling data and drug screening data, and clinical data from patients, SMPT process is a helpful tool for precision cancer medicine and individualized drug selection.

Citation Format: C Mignard, M Hillairet de boisferon, F Bichat, D France, O Duchamp. Single mouse preclinical trial: A tool for translational research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2170.
Abstract 2181: Functionalizing intratumoral signaling heterogeneity in triple negative breast cancer
Authors: Rinkenbaugh Amanda L. , Sinha Vidya C. , Zhang Xiaomei , Piwnica-Worms Helen
Published: August 2018

Tumors are highly heterogeneous populations of cells, and measures of intratumoral heterogeneity (ITH) and diversity correlate with worse prognosis in many cancers, including breast cancer. Emerging studies are highlighting functional interactions between subclones, as well as among subclones and components of the tumor microenvironment. However, these studies have largely focused on soluble factors without interrogating the spatial distribution of subclones defined by activated signaling pathways. Previous work in this area has been severely limited by technical restrictions – existing techniques allowing measurement of many biomarkers simultaneously lose all information about the tissue architecture, while those that do retain spatial information can only assay a handful of markers at once. We will circumvent these limitations by undertaking imaging mass cytometry (IMC), which allows for simultaneous measurement of 30-40 antigens while retaining the spatial organization of the sample. Our objective is to dissect the signaling heterogeneity in tumors from patients and patient-derived xenograft (PDX) models of triple negative breast cancer (TNBC), through two main approaches: (1) characterization of signaling heterogeneity in human tumors and PDX models of TNBC through the use of imaging mass cytometry (IMC) and (2) modeling cell signaling heterogeneity in cell line-based models to determine mechanisms of cell-cell interaction and communication. We have constructed an IMC panel of antibodies that combines markers for tissue architecture, cell phenotyping, and signaling pathway activation. Profiling of a panel of TNBC PDX models, including matched sets of pre- and post-chemotherapy treatment, indicates emerging patterns of pathway activation. We will utilize these results to inform functional studies in our isogenic cell line models. As it is becoming more clear that tumors are composed of heterogeneous subclones, it is crucial that we understand the communication between subclones and with components of the microenvironment. Ultimately, we plan to use these results to identify novel vulnerabilities in subclonal interactions that can be targeted therapeutically in TNBC.

Citation Format: Amanda L. Rinkenbaugh, Vidya C. Sinha, Xiaomei Zhang, Helen Piwnica-Worms. Functionalizing intratumoral signaling heterogeneity in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2181.
Abstract 2184: Enrichment and isolation of tumor cells using a unique flow-sorting approach to decrypt intratumoral heterogeneity in matched samples of squamous cell carcinoma of the lung
Authors: Krause Arthur , Lorber Thomas , Perrina Valeria , Barrett Michael T. , Ruiz Christian , Bubendorf Lukas
Published: August 2018

Background:

Genomic intratumoral heterogeneity in cancers is a driving force for progression or recurrence. Availability of pure tumor cell material is critical for studying clonal evolution. In general, tumors are highly mixed with benign cells with a mean tumor cell purity of only 49%1 shown in lung squamous cell carcinoma (LSCC). Using a unique flow-sorting based approach enables us to overcome this limitation by highly enriching for tumor cells. Here, we aimed at precisely identifying different tumor populations in primary LSCC and matched distant metastases from 18 patients.

Methods:

Nuclei from snap-frozen and FFPE tumor specimens were extracted and subjected to flow-sorting using DNA content/ploidy as a parameter. Pan-cytokeratin (pCK) was used to differentiate diploid tumor cell populations from benign diploid stromal cells. DNA has been extracted from these individual tumor cell populations and the mutational profile and copy number status are currently being analyzed using whole exome seqeuencing (WES).

Results:

We successfully enriched for tumor cells with a purity of higher than 95% using the multi parameter flow-sorting approach. Besides the aneuploid tumors with higher ploidies, we discovered near-diploid tumor populations after enrichment with the pCK antibody. The pCK negative fraction consisting of stromal cells can serve as a germ line control in further downstream analysis as WES.

Conclusion:

The present study illustrates a unique method that allows high enrichment for tumor cells. Avoiding the dilution of DNA by benign stromal cells, together with the purity of aneuploid tumor cells, the precision of genomic analysis highly increases. At the same time, the diploid and pCK negative stromal cells can serve as a germ line control. Comprehensive genomic profiling of flow-sorted aneuploid and pCK positive diploid tumor populations represent a powerful technique to study intratumoral heterogeneity.

References:

1. Zack, T. I. Pan-cancer patterns of somatic copy number alteration. Nature Genetics. 45, 10 (2013).

Citation Format: Arthur Krause, Thomas Lorber, Valeria Perrina, Michael T. Barrett, Christian Ruiz, Lukas Bubendorf. Enrichment and isolation of tumor cells using a unique flow-sorting approach to decrypt intratumoral heterogeneity in matched samples of squamous cell carcinoma of the lung [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2184.
Abstract 2217: Concordance of PIK3CA mutations in hormone receptor-positive, human epidermal growth factor receptor 2-negative breast cancer: A systematic literature review
Authors: Aguilar Alejandra , Dean Joni , Anderson Elizabeth , Mollon Lea , Davis Lisa , Warholak Terri , Aizer Ayal , Platt Emma , Bardiya Aditya , Tang Derek
Published: August 2018

Introduction: This systematic literature review sought to determine the concordance of PIK3CA mutations in hormone receptor-positive (HR+), human epidermal growth factor receptor 2-negative (HER2-) metastatic breast cancer (mBC) patients.

Methods: A comprehensive search of PubMed/MEDLINE, EMBASE, Cochrane Central, and select conference abstracts was performed by two independent researchers that included, but was not limited to, keywords: “breast neoplasm,” “PIK3CA protein,” “hormone receptor positive,” and “metastases.” Databases were searched for English-language publications in HR+, HER2- mBC published between January 1993 through August 2017. Studies were included if results reported were specific to patients with HR+, HER2- mBC and reported data comparing PIK3CA mutations from liquid biopsies versus tumor biopsies or primary tumor samples versus metastatic lesion samples. Concordance was assessed between tissue samples (mutations found in primary tumors versus those from metastatic lesions) and between biopsy methods (i.e., tumor biopsy versus liquid biopsy) when the assessment was done at a variety of time points including time of initial diagnosis and time of diagnosis at disease progression. Content analysis was employed to quantify collected data elements.

Results: Of 558 studies included for full-text review, four met inclusion criteria (number of patient samples [n]=358). One study (n = 9) found the concordance between the mutation status of primary breast tumors to the mutation status of metastatic lesions to be 100%. Three studies (n = 47; n = 55; n = 247) determined the concordance of PIK3CA mutations between tumor biopsies and liquid biopsies with concordance ranging from 70.4% to 94%. One study found that the concordance of circulating tumor DNA (ctDNA) against tumor biopsy was higher among metastatic lesions only (81.6%) relative to using all tumor samples (either primary or metastatic lesions) (70.4%).

Conclusions: Available evidence suggested high level of concordance across sampling methods as well as across time. However, additional evidence is needed to increase study generalizability as well as to assess other possible confounding factors, such as differential timing between tumor and liquid biopsies.

Citation Format: Alejandra Aguilar, Joni Dean, Elizabeth Anderson, Lea Mollon, Lisa Davis, Terri Warholak, Ayal Aizer, Emma Platt, Aditya Bardiya, Derek Tang. Concordance of PIK3CA mutations in hormone receptor-positive, human epidermal growth factor receptor 2-negative breast cancer: A systematic literature review [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2217.
Abstract 2218: Trim29 regulates hemangiomas neovascularization through targeting HMOX1
Authors: Huang Qiang , Li Wei , Ge Xin , Li Peng , Gao Ya
Published: August 2018

Infantile hemangiomas is the most common benign vascular tumors of childhood, characterized by rapid proliferation after birth and slow involution thereafter. Although several signaling pathways have been implicated in hemangiomas neovascularization, the mechanism is still unrevealed especially the initiative factor. Here we used gene microarray to profile proliferating and involuting phases of infantile hemangiomas and bioinformatic methods to find the distinguished genes. Log2FC>0.585 or <-0.585 and a nominal P value of 0.05 were used as the filtering criteria. A total of 354 significant genes were identified including 262 upregulated genes. 20 genes were selected for screening according to the microarray results. Trim29 was certified to be responsible for the proliferation of IH using Celigo cytometer method, which were reinforced in patient lesions. By overexpression of Trim29, proteomics was used to detect the downstream proteins.After comparing with the microarray results, HMOX1 was identified and selected for further study after reidentification in patient lesions. Through overexpression and knockdown assay in vitro, we found Trim29 could regulate the expression of HMOX1 and affect hemangiomas neovascularization. Propranolol could block this potential pathway to inhibit proliferation of IH in vivo. These results indicated Trim29 could regulate hemangiomas neovascularization through targeting HMOX1. This innovative pathway could be blocked by propranolol and gave a potential target gene for further investigation to find new drug treatment for IH.

Citation Format: Qiang Huang, Wei Li, Xin Ge, Peng Li, Ya Gao. Trim29 regulates hemangiomas neovascularization through targeting HMOX1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2218.
Abstract 2228: Differential expression of MT-ATPase and COXIV genes in colorectal adenopolyps
Authors: Wallace Lashanale , Cherian Anju , Aikhionbare Felix
Published: August 2018

Therapeutic decisions in colorectal cancer (CRC) will be enhanced if guided by more accurate prognostic and predictive biomarkers during the progression of adenomas to CRC. Given that most CRCs develop from adenopolyps via the adenoma-carcinoma sequence, a mechanism for the inhibition of this sequence in patients with a high risk of developing CRC is a pressing need. Variants in mitochondrial (mt) protein expressions have been correlated with several clinico-pathological features of cancers as the majority of energy for tumor transformation are of mitochondrial origin. Differences in mitochondrial efficiency may be reflected as in adenoma-carcinoma sequence. Reports have shown that cytochrome c oxidase (COX) is a key player in oxidative phosphorylation and reactive oxygen species (ROS) formation. In addition ATPase subunits are also associated with ROS formation and mtDNA maintenance. Here, we specifically searched for differentially expressed ATPase and COX subunits in early adenomas of CRC tissues as compared to late stages of CRC tissues. In addition mitochondria variants were analyzed in mitochondrial encoded subunits of complexes IV and V of the electron transport chain. Direct sequencing, high resolution restriction digestion, RT-qPCR and western blot techniques were used to assess differences in colorectal tumors. Tissue samples used included early adenomas classified as tubular adenoma (TA), tubulovillous adenoma (TV), and villous adenomas (v); cancer tissues, and normal surrounding tissues. Results suggest that most variants of complex IV were found in mitochondrial encoded cytochrome c oxidase subunit III (9207-9990). Of these variants 9414delC found in 60% TA and 20% CA samples was predicted to be disease causing. Furthermore, ATPase6 variant G9055A found abundantly in TA and V samples was confirmed using high resolution restriction digestion. Expression levels of ATPase6 progressively increased from early adenomas to late stage adenomas and cytochrome c oxidase mitochondrial subunits also varied within the adenoma carcinoma sequence. Interestingly, COX subunit 4 isoform 1 protein expression decreased by five-fold in cancer samples when compared to normal tissue and by three-fold when compared to TA. Therefore, this study suggest an important role of ATPase and COX IV-1 in tumor CRC progression in respect to the impact on mitochondrial ROS production and oxidative phosphorylation regulation.

Citation Format: Lashanale Wallace, Anju Cherian, Felix Aikhionbare. Differential expression of MT-ATPase and COXIV genes in colorectal adenopolyps [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2228.
Abstract 2230: Low frequency variant detection in cell free DNA by applying molecular identifiers to targeted NGS
Authors: Wood Ashley , Sandhu Sukhinder , Pezeshkian Mida , Kelchner Vanessa , RoseFigura Jordan , Lenhart Justin , Kurihara Laurie , Makarov Vladimir
Published: August 2018

The growing use of liquid biopsy for early detection and monitoring of disease necessitates accurate variant detection at <1% allele frequencies due to a low population of disease DNA within circulating, cell-free DNA (cfDNA). Reliable, low-frequency variant detection by next-generation sequencing (NGS) is challenging due to background noise from PCR and sequencing errors. We employed molecular identifiers (MIDs) to uniquely label individual DNA molecules prior to amplification, facilitating the distinction of true variants from PCR and sequencing errors. We incorporated MIDs in both our amplicon library prep that uses multiplex PCR for targeted NGS and our whole genome library prep followed by targeting with hybridization capture using an 800kb pan-cancer panel. We performed low frequency spike-in experiments at <1% allele frequencies. We prepared MID libraries with various amplicon panels including a 17 amplicon EGFR pathway panel and a 104 amplicon SNP panel. Deep sequencing to >30,000x was done to maximize MID family size (number of PCR duplicates) and optimize generation of a consensus sequence. This analysis identified all known variants present at 1%, 0.5%, and 0.25% allele frequencies. Next, the hybridization capture libraries were prepared with low-frequency spike-in samples, sequenced to >8000x, and all known variants at 1% and 0.5% allele frequencies were maintained in the consensus data. In both cases, the number of false positives was reduced, resulting in improved specificity. Further, EGFR amplicon libraries and hybridization capture libraries were prepared using cfDNA samples from lung, ovarian, liver, stomach, and colon cancers. Variant calling based on MID generated consensus sequences identified mutations in cfDNA samples as well as corresponding tumor and normal samples when available. This study highlights the ability of MID technology to enable low frequency variant detection, critical to track known variants and identify novel pathogenic mutations in cfDNA samples.

Citation Format: Ashley Wood, Sukhinder Sandhu, Mida Pezeshkian, Vanessa Kelchner, Jordan RoseFigura, Justin Lenhart, Laurie Kurihara, Vladimir Makarov. Low frequency variant detection in cell free DNA by applying molecular identifiers to targeted NGS [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2230.
Abstract 2236: Metformin and pancreatic cancer risk in Taiwanese patients with type 2 diabetes
Authors: Tseng Chin-Hsiao
Published: August 2018

Background: Whether metformin may reduce pancreatic cancer risk is controversial and has rarely been studied in Asian populations. This study evaluated pancreatic cancer risk in type 2 diabetes patients with and without metformin treatment. Methods: An original cohort of 16232 never users and 153408 ever users of metformin who were newly diagnosed of type 2 diabetes between 1999 and 2005 were enrolled from Taiwan's National Health Insurance. A propensity score matched cohort of 16232 ever users and 16232 never users were derived from this original cohort. The patients were followed up until December 31, 2011 and analyses were conducted in both the original cohort and the matched cohort. Hazard ratios were estimated by Cox regression incorporated with the inverse probability of treatment weighting using propensity score. Results: In the original cohort, the incidence rate of pancreatic cancer in never users and ever users were 43.59 and 28.85 per 100000 person-years, respectively, with an overall hazard ratio of 0.658 (95% confidence interval: 0.438-0.988, P=0.0436). While compared to never users, the hazard ratio (95% confidence interval) for cumulative duration of metformin use in the first (<22.10 months), second (22.10-46.70 months) and third tertile (>46.70 months) was 1.445 (0.950-2.196), 0.595 (0.384-0.922) and 0.157 (0.094-0.264), respectively. Results in the matched cohort were very similar, with an overall hazard ratio of 0.492 (0.252-0.961) and the hazard ratio in the respective tertile of cumulative duration was 0.900 (0.368-2.198), 0.648 (0.266-1.581) and 0.094 (0.013-0.692). Conclusions: Metformin significantly reduces pancreatic cancer risk in a dose-response pattern.

Citation Format: Chin-Hsiao Tseng. Metformin and pancreatic cancer risk in Taiwanese patients with type 2 diabetes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2236.
Abstract 2238: Self-microemulsifying drug delivery systems (SMEDDS) containing novel compounds for the chemoprevention of pancreatic cancer
Authors: Desai Preshita , Thakkar Arvind , Wang Jeffrey , Prabhu Sunil
Published: August 2018

Pancreatic cancer (PC) is the fourth leading cause of deaths in the United States, claiming approximately 43,000 lives every year. Existing trends suggest that it will be the second cause of death after lung cancer within the next 20 years. With mortality rates remaining high even after decades of research, scientists are now turning to develop chemopreventive strategies that may stop or delay the initiation and progression of the disease. Our study reports the chemoprevention potential of (1) a free drug combination of H1-receptor antagonist drug with Sulforaphane (SFN), a neutraceutical compound derived from broccoli and (2) lipid nanocarriers of H1-receptor antagonist drug (SP1 SMEDDS; formulation patent pending) with free SFN when administered at low doses in human pancreatic cancer cell lines (MIA PaCa-2 and Panc-1). IC50 concentrations were calculated for various treatment groups using MTS viability assay in accordance with published protocol, using 96-well microplates and incubation time of 72 h. The free drug combination revealed almost 70-fold and 20-fold enhancement in chemoprevention efficacy (based decrease in cancer cell viability) as compared to controls. Interestingly, the free drug combination (at 5µM) showed ~55 % (p<0.001) inhibition in cell lines whereas no measurable response was observed with individual free drug treatments at the same concentration. This confirmed the synergistic chemoprevention potential of the free drug combination. SP1 SMEDDS were optimized for particle size, encapsulation efficiency and chemoprevention efficacy. SP1 SMEDDS (10µM) by itself exhibited 54% (p<0.001) cell line inhibition whereas no measurable response was observed with free drug at that same concentration, confirming the potential of lipid nanocarriers in enhancing the chemoprevention activity. Moreover, the SP1 SMEDDS in combination with free SFN demonstrated synergistic activity with 500-fold, 140-fold and 7-fold enhancement in chemoprevention potential as compared to the free HI-receptor antagonist, SFN and the free drug combination, respectively. In conclusion, a novel lipid formulation of an H1-receptor antagonist in combination with free SFN was invented (provisional patent applied) to successfully elicit PC chemoprevention. Future studies will look into the efficacy of this novel formulation in in vivo PC models.

Citation Format: Preshita Desai, Arvind Thakkar, Jeffrey Wang, Sunil Prabhu. Self-microemulsifying drug delivery systems (SMEDDS) containing novel compounds for the chemoprevention of pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2238.
Abstract 2239: Is folic acid safe for non-muscle-invasive bladder cancer patients? An evidence-based cohort study
Authors: Tu Huakang , Dinney Colin P. , Ye Yuanqing , Grossman Barton H. , Lerner Seth P. , Wu Xifeng
Published: August 2018

Background: Cancer patients are highly concerned about food choices and dietary supplements that may affect their treatment outcomes. Excess folic acid (synthetic folate) from supplements or fortification can lead to accumulation of unmetabolized folic acid in the systemic circulation and urine, and may promote cancer growth, especially among those with neoplastic alterations.

Objective: We investigated the prospective association between synthetic versus natural folate intake and clinical outcomes in non-muscle-invasive bladder cancer (NMIBC), which is a highly recurrent disease.

Design: In a cohort of 619 NMIBC patients, folate intake at diagnosis was assessed with a previously validated food frequency questionnaire and categorized according to tertiles. After a median follow-up of 5.2 years, 303 tumor recurrence and 108 progression events were documented from medical record review. Multivariable Cox proportional hazards and logistic models were used to estimate adjusted hazard ratios (HR) and odds ratios (OR) with 95% confidence intervals (95% CI).

Results: Synthetic folic acid intake was positively associated with risk of recurrence among NMIBC patients (medium vs. low intake: HR=1.72; 95% CI=1.20, 2.48; P=0.003; high vs. low intake: HR=1.80; 95% CI=1.14, 2.84; P=0.01). Patients with higher folic acid intake were more likely to have multifocal tumors at diagnosis (medium/high vs. low: OR=2.08; 95% CI=1.08, 4.02; P=0.03). In contrast, natural folate intake tended to be inversely associated with risk of progression (medium/high vs. low: HR=0.68; 95% CI=0.44, 1.04; P=0.08).

Conclusions: High intake of synthetic folic acid, in contrast to the natural forms, is associated with increased risk of recurrence in NMIBC and multifocal tumors at diagnosis, suggesting that folic acid may be unsafe for NMIBC patients. These findings provide some evidence for nutritional consultation regarding folate intake among NMIBC patients.

Citation Format: Huakang Tu, Colin P. Dinney, Yuanqing Ye, Barton H. Grossman, Seth P. Lerner, Xifeng Wu. Is folic acid safe for non-muscle-invasive bladder cancer patients? An evidence-based cohort study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2239.
Abstract 2258: Chromothripsis and survival in human malignancies
Authors: Mansfield Aaron S. , Garcia-Rivera Enrique
Published: August 2018

Chromothripsis is a complex genomic event characterized by a high number of chromosomal rearrangements and copy number changes that typically localize to a specific region on a single chromosome. Next generation sequencing has led to the initial discovery and description of these events which have since been observed in multiple human cancers. Whereas most mutagenic processes occur gradually, the multiple structural variations of each chromothriptic event likely occur at once. The clinical significance of chromothripsis remains uncertain, so we sought to characterize the relationship between chromothripsis and survival across human malignancies.

We analyzed 13,318 tumors of 36 types using publicly available data from The Cancer Genome Atlas with CTLPScanner, which uses a sliding window scan statistic to identify events consistent with a chromothripsis-like pattern (CTLP). Our cutoffs for CTLP of copy number variation ≥ 20 and a log10 likelihood ratio ≥ 8 were derived from a clinical training set previously described by CTLPScanner.

We detected one or more events consistent with a CTLP in 8,276 tumors (62.1%) for a total 24,879 events. There were no events in 5,042 cases (37.86%), a significant decrease from established rates of CTLPs. CTLPs were more common in ovarian serous cystadenocarcinomas (89.8%), esophageal carcinomas (86.5%) and sarcomas (81.2%) than in thymomas (26.6%) and thyroid carcinomas (15.2%). Chromosomes 8, 1 and 6 were most frequently involved with CTLPs. CTLPs in chromosome 6 were associated with uveal melanoma, chromophobic renal cell carcinoma and cholangiocarcinomas whereas CTLPs involving chromosome 12 were associated with testicular germ cell tumors. Multiple CTLPs were found in 5,262 tumors (39.5%, range of events 2-18+) and were most common in ovarian serous cystadenocarcinomas and sarcomas. The presence of CTLPs was associated with diminished overall survival across all tumor types (HR 1.5, p<2e-16). Given the potential for multiple CTLPs to have a greater effect on outcomes, we compared the survival of patients whose tumors contained 3 or more CTLPs (n=3,255, 24.4%) to those with 0-1 or 2 CTLPs. The presence of 3 or more CTLPs was associated with the worst survival amongst these groups (HR 1.67, p<2e-16).

We identified that CTLPs are common in human cancers despite their prior descriptions as rare events. This discrepancy is likely due to our detection parameters. In addition, we identified that having multiple co-occurring CTLPs is associated with a worse prognosis, suggesting this type of event is more clinically relevant than a single CTLP and can be used as a negative prognostic marker in human malignancies.

Citation Format: Aaron S. Mansfield, Enrique Garcia-Rivera. Chromothripsis and survival in human malignancies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2258.
Abstract 2262: Inference of kinase activity for cancer phosphoproteomics using substrate prediction scores
Authors: Liao Peter , Yori Jennifer , Keri Ruth , Koyuturk Mehmet , Barnholtz-Sloan Jill
Published: August 2018

Background: Quantification of global protein phosphorylation abundance levels with residue-level resolution is feasible with mass spectrometry and phosphopeptide enrichment methods. Researchers have inferred kinase activity from phosphoproteomics data using a variety of methods to extract interpretable and biologically relevant information, but analysis of phosphoproteomics data is limited by the fact that detected phosphorylation sites often have unknown function and relevance.

Methods: We developed a novel method for aggregating and interpreting phosphoproteomics data that combines kinase prediction scores from NetworKIN with experimental summary statistics to estimate abundance changes in predicted kinase substrates. By weighting student t-statistic scores by kinase prediction scores and summing cumulative scores across all phosphopeptides detected in a given screen, we generated kinase activity scores that reflect the overall direction, magnitude and significance of observed changes in predicted kinase substrates. These kinase scores were assessed using permutation testing to determine their significance versus changes that would be expected from random chance. To evaluate our method, we applied it to a shotgun phosphoproteomic dataset generated to study phosphorylation responses to rapamycin, dasatinib and combination treatment in MDA-MB-231 breast cancer cells.

Results: We were able to confirm phosphoproteomic perturbations in expected “hallmark” kinase activities using prediction-based kinase activity inference scores, including decreased phosphorylation of Src and Abl substrates in response to dasatinib treatment, as well as decreases in p70S6K substrate phosphorylation in response to rapamycin. Compared to KSEA, we identified changes in substrate abundance for a variety of potential downstream kinases including DNAPK, PAK2, CDK3, and multiple members of the MAPK family that were observed to be downregulated in single-agent and in combination treatment.

Conclusions: Our novel method provides a representation of phosphoproteomic changes based on abundance of predicted kinase substrates. Using predicted substrates allows for a global view of phosphoproteomic changes that extends beyond the relatively small number of known kinase-substrate relationships. Using a drug combination with potential application in breast cancer as an example, we demonstrate that this method can be used to identify phosphoproteomic changes and can potentially be used to rationally design and investigate novel drug combinations.

Citation Format: Peter Liao, Jennifer Yori, Ruth Keri, Mehmet Koyuturk, Jill Barnholtz-Sloan. Inference of kinase activity for cancer phosphoproteomics using substrate prediction scores [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2262.
Abstract 2265: viSNE in Cytobank enables rapid exploratory data analysis for RNA-seq biomarker discovery
Authors: Sethi Ashu , Polikowsky Hannah , Drake Katherine A.
Published: August 2018

Biomarkers provide great potential for understanding and predicting patient outcomes. However, the large numbers of putative biomarkers assayed by many discovery technologies can be difficult to parse quickly to understand their potential as predictors of an outcome of interest. viSNE is a non-linear dimensionality reduction algorithm available on the Cytobank informatics platform that can rapidly assess whether a set of biomarkers can meaningfully group samples. We establish a method for applying viSNE to RNA-seq data. We demonstrate this method using data from The Cancer Genome Atlas for 1,011 samples from 5 different types of kidney cancer and matched normal tissue samples for 139 of the subjects. The tumors ranged from stage I to stage IV, and subjects varied by age, gender, and whether they were living when the sample was taken. Using FPKM data from the 806 most variable transcripts in these samples, viSNE was able to group the samples into six distinct “islands” that separated cancer samples from each of the five disease types and the matched normal tissue. We demonstrate that viSNE is robust to noise and is able to group the samples even when variables that do not contribute to the signal are present in the data, and illustrate how this can be leveraged as part of a larger biomarker discovery workflow with RNA-seq and other data types. viSNE allows rapid exploratory data analysis that helps to build understanding of correlations between biomarkers and patient outcomes and improve overall time-to-results in biomarker discovery pipelines.

Citation Format: Ashu Sethi, Hannah Polikowsky, Katherine A. Drake. viSNE in Cytobank enables rapid exploratory data analysis for RNA-seq biomarker discovery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2265.
Abstract 2268: Differential splicing analysis of doxorubicin treatment response in cancer cells
Authors: Simpson Edward , Liu Yunlong
Published: August 2018

Background:Splicing of transcripts is an important epigenetic control mechanism that significantly influences expression of protein isoforms in a cell. Alternative splicing is known to contribute to development and progression of cancer, however the impact of cellular splicing profiles on cancer drug response has been largely unexplored. In this study, we integrated two large public data sets and report findings on the basal splicing profiles between doxorubicin treated sensitive and resistant cancer cell lines. We introduced a new method to analyze of splicing data using the quasi-binomial distribution that is incredibly simple, powerful and well suited for comparison of large groups of samples. We also identified exons whose inclusion or exclusion level is likely to be damaging to intended gene products. Finally, we performed RNA-binding protein motif enrichment at these identified exons to characterize proteins that may play a role in their regulation.

Methods:Drug response data from the Cancer Therapeutic Response Portal (CTRP) was integrated with RNAseq data from the Cancer Cell Line Encyclopedia (CCLE). AUC values from drug-response time curves in CTRP were used to classify cells as either doxorubicin sensitive, intermediate or resistant. The upper and lower tertiles provided a total of 253 sensitive and 258 resistant cell lines respectively. Splice junction read counts for skipped-exon events were calculated using the matched cell line data from CCLE. Response groups were then used to train a generalized linear model with quasi-binomial family. Results were filtered by group weight significance at an FDR of <=0.01. The remaining events were again filtered for >=10% difference in mean exon inclusion ratio.

Results:In total we identified 277 differentially spliced events between doxorubicin sensitive and resistant groups. When performing GO term over-representation our results demonstrated significantly enriched biological processes supporting the role of alternative splicing in EMT and cellular differentiation. This further confirms previous studies linking alternative splicing to these cancer hallmarks, suggesting that splicing may facilitate acquired drug resistance through survival mechanisms similar to those seen in cancer stem cells.

Citation Format: Edward Simpson, Yunlong Liu. Differential splicing analysis of doxorubicin treatment response in cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2268.
Abstract 2269: Transcription factor relationships associated with androgen-deprivation therapy response and metastatic progression in prostate cancer
Authors: Sharma Nitya V. , Pellegrini Kathryn L. , Ouellet Veronique , Giuste Felipe O. , Ramalingam Selvi , Watanabe Kenneth , Adam-Granger Eloise , Fossouo Lucresse , You Sungyong , Freeman Michael R. , Vertino Paula , Conneely Karen , Osunkoya Adeboye O. , Trudel Dominique , Mes-Masson Anne-Marie , Petros John A. , Saad Fred , Moreno Carlos S.
Published: August 2018

Patients with recurrent, aggressive prostate cancer typically undergo androgen-deprivation therapy (ADT), but the benefits are often short-lived, and responses are variable. Failure to respond to ADT invariably leads to metastatic disease, and ultimately death. To investigate differential responses to ADT, we performed whole-transcriptome analysis of 20 patient-matched pre-ADT biopsies and post-ADT prostatectomy specimens, and observed that all patients lost transcriptional signatures indicative of the androgen receptor (AR)-dependent subtype, after treatment. We also identified two subgroups of patients with either a strong or weak transcriptional response to ADT. The strong responders maintained the more aggressive subtype signal, while the weak responders lost expression of these genes and more resembled an AR-suppressed, basal subtype. We generated a strong responder transcriptional network using the PANDA program and integrated expression data from our cohort, protein-protein interaction, and DNA binding motif data. We also leveraged the expression data from a large public dataset of over 800 metastatic and primary samples to construct a metastatic lesion transcriptional network. We identified 20 common transcription factor coordinated groups (TFCGs) associated with both the strong responders and metastatic lesions, including GLI3/GLI2, SOX4/FOXA2/GATA4, ERF/ETV5/ETV3/ELF4, and a TFCG containing JUN, JUNB, JUND, FOS, FOSB, and FOSL1. Many TFCGs in the metastatic network were subsets of larger groups in the strong responders network, implicating these transcription factor associations as potentially critical for both the differential ADT response and metastatic disease progression.

Citation Format: Nitya V. Sharma, Kathryn L. Pellegrini, Veronique Ouellet, Felipe O. Giuste, Selvi Ramalingam, Kenneth Watanabe, Eloise Adam-Granger, Lucresse Fossouo, Sungyong You, Michael R. Freeman, Paula Vertino, Karen Conneely, Adeboye O. Osunkoya, Dominique Trudel, Anne-Marie Mes-Masson, John A. Petros, Fred Saad, Carlos S. Moreno. Transcription factor relationships associated with androgen-deprivation therapy response and metastatic progression in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2269.
Abstract 2279: The GenePattern Notebook environment for reproducible cancer research
Authors: Reich Michael M. , Tabor Thorin T. , Liefeld Ted , Hill Barbara , Thorvaldsdottir Helga , Mesirov Jill P.
Published: August 2018

As the availability of genetic and genomic data and analysis tools from large-scale cancer initiatives continues to increase, the need has become more urgent for a software environment that supports the entire “idea to dissemination” cycle of an integrative cancer genomics analysis. Such a system would need to provide access to a large number of analysis tools without the need for programming, be sufficiently flexible to accommodate the practices of non-programming biologists as well as experienced bioinformaticians, and would provide a way for researchers to encapsulate their work into a single “executable document” including not only the analytical workflow but also the associated descriptive text, graphics, and supporting research. To address these needs, we have developed GenePattern Notebook, based on the GenePattern environment for integrative genomics and the Jupyter Notebook system. GenePattern Notebook unites the phases of in silico research - experiment design, analysis, and publication - into a single interface.

GenePattern Notebook presents a familiar lab notebook format that allows researchers to build a record of their work by creating “cells” containing text, graphics, and executable analyses. Researchers add, delete, and modify cells as the research evolves, supporting the initial research phases of prototyping and collaborative analysis. When an analysis is ready for publication, the same document that was used in the design and analysis phases becomes a research narrative that interleaves text, graphics, data, and executable analyses. The online notebook format allows researchers to explain the analytical and scientific considerations of each step in any level of detail, promoting reproducibility and adoption. Notebooks can also be shared between researchers for collaborative development.

GenePattern Notebook features are designed to help nonprogramming users create and adapt notebooks. We have developed additional cell types allowing users to choose analyses, specify inputs, navigate results, send result files to new analyses, and create richly formatted text, all without the need for programming.

A free online GenePattern Notebook workspace is available at http://www.genepattern-notebook.org, where researchers can develop, share, and publish notebook documents. We have provided a collection of template notebooks that walk users through various genomic and machine learning analyses, and are collaborating with cancer research laboratories to create integrative cancer genomics notebooks.

Citation Format: Michael M. Reich, Thorin T. Tabor, Ted Liefeld, Barbara Hill, Helga Thorvaldsdottir, Jill P. Mesirov. The GenePattern Notebook environment for reproducible cancer research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2279.