bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4213: Stool-derived eukaryotic RNA (seRNA) assay for noninvasive detection of colorectal cancer and high-risk adenomas
Authors: Barnell Erica K. , Kang Yiming , Campbell Katie M. , Kruse Kimberly R. , Barnell Andrew R. , Wurtzler Elizabeth M.
Published: August 2019

Colorectal cancer (CRC) is the second leading cause of cancer related deaths in the United States. The high mortality rate for CRC is largely attributable to the frequency of late-stage diagnoses, caused by low patient compliance with screening guidelines. A novel nucleic acid extraction method that isolates stool-derived eukaryotic RNA (seRNA) has permitted development of a colorectal cancer stool diagnostic test (CRC-SDT) that uses a fecal immunochemical test (FIT) and 11 seRNA transcripts to serve as a reliable and noninvasive screening alternative to lower mortality associated with CRC. Stool samples were obtained from 190 individuals prior to undergoing a screening colonoscopy. Patients were diagnosed as either having colorectal cancer, having high-risk adenomas (high-grade dysplasia, villous growth pattern, or >1.0cm in size), or healthy (low-risk adenomas, benign polyps, and/or no findings on a colonoscopy). FITs were obtained for each sample. Samples that had a positive FIT were considered positive for the CRC-SDT. Samples that had a negative FIT underwent seRNA isolation, library preparation (Illumina TruSeq Targeted RNA) and subsequent sequencing (Illumina NextSeq 550). A random forest model was built using 11 transcripts that were differentially expressed (log2 fold-change > 1; ANOVA p < 0.05) between diseased patients (CRC and high-risk adenomas) relative to the healthy cohort. Internal 10-fold cross-validation was performed for the training set and a receiver operating characteristic (ROC) area under the curve (AUC) determined model accuracy for cancer and high-risk adenomas relative to the healthy cohort. Model predictions for an independent hold-out test set were used to determine model accuracy for colorectal cancer and high-risk adenomas. Internal cross-validation for 154 samples attained a ROC AUC of 0.82. The trained model was employed on the independent hold-out test set of 36 samples and model predictions were compared to colonoscopy results. The model attained a 100% sensitivity for CRC (n = 7), a 60% sensitivity for high-risk adenomas (n = 5), and an 88% combined specificity for the healthy cohort (n = 24). CRC-SDT uses 12 biomarkers (FIT and expression from 11 seRNA transcripts) to accurately detect CRC and high-risk adenomas. Use of seRNA biomarkers dramatically improves detection of high-risk adenomas relative to existing noninvasive screening methods for CRC.

Citation Format: Erica K. Barnell, Yiming Kang, Katie M. Campbell, Kimberly R. Kruse, Andrew R. Barnell, Elizabeth M. Wurtzler. Stool-derived eukaryotic RNA (seRNA) assay for noninvasive detection of colorectal cancer and high-risk adenomas [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 4213.
Abstract 4216: The microbiota associated to cervical and anal HPV infections in a Hispanic population
Authors: Vázquez-Sánchez Frances , Ortiz Gilmary , Ortiz Ana P. , Godoy-Vitorino Filipa
Published: August 2019

Anogenital human papillomavirus (HPV) are the world’s most commonly diagnosed sexually transmitted infections and high-risk types are linked to dysplasia. Susceptibility to HPV infections is related to the microbial communities of these genital surfaces, which are interfaces between the host and environment. Microbes are a predicted cause of malignancies, revealing a tremendous potential of microbiome-related processes for cancer prevention and diagnostics. The cervix and anus share a susceptible transformation zone, characterized by a metaplastic epithelial site. In fact, in women, anal and cervical squamous intraepithelial lesions tend to occur concurrently, an observation that could be explained by the fact that anal and cervical HPV infections are strongly correlated. We hypothesized that bacterial communities may differ in the anus and cervix and may reveal populations associated to HPV infections in these two body sites. To test this hypothesis we characterized the microbiota of a cross-sectional population-based sample of Puerto Rican women (self-sampled) from the San Juan metropolitan (n=300 samples) and related them to anogenital HPV infections (HPV typing performed by PCR). The microbiota of resident cervical and anal bacterial communities was performed through sequencing of the 16S ribosomal RNA V4 region with the Illumina platform. Data was analyzed at first with QIIta, using the SILVA database as taxonomic reference, and community analyses were performed in QIIME and R. Significant differences in community structure (betadiversity) were found between cervical and anal communities (p-value = 0.001), but not according to HPV (p-value = 0.212) in any of the body sites. Indeed, overall anal communities were dominated by OTUs within Prevotella, Bacteroides and Clostridiales, while cervical samples were dominated by Lactobacillus and Bifidobacteraceae (Gardnerella). Despite the common core communities at each body site, cervical samples of HPV positive patients revealed an enrichment of Ureaplasma and Prevotella while Peptinophilus was associated with anal HPV infections. Although more analyses are needed, our data suggests cervical and anal bacteria are associated to HPV infections which could pave the way to the development of early detection methods or novel probiotics for in women living in Puerto Rico.

Citation Format: Frances Vázquez-Sánchez, Gilmary Ortiz, Ana P. Ortiz, Filipa Godoy-Vitorino. The microbiota associated to cervical and anal HPV infections in a Hispanic population [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 4216.
Abstract 4221: Development and evaluation of cell line-derived FFPE reference material for MSI assay validation
Authors: Matsusaka Takahiro , Surmann Eva-Maria , Constantine Sian , Child Hannah , Wickenden Julie
Published: August 2019

Microsatellite Instability (MSI) is defined by variance in the repeat count of microsatellite motifs and occurs in cells that are deficient in one or more mismatch repair proteins. MSI is present in varying cancer types, but is most commonly found in colorectal, gastric and endometrial cancer. Patients with early stage colorectal cancers that display MSI have a better prognosis and show a better response to chemotherapy compared to those with microsatellite stable tumors. MSI alongside additional markers such as tumor mutational burden is also a positive predictive biomarker for immune checkpoint inhibition Identification of MSI tumors in the diagnostic laboratory is traditionally performed by fluorescent multiplex PCR, evaluating the microsatellite length of two mononucleotide repeats and three dinucleotide repeats (recommended NCI Panel) or a commercially available kit, consisting of five mononucleotide markers alongside IHC staining for the four MMR proteins MSH2, MSH6, MLH1, and PMS2. With the increase in MSI testing related to the recent FDA approval of Keytruda®, several companies and laboratories are now developing newer and better PCR-based and next-generation sequencing assays to assess MSI. To control for error, we have developed a pair of cell line-derived MSI/MSS reference samples covering the most commonly used MSI biomarkers. MSI/MSS cell lines were mixed at biologically-relevant ratios and processed into FFPE to serve as a whole-process control. Our data support the suitability of this material on a variety of different platforms and with a high degree of consistency throughout various FFPE batches. In conclusion, our cell line-derived reference samples represent a commutable control to support MSI assay development and validation.

Citation Format: Takahiro Matsusaka, Eva-Maria Surmann, Sian Constantine, Hannah Child, Julie Wickenden. Development and evaluation of cell line-derived FFPE reference material for MSI assay validation [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 4221.
Abstract 4222: Omega-3 fatty acids produce DNA methylation changes in inflammation-related genes and pathways with implication of toll-like receptor signaling
Authors: Frankhouser David E. , Woelke Sarah , Sovic Michael , Bundschuh Ralf , Yan Pearlly , Yee Lisa D.
Published: August 2019

Introduction Omega-3 polyunsaturated fatty acids (n-3 PUFA) have been studied for potential health benefits in many diseases including breast cancer. The preventive effects of n-3 PUFAs may relate in part to inhibition of chronic, low-grade inflammation. Of interest is the role of n-3 PUFAs in modulating pro-inflammatory gene expression via epigenetic factors such as DNA methylation (DNAm).

Methods DNA methylation of PBMCs obtained at 0 and 6 months of n-3 PUFA supplementation was assessed via reduced representation bisulfite sequencing (RRBS). PBMC samples were obtained from women at high risk for breast cancer during a randomized clinical trial investigating the effects of different n-3 PUFA doses. The dosing arm selected for this study was 5 g of EPA+DHA/day, with baseline and 6 month samples (n=10). DNAm was quantified using Bismark from trimmed, pass filter reads and analyzed with MethylKit to determine n-3 PUFA treatment specific DNAm changes.

Results Global DNAm showed no change after 6 months of n-3 PUFA treatment; however, we detected 30,974 differentially methylated CpGs (DMCs) across the genome. DMCs, both genome-wide and in gene promoters, where DNAm can regulate gene expression, were significantly enriched for hypermethylation events after treatment. Focusing the analysis on pro-inflammatory signaling mediators led to identification of candidate gene promoter DMCs involved in several inflammation-related pathways. Four pathways were significantly enriched for both DMCs and DMC hypermethylation events even when accounting for the genome-wide trend toward hypermethylated DMCs (hypergeometric test p-value < 0.001). The Toll-Like Receptor Pathway (TLR) genes harbored the most DNAm changes post n-3 PUFA treatment.

Conclusion Our findings demonstrate that n-3 PUFA supplementation can result in inflammation-related changes stemming from PBMC methylome perturbation. The results suggest the TLR pathway as a potential mechanism for the anti-inflammatory effects of EPA and DHA. Functional studies are needed to confirm our current observation.

Citation Format: David E. Frankhouser, Sarah Woelke, Michael Sovic, Ralf Bundschuh, Pearlly Yan, Lisa D. Yee. Omega-3 fatty acids produce DNA methylation changes in inflammation-related genes and pathways with implication of toll-like receptor signaling [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 4222.
Abstract 4224: SGLT2 is a diagnostic target for early stage lung adenocarcinoma
Authors: Villegas Brendon , Koziolek Eva , Liu Jie , Wallace W. Dean , Elashoff David , Aberle Denise R. , Shackelford David B. , Barrio Jorge R. , Yanagawa Jane , Dubinett Steven M. , Scafoglio Claudio
Published: August 2019

Lung cancer is the leading cause of cancer-related death, and lung adenocarcinoma (LUAD) is the most frequent histology. Early diagnosis and treatment are essential; however, there are no targeted diagnostic and therapeutic approaches for early LUAD. An important hallmark of cancer is the increased glucose uptake via GLUT transporters. GLUT activity is imaged in cancer by positron emission tomography (PET) with 2-[18F] fluorodeoxyglucose (FDG). FDG PET is a standard tool for staging advanced lung cancer, but has low sensitivity for early-stage LUAD. This is considered a consequence of slow growth and low requirement of glucose. However, we discovered a novel system of metabolic supply not detected by FDG PET: the sodium glucose transporter 2 (SGLT2)1. SGLT2 activity can be measured in vivo with the PET tracer methyl-4-[18F] fluorodeoxyglucose (Me4FDG). We identified high expression of SGLT2 in human lung premalignancy and early-stage LUAD. Me4FDG detects early-stage, FDG-negative LUAD in mouse models. Targeting SGLT2 with FDA-approved inhibitors significantly reduces tumor growth and prolongs survival in genetic and patient-derived murine models, confirming an important role of SGLT2 in early-stage LUAD2. The reliance of early stage LUAD on SGLT2 opens exciting diagnostic and therapeutic opportunities. The National Lung Screening Trial showed a 20% reduction in lung cancer mortality in high risk individuals using low-dose helical computed tomography (CT). CT is highly sensitive for detecting lung nodules, but is limited by low specificity, especially for LUAD. On CT, LUAD may appear as solid or subsolid nodules. Most subsolid nodules are not cancer, and many will remain stable or resolve; however, subsolid lesions can represent premalignant lesions or adenocarcinoma in situ. These lesions in the early spectrum of LUAD may persist for months to years before transforming into invasive disease. As a result, current standard of care is to follow these patients with CT imaging to monitor these indeterminate lesions for radiologic signs of malignant progression. The identification of novel biomarkers to predict the malignant potential of these nodules at their initial identification is of paramount importance. 1Scafoglio et al. Proc Natl Acad Sci U S A 2015;112(30):E4111-4119 2Scafoglio et al. Sci. Transl. Med. 10, eaat5933 (2018)

Citation Format: Brendon Villegas, Eva Koziolek, Jie Liu, W. Dean Wallace, David Elashoff, Denise R. Aberle, David B. Shackelford, Jorge R. Barrio, Jane Yanagawa, Steven M. Dubinett, Claudio Scafoglio. SGLT2 is a diagnostic target for early stage lung adenocarcinoma [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 4224.
Abstract 4225: Is biomarker-driven precision medicine possible by using high dimensional augmented intelligence assisted analysis of cancer immune responses
Authors: Krieg Carsten , Cardenas Luis , Guglietta Silvia , Wrangle John , Rubinstein Mark , Robinson Mark
Published: August 2019

Checkpoint inhibitors have significantly accelerated cancer treatment but still a majority of patients do not respond. Biomarker driven patient stratification early to the right immunotherapeutic might enhance response and patient survival. Here we used high-dimensional mass cytometry (CyTOF) combined with machine-learning bioinformatics for the in-depth characterization of immune responses before and during anti-PD-1 immunotherapy. CyTOF allows us to monitor protein expression of 34 markers on a single cell while running 20 samples simultaneously. The analysis is data driven, can be adapted to high throughput approaches and can model arbitrary trial designs such as batch effects and paired designs and is quantitative over millions of events. Using CyTOF as a precision medicine tool we could predict response to anti-PD-1 using liquid blood biopsies. Biobanked peripheral blood mononuclear cells (PBMCs) from 51 patients with stage IV melanoma before and after 12 weeks of anti-PD-1 therapy was analyzed. We observed a clear T cell response on therapy. The most evident difference in responders before therapy was an enhanced frequency of CD14+ CD16+HLA-DRhi classical monocytes. We validated our results using conventional flow and found a clear correlation of enhanced monocyte frequencies before therapy initiation with clinical response such as lower hazard and extended progression-free and overall survival. In a second study we used CyTOF to monitor immune response in 21 non small cell lung cancer (NSCLC) patients that initially responded and then progressed under anti-PD-1 to a novel combination immunotherapy of anti-PD-1 plus an IL-15 super-agonist (ALT-803). In this phase Ib clinical study a response in the CD8+ T cell compartment was observed. Unexpected our high dimensional unbiased analysis was able to detect and characterize a strong expansion of innate tumor-reactive effector NK cells starting around day 4 of therapy. Taken together, our unbiased artificial intelligence driven immune workflow might support patient selection prior to therapy, and serve as a novel tool for precision medicine to select the right drug combination and identify new drug-able cell populations.

Citation Format: Carsten Krieg, Luis Cardenas, Silvia Guglietta, John Wrangle, Mark Rubinstein, Mark Robinson. Is biomarker-driven precision medicine possible by using high dimensional augmented intelligence assisted analysis of cancer immune responses [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 4225.
Abstract 4244: Novel expressed long non-coding RNAs in uveal melanoma
Authors: Rodriguez Daniel A. , Kuznetsov Jeffim N. , Sanchez Margaret I. , Kurtenbach Stefan , Harbour J. William
Published: August 2019

Uveal melanoma (UM) is a highly aggressive eye cancer that leads to metastatic death in up to half of patients. UMs can be divided into two prognostic groups based on their gene expression profile (GEP). The class 1 GEP is associated with low metastatic risk and the class 2 GEP with high metastatic risk. Class 1 tumors are associated with EIF1AX or SF3B1 mutations while Class 2 tumors are associated with inactivating mutations in the tumor suppressor BAP1. Class 1 and Class 2 UMs have been shown to differ in their expression of numerous known micro-RNAs and long non-coding RNAs (lncRNA). Here, we sought to identify novel differentially expressed lncRNAs using a publicly available RNA-Seq database. Raw RNA-Seq fastq files from 80 TCGA UM samples were obtained from the Cancer Genomics Hub (CGHub), quality controlled using FastQC (v0.11.3), and trimmed using trim-galor (v0.4.1). Sequences were aligned to the human genome (GRCh38) and accompanying general transfer format file (gtf) (Gencode v28) using STAR (v2.5). Transcript discovery was performed using Cufflinks (v2.2.1). Protein coding probability was calculated using CPC (v2.0), and transcripts predicted to be non-coding with transcript length >200bps were retained. 1671 novel transcripts were added to the gtf file, and fastq files were realigned with the new annotation. Estimated counts for all known and novel transcripts were generated using RSEM (v1.3.0) after STAR alignment. A cutoff of RPKM > 1 in at least 35% of tumors was used as a threshold for transcripts of interest, resulting in 61 novel transcripts, 32 of which were differentially expressed at FDR < 0.05 between Class 1 and Class 2 tumors, including 7 upregulated and 25 downregulated in Class 2 tumors. Further work is underway to elucidate the function of these novel transcripts in UM pathogenesis.

Citation Format: Daniel A. Rodriguez, Jeffim N. Kuznetsov, Margaret I. Sanchez, Stefan Kurtenbach, J. William Harbour. Novel expressed long non-coding RNAs in uveal 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 4244.
Abstract 4259: Defining subtle cancer subtypes using the darkest DNA
Authors: Parida Laxmi , Haferlach Claudia , Rhrissorrakrai Kahn , Utro Filippo , Levovitz Chaya , Wolfgang Kern , Nadarajah Niroshan , Hutter Stephan , Meggendorfer Manja , Walter Wencke , Baer Constance , Haferlach Torsten
Published: August 2019

The confluence of deep sequencing and powerful machine learning is providing an unprecedented peek at the darkest of the dark genomic matter. While deep sequencing uncovers rare tumor variants, the heterogeneity of the disease confounds the best of machine learning (ML) algorithms. Here we set out to answer if the dark-matter of the genome encompass signals that can classify the fine subtypes of disease that are otherwise gnomically indistinguishable. We introduce a novel stochastic regularization, ReVeal, that empowers ML to classify subtle cancer subtypes even from the same ‘cell of origin’. Analogous to heritability, implicitly defined on whole genome, we use predictability (F1 score) definable on portions of the genome. In an effort to classify cancer subtypes using dark-matter DNA, we applied ReVeal to a new WGS dataset from 727 patient samples with seven forms of hematological cancers and assessed the predictivity over several genomic regions including genic, non-dark, non-coding, non-genic, dark. ReVeal allowed the classification of all segments of the genome better than standard ML algorithms. The non-genic, non-coding and the dark-matter had the highest F1 scores with dark-matter having the highest level of predictability (F1 = 0.78). Based on ReVeal’s predictability of different sectors of the genome, dark matter contains signal significant enough to classify fine subtypes of disease. The agglomeration of rare variants, even in the hitherto unannotated and ill-understood regions of the genome, may play a substantial role in the disease etiology and deserve much more attention.

Citation Format: Laxmi Parida, Claudia Haferlach, Kahn Rhrissorrakrai, Filippo Utro, Chaya Levovitz, Kern Wolfgang, Niroshan Nadarajah, Stephan Hutter, Manja Meggendorfer, Wencke Walter, Constance Baer, Torsten Haferlach. Defining subtle cancer subtypes using the darkest DNA [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 4259.
Abstract 4276: Inhibition of USP14 decrease tumorigenesis via autophagy in lung cancer
Authors: PARK MINSOO , Kim Min Ji , Lee Peter Chang Whan
Published: August 2019

The ubiquitin proteasome system (UPS) is the primary pathway through which the levels of regulatory proteins are controlled. Dysregulation of components within the UPS have been linked to both hereditary and sporadic forms of cancer. The deubiquitinating enzyme USP14 is associated with proteasome where it is trimming ubiquitin chain on the substrate. In our current study, we unexpectedly found that USP14 levels were elevated in lung cancer patients. USP14 inhibitor, IU1-47 and siUSP14, significantly decreased cell proliferation, migration, and invasiveness in lung cancer cells. Inhibition of USP14 induced the alteration of LC3-I to LC3-II which leads to autophagic cell death not but apoptosis. Thus our finding suggests that USP14 plays a crucial role in tumorigenesis and USP 14 inhibitor is a potent drug for lung cancer treatment.

Citation Format: MINSOO PARK, Min Ji Kim, Peter Chang Whan Lee. Inhibition of USP14 decrease tumorigenesis via autophagy in 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 4276.
Abstract 4303: TanshinoneIIA, an isolated compound from Salvia miltiorrhiza, inhibits cell growth in colorectal cancer via activation of p38MAPK signaling pathway
Authors: Wang Yan , Zhou Lihong , Ji Qing , Sui Hua , Hu Xueqing , Cai Gang , Li Qi
Published: August 2019

Tanshinone IIA (TSIIA) is an active ingredient extracted from the root of Danshen (Salvia miltiorrhiza Bunge), a Chinese traditional herb. Recent studies have indicated that TSIIA is a natural anti-tumor agent, however, the underlying mechanisms remain largely unknown. We studied the anti-tumor efficacy of TSIIA on human colon cancer cell lines in vitro and in vivo, and have further demonstrated that the molecular anti-cancer property of TanIIA is dependent on its inhibition of proliferation and induction of apoptotic cell death via p38MAPK signaling pathway.

The results indicated that TanIIA were markedly more effective than control group in preventing tumor growth and increasing survival time. This phenomenon was accompanied by a decrease in cell growth in a concentration- and time-dependent manner. Hoechst 33258 stainning showed an increased number of apoptotic bodies in the cells after treatment with TanIIA. Flow cytometry analysis showed TanIIA could cause an obvious colon cacer cell apoptosis and arrest cells in the G0/G1 phase. After p38MAPK signaling pathway was blocked, the cell apoptotic rates and cell ratio of G0/G1 phase were decreased significantly. In addition, TanIIA increased p38MAPK phosphorylation, and up-regulated the protein expression of ATF-2, The ATF-2 expression was found to be significantly decreased in cells treated with p38MAPK-specific inhibitor. From our results, it is speculated that TanIIA may induce human colon cancer cells apoptosis and arrest cells in the G0/G1 phase involve up-regulation the expression of the ATF-2 mRNA via p38MAPK signal transduction pathway.

Note: This abstract was not presented at the meeting.

Citation Format: Yan Wang, Lihong Zhou, Qing Ji, Hua Sui, Xueqing Hu, Gang Cai, Qi Li. TanshinoneIIA, an isolated compound from Salvia miltiorrhiza, inhibits cell growth in colorectal cancer via activation of p38MAPK signaling pathway [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 4303.
Abstract 4304: Anti-proliferative activity of nodosin is associated with the regulation of wnt signaling pathway in colon cancer cell
Authors: Bae Eunseo , Kim Donghwa , Byun Woong sub , Lee Sang Kook , Chin Young-Won
Published: August 2019

Wnt signaling is a critical mechanism of biological processes, including cell proliferation, tissue homeostasis and development. The aberrant activity of Wnt signaling pathway is highly correlated with the colorectal carcinogenesis. Therefore, the effective compounds targeting Wnt signaling pathway could be applicable for colorectal cancer treatment. The bioactivity of nodosin, a component of Isodon serra, was evaluated in HCT116 colorectal cancer cells. Nodosin exhibited a potential growth inhibition of colon cancer cells. Nodosin also showed an effective inhibition upon wnt/β-catenin reporter gene assay in HEK293 and HCT116 cells. In addition, Wnt target genes such as β-catenin, Axin2, cyclin D1 and survivin were suppressed by nodosin in HCT116 cells. The inhibition of cell proliferation by nodosin was in part associated with the G2/M phase cell cycle arrest in colon cancer cell. These findings suggest that the anti-proliferative activity of nodosin against colorectal cancer cell should be associated with the regulation of Wnt/β-catenin signaling pathway.

This work was supported by a National Research Foundation of Korea (NRF) Grant funded by the Korean Government (MEST) (NRF-2016M3A9B6903499).

Citation Format: Eunseo Bae, Donghwa Kim, Woong sub Byun, Sang Kook Lee, Young-Won Chin. Anti-proliferative activity of nodosin is associated with the regulation of wnt signaling pathway in colon 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 4304.
Abstract 4323: 1,25-Dihydroxyvitamin D3 inhibits oral squamous cell carcinoma cell growth via microRNA regulation
Authors: Hussein Heba Said Ismail , Wang Wei , Shan Liang , Thompson Karl , Washington Kareem , Madkour Gihane , Gu Xinbin
Published: August 2019

Objective: Oral squamous cell carcinomas (OSCC) is one of top ten cancers lead to death in USA. This study focused on the impacts of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) treatment on the inhibition of OSCC growth in vitro and the alteration of microRNA (miRNA) expression profile by the treatment.

Materials and Methods: 1,25(OH)2D3-associated apoptosis, cell cycle arrest, and proliferative effect in cultured OSCC cells were assessed using flow cytometry and western blotting methods. miRNA expression profiles were measured using nanoString Sprint Profiller and the Nanostring human miRNA panel. More miRNAs functional pathways were retrieved through bioinformatics using Qiagen IPA system.

Results: 1,25(OH)2D3 was found to inhibit the growth of human JHU-22 OSCC cells in a dose-dependent manner with IC50 of 1.56 x 10-6 M. High levels of apoptotic cells and related biomarkers were obtained when the cells were treated with 1,25(OH)2D3. Over 20 miRNAs were upregulated and 23 downregulated by more than two folds, in 1,25(OH)2D3 treated versus untreated JHU-22 cells. Bioinformatics analysis showed molecular functions of most dysregulated miRNAs. For example, MiR-125b-5p upregulated caspases number 2, 6, 7 in addition to upregulating apoptosis facilitator like BCL-2, BIM, and AIF.

Conclusion: Our data suggested that 1,25(OH)2D3 function as a OSCC inhibiter is through regulating miRNA expression profile and miRNA function directly or indirectly. 1,25(OH)2D3 has potential to be an anticancer agent for OSCC prevention and treatment.

Fold change of top ten unregulated and down regulated miRNAs at nine hour treatment.miRNAControl (C9)Vitamin D (D9)C9/D9hsa-miR-624-3p8283.5hsa-miR-52110272.7hsa-miR-221-5p11292.64hsa-miR-1301-3p7182.57hsa-miR-520a-3p8202.5hsa-miR-153-3p12282.33hsa-miR-122-5p16372.31hsa-miR-120615342.27hsa-miR-125b-5p68615472.26hsa-miR-450b-3p492.25hsa-miR-613219-2.33hsa-miR-147b2611-2.36hsa-miR-525-3p125-2.40hsa-miR-5196-3p+hsa-miR-6732-3p187-2.57hsa-miR-181b-5p+hsa-miR-181d-5p218-2.63hsa-miR-182-3p3212-2.67hsa-miR-941228-2.75hsa-miR-671-3p176-2.83hsa-miR-944186-3.00hsa-miR-1245b-3p246-4.00

Citation Format: Heba Said Ismail Hussein, Wei Wang, Liang Shan, Karl Thompson, Kareem Washington, Gihane Madkour, Xinbin Gu. 1,25-Dihydroxyvitamin D3 inhibits oral squamous cell carcinoma cell growth via microRNA regulation [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 4323.
Abstract 4324: Prognostic potential of DNA methylation levels of EPDR1 and CHST10 in colorectal cancer
Authors: Chu Chun-Ho , Chang Shih-Ching , Wang Hsiu-Hua , Yang Shung-Haur , Lee Te-Chang , Lai Kuo-Chu
Published: August 2019

Chromosomal instability (CIN), microsatellite instability (MSI), and the CpG island methylator phenotype (CIMP) are well-characterized molecular features of colorectal cancer (CRC). Aberrant DNA methylation may associate with MSI-high and CIMP-high phenotype in CRC. Studies on aberrant DNA methylation are likely to help in the identification of biomarkers clinically relevant to the process of tumorigenesis. In this study, we explored DNA methylation profile changes in CRC with MSI through genome-wide DNA methylation profiling analysis. Of 34 altered genes, three hypermethylated (pidermal growth factor, EGF; carbohydrate sulfotransferase 10, CHST10; ependymin related 1, EPDR1) candidates were further validated in 75 CRC patients. All validated genes, except EGF, were significantly correlated with MSI status. In addition, methylation of EPDR1 or CHST10 was significantly correlated with better prognosis and mutations in BRAF and TGFβR2. Beside, we found a positive correlation between the methylation of EPDR1 and CHST10. Methylation of EPDR1 was also significantly correlated with node negativity and a lower tumor stage. Negative correlations between mRNA expression and DNA methylation level of both EPDR1 and CHST10 were reported in The Cancer Genome Atlas (TCGA) dataset, revealing that DNA methylation has a crucial function in modulating expressions of EPDR1 and CHST10 in CRC cells. These results suggest that DNA methylation levels of EPDR1 and CHST10 may serve as potential prognostic markers for CRC.

Citation Format: Chun-Ho Chu, Shih-Ching Chang, Hsiu-Hua Wang, Shung-Haur Yang, Te-Chang Lee, Kuo-Chu Lai. Prognostic potential of DNA methylation levels of EPDR1 and CHST10 in colorectal 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 4324.
Abstract 4329: Pharmaceutical means of targeting the fusion oncogene EWS-FLI1 in the Ewing family of tumors
Authors: Heisey Daniel A. , Lochmann Timothy , Calbert Marissa , Ghotra Maninderjit , Maves Yuki Kato , Boikos Sosipatros , Benes Cyril , Reynolds C. Patrick , Faber Anthony
Published: August 2019

The EWS-FLI1 translocation is the hallmark genomic alteration in the Ewing Family of Tumors (EWFT) a malignancy of the bone and surrounding tissue, predominantly affecting children and adolescents. Although significant progress has been made for the treatment of localized disease, patients with metastasis or who relapse after chemotherapy have less than a 30% five year survival rate. EWS-FLI is currently not pharmaceutically druggable, driving the need for more effective targeted therapies. It is well known that the EWS-FLI1 translocation induces a variety of epigenetic changes which impact tumorigenesis and disease progression. Using high throughput drug screening we have identified a novel epigenetic susceptibility in EWFT to the H3K27 demethylase inhibitor GSK-J4 (GlaxoSmithKline). Subsequent treatment with GSK-J4 leads to a decrease in H3K27 acetylation and ultimately silencing of EWS-FLI1 gene targets. We sought to fully characterize the hypersensitivity of EWFT to GSK-J4 and to elucidate the mechanisms of histone modifications caused by the EWS-FLI1 translocation in EWFT. We are examining key shifts in histone modifications at FLI1 target gene enhancer elements in the presence of GSK-J4 as a means of directly regulating FLI1 tumorigenesis. Additionally, we seek to determine the efficacy of GSK-J4 in combination with a CDK7 inhibitor (THZ1), which have shown synergy in vitro, through the utilization of patient derived xenograft models (PDX) and the identification of biomarkers of sensitivity to rationalize the use of this combination for clinical trials.

Citation Format: Daniel A. Heisey, Timothy Lochmann, Marissa Calbert, Maninderjit Ghotra, Yuki Kato Maves, Sosipatros Boikos, Cyril Benes, C. Patrick Reynolds, Anthony Faber. Pharmaceutical means of targeting the fusion oncogene EWS-FLI1 in the Ewing family of tumors [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 4329.
Abstract 4338: Enhancer mapping in triple negative breast cancer as a tool for biomarker and oncogene discovery
Authors: Raisner Ryan , Bainer Russell , Gascoigne Karen
Published: August 2019

Triple Negative Breast Cancer (TNBC) represents a heterogeneous disease with no common drivers or effective targeted therapies. Here we use ChIP-Seq combined with RNA-Seq to map the gene-regulatory landscape of TNBC in cell lines and primary tumors. Using this approach we identify novel actionable subtypes of the disease based on enhancer activity. We also identify novel tumor-specific enhancers and associated enhancer-driven oncogenes, and confirm enhancer status as a predictive biomarker of gene dependency.

Citation Format: Ryan Raisner, Russell Bainer, Karen Gascoigne. Enhancer mapping in triple negative breast cancer as a tool for biomarker and oncogene discovery [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 4338.
Abstract 4346: PI3K pathway mediated splicing defects in ER+ breast cancers
Authors: Ladewig Erik , Fairchild Lauren , Scaltriti Maurizio , Leslie Christina , Toska Eneda , Baselga Jose
Published: August 2019

Activating mutations in PIK3CA, the gene encoding for the catalytic subunit (p100a), are the most common oncogenic alterations in estrogen receptor-positive (ER+). The majority of PIK3CA mutations occur within two hot spots; exons 9 and exon 20 which encode the helical (E545K) and kinase domains (H1047R), respectively. These mutations result in hyperactivation of the PI3K/AKT/mTOR pathway and provide the rationale for the development of inhibitors targeting the PI3K pathway. To this end, PI3K α-specific inhibitors are showing antitumor activity in patients with PIK3CA-mutant, ER-positive breast cancer. Evidence of alternative mRNA regulation and splicing in various cancers has been described in the literature. Although, the majority of events appear to have unknown clinical significance, there is evidence alternative splicing can lead to drug resistance. The role of the PI3K pathway on transcriptional regulation and mRNA processing is not well studied. Through transcriptome analysis and cell assays in mouse MEF and human MCF10A cells we demonstrate splicing defects accrue as a result of the PI3K pathway activation by the PIK3CA H1047R mutation. PI3Ka pathway inhibitors were able to restore wildtype exon inclusion levels in these mutants, suggesting a potential clinical benefit. We propose that PIK3CA H1047R imposes mRNA differential isoform regulation by acting through the most commonly mutated PI3K pathway in ER+ breast cancers and that such mutations are targetable with PI3K pathway inhibitors.

Citation Format: Erik Ladewig, Lauren Fairchild, Maurizio Scaltriti, Christina Leslie, Eneda Toska, Jose Baselga. PI3K pathway mediated splicing defects in ER+ breast cancers [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 4346.
Abstract 4351: Single-cell RNA sequencing reveals transcriptomic heterogeneity in response to epigenetic inhibitors
Authors: Conery Andrew R. , Park Sungmi , Steinbaugh Michael J. , Bryant Barbara M. , Apte Shruti , Keller Patricia J. , Yuan C. C. , Bradley Bill , Bommi-Reddy Archana , Sims Robert J.
Published: August 2019

Histone modification is a fundamental regulatory mechanism of gene transcription and is associated with multiple diseases including cancer and inflammatory diseases. The factors that place and read these modifications can be co-opted in pathological conditions to give rise to disease-promoting transcriptional states, and thus represent promising targets for therapeutic small molecule inhibition. A central challenge in the development of epigenetic cancer therapy is the identification of transcriptionally sensitive cells within a heterogeneous population as a way to maximize therapeutic efficacy. To explore this challenge, we used single cell RNA-sequencing to characterize the transcriptional response of intrinsically heterogeneous human cancer and primary cell populations to small molecule inhibitors of epigenetic factors including the BET bromodomains, EZH2 methyltransferase, and CBP/EP300 acetyltransferase. Through clustering and differential expression analysis, we show that bulk transcriptional response in a mixed population of primary or tumor cells can be driven by a profound response in a hypersensitive subpopulation. Further, through the use of trajectory analysis, we show that epigenetic inhibitors can skew cell fate or differentiation status depending on the heterogeneity of the starting population. Overall, our results demonstrate the value of single cell transcriptomics for understanding the response of cell populations to epigenetic small molecule inhibitors and for enhancing the therapeutic potential of targeting pathogenic transcriptional programs.

Citation Format: Andrew R. Conery, Sungmi Park, Michael J. Steinbaugh, Barbara M. Bryant, Shruti Apte, Patricia J. Keller, C. C. Yuan, Bill Bradley, Archana Bommi-Reddy, Robert J. Sims. Single-cell RNA sequencing reveals transcriptomic heterogeneity in response to epigenetic inhibitors [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 4351.
Abstract 4384: Role of EIF4G1 in non-small cell lung cancer pathogenesis and targeted therapy
Authors: Qin Zhiqiang , Dai Lu , Valle Luis Del
Published: August 2019

Non-small cell lung cancer (NSCLC) accounts for about 85-90% of lung cancer cases, which represents the number one killer among cancers in US. The majority of lung cancer patients doesn't respond well to conventional chemo-/radio-therapeutic regimens and have a dismal 5-year survival rate of ~15%. The recent introduction of targeted therapy and immunotherapy gives new hopes to NSCLC patients, but their outcome/prognosis is far from satisfactory. The translation initiation EIF4F complex has been shown to play important roles in cancer progression. As an important component of the EIF4F complex, EIF4G1 serves as a scaffold and interacts with several other initiation factors such as EIF4E and EIF4A, and help to initiate cap-dependent translation in mammalian cells. EIF4G1 is overexpressed in a variety of cancers, but its functional role, clinical relevance and potential role as a therapeutic target in NSCLC remain largely unknown. Our recent data demonstrate that EIF4G1 expression level is much higher in NSCLC primary tumors than in paired adjacent normal tissues as well as in NSCLC cell lines than in the normal bronchial epithelial cells. Directly targeting EIF4G1 by RNAi or selective small-molecule inhibitors significantly reduce NSCLC cell proliferation, anchorage-independent growth in vitro as well as tumor progression in vivo. Our recent protein array and proteomics analyses indicate that EIF4G1: 1) has a complex interactome network in NSCLC cells; 2) appears to control the expression of a unique subset of the cellular proteome when compared to normal cells, which are closely related to NSCLC cells survival. Taken together, our data support that EIF4G1 plays a critical role in NSCLC survival, oncogenesis and tumor progression, and may serve as a novel and promising therapeutic target for improving NSCLC treatment.

Citation Format: Zhiqiang Qin, Lu Dai, Luis Del Valle. Role of EIF4G1 in non-small cell lung cancer pathogenesis and targeted therapy [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 4384.
Abstract 4391: Disruption of the translation initiation complex by eIF4A mutant inhibits prostate tumor growth in vivo
Authors: Singh Puja , Chen Hanyong , Li Hanxuan , Chi Young-In , Liu Bin , Lu Junxuan , Li Wei , Dong Zigang , Deng Yibin
Published: August 2019

Translation initiation in cancer cells is the rate-limiting step of oncogenic mRNAs translation/protein synthesis and is primarily mediated by the eukaryotic translation initiation factor 4 F (eIF4F) complex that consists of three subunits: eIF4E, which binds the cap of mRNA; eIF4A, an RNA helicase implicated in unwinding mRNA structure; and a scaffold protein eIF4G. Our prior crystal structure determination of human eIF4A in complex with Heat 1 domain of eIF4GI (722-999) revealed that eIF4G interacts with both N- and C-terminal domains of human eIF4A (eIF4A1-NTD and eIF4A1-CTD). Utilizing structural information gained from this complex, we generated a series of eIF4A mutants (eIF4A1-NTD: E41K, R45D, Y48A and eIF4A1-CTD: T271A, R324D, D296A/T298A) in order to identify the crucial site(s) of interaction with eIF4G Heat 1 domain. Using in vitro binding studies, we demonstrated that amongst various mutants tested, eIF4A-CTD (eIF4A1R324D) mutant disrupted the eIF4A/eIF4G Heat 1 complex formation, mirroring the binding residue E809K mutant of eIF4G that also interrupted eIF4A/eIF4G Heat 1 interaction. Given that eIF4G has an additional eIF4A-binding site named Heat 2 domain, we further investigated whether eIF4A1R324D mutant is able to disrupt binding to full-length eIF4G protein in vivo. Surprisingly, overexpression of Flag-tagged eIF4A1R324D in prostate cancer cell line blocked interaction with exogenous eIF4G as well as endogenous eIF4G. Taken together, these results strongly suggest that eIF4A1R324 residue plays a crucial role in mediating eIF4A/eIF4G complex formation in vivo. Furthermore, overexpression of eIF4A1R324D mutant significantly blocked oncogene c-myc and Bcl-2 mRNA translation thereby inhibiting prostate tumor growth in vivo. To conclude, our studies provide a previously unexplored strategy to identify small-molecule compounds disrupting eIF4A-eIF4G complex by targeting the pocket spanning eIF4AR324 and its binding site residues on eIF4G for cancer therapy.

Citation Format: Puja Singh, Hanyong Chen, Hanxuan Li, Young-In Chi, Bin Liu, Junxuan Lu, Wei Li, Zigang Dong, Yibin Deng. Disruption of the translation initiation complex by eIF4A mutant inhibits prostate tumor growth in vivo [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 4391.
Abstract 4471: Commercial gene expression tests for prostate cancer prognosis provide paradoxical estimates of race-specific risk
Authors: Creed Jordan H. , Berglund Anders E. , Rounbehler Robert J. , Awasthi Shivanshu , Cleveland John L. , Park Jong Y. , Yamoah Kosj , Gerke Travis A.
Published: August 2019

Background: Current National Comprehensive Cancer Network (NCCN) guidelines recommend three gene expression-based tests for prostate cancer (PCa) prognosis in men with low or favorable intermediate risk disease: Decipher, Oncotype DX Prostate, and Prolaris. The three tests feature varying numbers of genes with minimal overlap. Importantly, development and validation efforts for all three panels were undertaken in predominantly European American men (EAM) cohorts, and limited research exists on the value of such signatures in African American men (AAM), who have poorer PCa outcomes. Here, we explored differences in gene expression between EAM and AAM for the three panels recommended by the NCCN for PCa prognosis.

Methods: 232 EAM and 95 AAM patients provided radical prostatectomy specimens. Gene expression was quantified using Nanostring for 60 genes spanning the Oncotype DX Prostate, Prolaris, and Decipher panels. Differential expression and intrapanel co-expression by race were assessed using Mann-Whitney tests and Spearman’s correlations, respectively. A continuous expression-based risk score was approximated for each panel with higher scores indicating worse outcomes. Race-specific risks were compared using Mann-Whitney tests and Spearman’s correlations.

Results: Clinical and pathologic features were similar between AAM and EAM. Differential expression by race was observed for 48% of genes measured, though the magnitudes of expression differences were small. Co-expression patterns were more strongly preserved by race group for Oncotype DX and Decipher versus Prolaris (integrative correlations of 0.87, 0.73, and 0.62, respectively). Paradoxically, poorer prognosis was estimated in EAM versus AAM for Prolaris and Oncotype DX (p = 0.01 for both), whereas worse prognosis was predicted for AAM versus EAM using Decipher (p < 0.001).

Discussion: Due to observed racial differences across three commercial gene expression panels for PCa prognosis, caution is warranted when applying these panels in clinical decision-making in AAM. Replication of our findings directly on the commercial panels with long-term follow-up is warranted.

Citation Format: Jordan H. Creed, Anders E. Berglund, Robert J. Rounbehler, Shivanshu Awasthi, John L. Cleveland, Jong Y. Park, Kosj Yamoah, Travis A. Gerke. Commercial gene expression tests for prostate cancer prognosis provide paradoxical estimates of race-specific risk [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 4471.