bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4156: Multiple rare germline variants in a thyroid cancer family
Authors: Nieminen Taina T. , Comiskey Daniel F. , Wang Yanqiang , Liyanarachchi Sandya , Brock Pamela , Peltomaki Paivi , He Huiling , Chapelle Albert de la
Published: August 2019

Thyroid cancer is the 12th most common cancer in the USA. Four main types exist: the majority (85-90%) is papillary thyroid cancer (PTC). Familial form of PTC represents 5 to 15 % of all thyroid cancers. We have access to 155 PTC families including clinical data and biological samples. Our aim was to search for highly penetrant gene variants in 17 PTC families. Data from one of the families in which PTC is segregating in three generations are described here. Whole genome sequencing was performed in three family members affected by PTC. Sanger sequencing at germline DNA and RNA levels followed by TOPO cloning was used to study the effects of mutations. We found 4 different either novel or ultra-rare mutations in the ITGAD, AARS and PDPR genes on chromosome 16 (Table). All mutations segregated perfectly with PTC in family members (n=4) and were absent in unaffected members (n=3). We Sanger sequenced cDNA from two of the PTC patients and cloned the products into the pCR 2.1-® TOPO vector. Based on the cDNA sequencing and cloning results, all of the mutations will create a premature stop codon leading to a truncated protein. We will verify the effects of the mutations by protein analysis as well. In addition, structural variation analysis will be done to exclude large genomic rearrangements. The germline events leading to PTC are neither well known nor extensively researched. When occurring in families PTC regularly shows autosomal dominant inheritance with incomplete penetrance. Only a few of probable mutations have been reported. Nevertheless, our finding of the truncating mutations in 3 genes on chromosome 16 that are cosegregating with PTC in a 3-generation family is surprising. Even more so: is the localization of the three genes in one chromosome coincidental? Preliminary findings in some of the other 16 PTC families suggest that the occurrence of more than one truncating mutation is not a unique event. We look forward to answer the question whether combination of two or more mutant genes can be responsible for one disease segregating in families.

Citation Format: Taina T. Nieminen, Daniel F. Comiskey, Yanqiang Wang, Sandya Liyanarachchi, Pamela Brock, Paivi Peltomaki, Huiling He, Albert de la Chapelle. Multiple rare germline variants in a thyroid cancer family [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 4156.
Abstract 4164: Comprehensive analysis of germline variants in patients with hereditary breast and ovarian cancer susceptibility from 4 countries of Latin America
Authors: Vaca-Paniagua Felipe , Quezada-Urban Rosalia , Velásquez Clara Estela Díaz , García Eva María Gómez , Catalá Claudia Fabiola Méndez , Oliver Javier , Franco Alejandra , Frecha Cecilia , Riggi Cecilia , Carranza Claudia , Altamirano Carlos Castañeda , Gómez Ana Milena , Montealegre Ana Lorena , Chaparro Sandra Gaitán , López Juan Javier , Perdomo Sandra
Published: August 2019

Hereditary breast and ovarian cancer syndrome (HBOC) is an autosomal dominant disease mainly associated to high-risk pathogenic alleles in the BRCA1 and BRCA2 genes, but only in ~25% of HBOC cases. With the emergence of broader multi-gene panels, population-based studies have revealed that 3-4% of high-risk individuals have germline pathogenic variants in cancer risk genes other than BRCA1 and BRCA2, including ATM, CHEK2, PALB2, PTEN, TP53, and others. One of the understudied population with HBOC is the Latin American, and in this study, we aimed to identify the prevalence of high, moderate and new pathogenic alleles within two panels of cancer predisposition genes (143 and 86 genes) in 217 Latino breast cancer patients that met the NCCN criteria for panel testing in 4 countries. The Latino population was integrated by 68 Mexicans (31.3%), 19 Guatemalan (8.8%), 56 Argentinians (25.8%) and 74 Colombians (34.1%). We detected (i) 19.4% patients with pathogenic variants (42/217; Mexicans: 12, 5.5%; Guatemalans: 3, 1.4%; Argentinians: 10, 4.6%; Colombians: 17, 7.8%); (ii) 36.9% harbored variants with unknown clinical significance (VUS) (80/217; Mexicans: 24, 11.1%; Guatemalans: 6, 2.7%; Argentines: 26, 12%; Colombians: 24, 11.1%) and (iii) 43.7% were negative (95/217; Mexicans: 32, 14.7%; Guatemalans: 10, 4.6%; Argentines: 20, 9.2%; Colombians: 33, 15.2%). Moreover, most of the pathogenic variants (66%, 28/42) were found in high-risk genes including BRCA1/2, MSH2, MSH6 and PALB2. Our findings show the high locus heterogeneity of HBOC in the Latin American population. To establish the level of risk and the ultimate clinical utility of the variants detected in expanded panels tests, further international efforts are necessary in a population-based context.

Citation Format: Felipe Vaca-Paniagua, Rosalia Quezada-Urban, Clara Estela Díaz Velásquez, Eva María Gómez García, Claudia Fabiola Méndez Catalá, Javier Oliver, Alejandra Franco, Cecilia Frecha, Cecilia Riggi, Claudia Carranza, Carlos Castañeda Altamirano, Ana Milena Gómez, Ana Lorena Montealegre, Sandra Gaitán Chaparro, Juan Javier López, Sandra Perdomo. Comprehensive analysis of germline variants in patients with hereditary breast and ovarian cancer susceptibility from 4 countries of Latin America [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 4164.
Abstract 4165: Unstable microsatellite instability proportion among unselected ovarian and endometrial cancer patients among Korean population
Authors: Kim Min Kyu
Published: August 2019

Background: There are several availability of microsatellite instability(MSI) among ovarian and endometrial cancer for detection of Lynch syndrome and biomarker of immune chemotherapeutic treatment. We investigated to know proportion of abnormal microsatellite instability (MSI-L/H).

Methods: Through retrospective search,we identified 51 cases of MSI samples from ovary and endometrial cancer visiting hereditary gynecologic cancer center.

Results: We found 34 ovary cancer, 13 endometrial cancer and 4 colon cancer patients. Median age was 56.6(18~78). About thirty percent have family cancer history among patient relatives (14/45(31.1%)). Early stage cancer (I~II) (4/25,16.0%) have higher incidence than late stage cancer (III~IV) (2/28,7.1%). Abnormal MSI have three serous type and endometrioid type pathology. Among abnormal MSI, we found two MSI-L and four MSI-H (6/51(11.8%)). We found one MSI-H ovary cancer,3 MSI-H endometrial cancer patients (1/34(2.9%),3/13(23.1%)).

Conclusions: There are about 10 percent of abnormal MSI in this study group

Citation Format: Min Kyu Kim. Unstable microsatellite instability proportion among unselected ovarian and endometrial cancer patients among Korean 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 4165.
Abstract 4194: Rare cancer’s ‘valley of death’: Critical gaps in data, research, and funding
Authors: Treuting Robert L. , Murphy Sean , Murphy Niall , Rao Bovey , Goyal Anekha , Tuccillo Nico , Kim Ryan Ki-Hoon , Parker Dylan , Arline Katherine
Published: August 2019

Over 370 forms of rare cancer compose at least 29.7% of all U.S. cancer diagnoses, or over 500,000 Americans per year. And yet, available data, research, and public funding related to these indications is insufficient in comparison with the 20 forms of non-rare cancers. Rare cancer is defined by the American Cancer Society as a cancer having an incidence of <6 per 100,000 per year. A review of the AACR Annual Proceedings 2018 showed that at least 150 rare cancers were not the focus of any abstract. Non-rare forms of breast cancer, expected to represent 11.9% of new cancer cases in 2018, had almost the same coverage (1081 abstracts, 25.6%) as all rare cancers combined (1155 abstracts, 27.3%). Rare cancers which were included in AACR 2018 were the focus of an average of 5 abstracts each, while the 20 non-rare cancers were the focus of an average of 154 each. That gap in basic science is also visible in broader data sources. A computational review of the 10,000 most recent cancer-related publications in PubMed showed that over 100 rare cancers had no publications, while that was true of only 1 non-rare cancer. Included rare cancers had an average of 3.2 mentions in PubMed abstracts, while non-rare cancers had an average of 115. Adequate patient-derived tumor gene expression data is critical for targeted drug development. Analysis of the Gene Expression Omnibus (GEO) repository demonstrated that, while all 20 non-rare cancers had DataSets, over 100 rare cancers had none. On average, each rare cancer included in GEO had 1.04 DataSets, while each non-rare cancer had 22.8. Government grants to companies are an important tool for bridging the drug development “valley of death” between basic science and the clinic. Between 2013 and 2017, 781 SBIRs and STTRs related to cancer research, development, or treatment were identified. 489 of them related to a specific cancer or cancers. Of those grants, 41.5% were related to breast, lung, or prostate cancers. 22.3% were related to rare cancers. Among rare cancers, glioblastoma was the specific focus of the most grants (18). 356 forms of rare cancer were not the specific focus of any grant. Pediatric cancers, which are all rare, were the focus of 8 grants (1%). These data highlight a significant gap in rare cancer-focused data, research, and public funding which contributes to lower availability of clinical trials and therapeutics for over half a million U.S. patients per year.

Citation Format: Robert L. Treuting, Sean Murphy, Niall Murphy, Bovey Rao, Anekha Goyal, Nico Tuccillo, Ryan Ki-Hoon Kim, Dylan Parker, Katherine Arline. Rare cancer’s ‘valley of death’: Critical gaps in data, research, and funding [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 4194.
Abstract 4227: Salvage genetic testing on buccal swab samples using liquid in situ amplification identifies genetic mutations from previous test failures
Authors: Weiss Glen J. , Ford Andrew , Brown Charmaine , Caver Elizabeth , Vallejo Matthew , Adeyemi Claribel , Collins Forrest , Yeh Chen-Hsiung
Published: August 2019

Background: NCCN guidelines version 2.2019 address BRCA1/2 testing for men with a personal history of prostate cancer limited to Gleason ≥7 and specific family history features. Inherited genetic mutations have been identified in up to 12% of metastatic prostate cancer, primarily in DNA repair genes. Here we report liquid in situ amplification (LISA) technique followed by hereditary testing on buccal swab samples that had previously failed to yield a genetic testing result.

Methods: Previously failed buccal swab samples from another CLIA-certified laboratory were re-prepared using LISA. Qubit quantification following LISA revealed goodDNA concentrations even for these poor-quality swab samples ranging from 5 to 70 ng/uL, which is sufficient for next-generation sequencing analysis (NGS). Coding regions of ATM, BRCA1, BRCA2, CHEK2, PALB2, and RAD51D genes were amplified by a panel of specific primer pools followed by massively parallel sequencing for the identification of germline mutations. Minimal sequencing coverage was set as 50X, and pathogenic, likely pathogenic, and variants of unknown significance (VUS) were classified and reported.

Results: Buccal swab samples from 29 men with at least intermediate-risk prostate cancer were received as low-yield, low-quality DNA (n=12), pre-cut swabs in preservation solution (n=6), and aged swab samples (n=11). LISA and subsequent NGS testing was able to salvage results for 24/29 (82.8%) (failed samples included 4 aged swab and 1 pre-cut swab). 1 patient had a pathogenic BRCA1 mutation (c.4309delT) and 3 patients had VUS (BRCA1 c.4776C>G, BRCA1 c.1846_1848delTCT, and RAD51D c.268G>A). The remaining 20/29 (69.0%) samples have either benign or likely benign variants.

Conclusions: LISA applied to these previously failed samples was able to salvage results for over 80% of cases, including the identification of a pathogenic BRCA1 mutation which led cascade hereditary testing for immediate family members. It also provided confirmation for nearly 70% of cases about the absence of hereditary risk for the genes on the panel.

Citation Format: Glen J. Weiss, Andrew Ford, Charmaine Brown, Elizabeth Caver, Matthew Vallejo, Claribel Adeyemi, Forrest Collins, Chen-Hsiung Yeh. Salvage genetic testing on buccal swab samples using liquid in situ amplification identifies genetic mutations from previous test failures [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 4227.
Abstract 4231: Association between age of first full-term pregnancy and subsequent breast cancer risk
Authors: Tabassum Neha
Published: August 2019

Introduction

Amongst the various risk factors for breast cancer (BC), age at first full-term pregnancy is still a complex problem. Early first full-term pregnancy (before 25 years of age) is believed to confer protection towards the development of BC after menopause compared to the risk in nulliparous women but is also correlated with a transient increase in the risk of developing BC soon after pregnancy. On the other hand, a late first pregnancy (after 35 years of age) is believed to increase the risk of developing breast cancer after menopause, equating or increasing the risk compared to nulliparous women.

Material and Methods

In our project, currently, we aim to do a pilot study with 4 fresh frozen normal samples of nulliparous and early-and late-parous women from Komen tissue bank (USA) and to create a mathematical model to determine how rates of both drivers and passengers mutations are affected by pregnancy and how the risk can be determined in parous and nulliparous women. We plan to measure low-frequency mutations from fresh frozen normal breast samples from patients with different reproductive stages using both Whole Genome Sequencing in this pilot group,and later on to expand the findings with Exome Sequencing on the remaining cohort of 55 normal samples.

Results and Discussions

We are currently in the process of analysing the data from the whole genome sequencing and whilst we do this, we are also collecting DNA from laser-capture microdissected epithelial and stromal cells, for the remaining samples. Bioinformatics tools are used to eliminate germline mutations from the stroma and to determine where the mutations are located within the genome, and how their frequency changes within the sample cohort.

Conclusion

While this study is aimed to understand the scientific basis of breast cancer and therefore it is not clinically applicable in the immediate future, understanding the cancer risk associated with age of pregnancy will provide future patients, in particular from at-risk categories, with an informed choice when deciding to plan a pregnancy and a surveillance programme could also be implemented to closely monitor any changes in the breast after a late pregnancy and improve early detection. Furthermore, we could hypothesise that in the long-term future, with the wider application of mammary ductoscopy, breast samples could be analysed in the clinic to calculate the mutation rate of the patient and identify individual risk. This risk stratification along with available predictors such as the ‘Gail model’ could be applied in breast cancer surveillance programmes.

Note: This abstract was not presented at the meeting.

Citation Format: Neha Tabassum. Association between age of first full-term pregnancy and subsequent breast cancer 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 4231.
Abstract 4237: CC chemokines are differentially expressed in breast cancer and are associated with racial disparity
Authors: Thomas Jeronay K. , Mir Hina , Kapur Neeraj , Singh Shailesh
Published: August 2019

Despite recent advances in diagnosis and treatment Breast cancer (BrCa) still impacts women’s lives and this impact is disproportional in African Americans (AA) compared to European Americans (EA). Addressing socioeconomic and behavioral status has not reduced the race-specific gap in BrCa outcome, suggesting contribution of biological differences in BrCa disparity. We have previously shown involvement of chemokines in the pathogenesis of BrCa. In this study, we have determined the expression of CC chemokines in BrCa tissues and normal tissues utilizing the ONCOMINE database. Further, we determined clinical parameters associated with the CC chemokines overexpressed in BrCa tissues using The Cancer Genome Atlas (TCGA). Additionally, using Bc-GenExMiner and KMplotter we determined the effects of CC chemokines on reoccurrence, overall and relapse-free survival. Our analysis shows overexpression of CCL5, CCL7, CCL11, CCL17, CCL20, CCL22 and CCL25 mRNA in BrCa tissues compared to normal. Overexpression of CCL21 and CCL22 were significantly correlated with metastatic recurrence. High mRNA levels of CCL7, CCL8, CCL17, CCL20 and CCL25 predicted a decrease in overall survival and CCL7 and CCL8 expression showed a trend in decreased relapse-free survival. Furthermore, overexpression of CCL17 and CCL25 was associated with decreased overall survival in AA whereas in EA, CCL8 was associated with a decrease in overall survival. Interestingly, expression of CCL5, CCL8, CCL17, CCL20 and CCL25 were highest in TNBC tissues. Expression of CCL11 and CCL22 were associated with HER2. In addition to these, there was an association with CC chemokines expression with age in BrCa. Higher CCL11 expression was noted in younger women and CCL8, CCL20, CCL22 and CCL25 expression was higher in older women. Furthermore, CCL25 was significantly elevated and CCL8 was nearly significant in AA tissues when compared to EA. Expression of CCL7, CCL8, and CCL25 were associated with stage. In conclusion, our analysis suggests an association of CC chemokines in BrCa progression, overall survival and observed disparity in disease outcome between AA and EA patients.

Citation Format: Jeronay K. Thomas, Hina Mir, Neeraj Kapur, Shailesh Singh. CC chemokines are differentially expressed in breast cancer and are associated with racial disparity [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 4237.
Abstract 4246: Association of transcriptional levels of folate-mediated one-carbon metabolism related genes in cancer cell lines with drug treatment response
Authors: Krushkal Julia , Vural Suleyman , Min Dong-Joon
Published: August 2019

Folate-mediated one-carbon metabolism (OCM) is essential for growth and survival of cancer cells. It affects biosynthesis of nucleotides and amino acids, regulation of redox status, methylation of nucleic acids and proteins, and genome maintenance. We investigated whether the response of cancer cells to antitumor therapy treatment may be partially influenced by variation in expression of one-carbon metabolism genes. We used publicly available gene expression data and drug response measures for 251 antitumor agents in 635 cancer cell lines with matching information from the Cancer Cell Line Encyclopedia and the Genomics of Drug Sensitivity in Cancer resources. We examined whether pre-treatment expression levels of OCM-related genes were associated with drug response. Among the 34 OCM genes examined, expression of GART, TYMS, SHMT2, MTR, ALDH2, BHMT, MAT2B, MTHFD2, NNMT, and SLC46A1 showed modest correlations with response to treatment with a variety of antitumor agents. Higher expression levels of the SLC46A1 transporter gene were associated with resistance to multiple drugs, whereas elevated expression of GART, TYMS, SHMT2, MTR, BHMT, and MAT2B was associated with chemosensitivity to multiple antitumor agents. NNMT expression was bimodally distributed and showed different directions of association with various agents. Correlation of increased NNMT expression with sensitivity to dasatinib was validated in the NCI-60 cancer cell line panel. Expression of several OCM genes was strongly associated with expression of multiple components of drug target pathways. For example, expression of both TYMS and GART was strongly positively correlated with BRCA1 expression, NNMT expression was associated with expression of multiple drug target genes including EGFR and ABL2, and the expression of TYMS, DHFR, and SHMT1 was positively correlated with AURKB expression. Pretreatment expression levels of many OCM genes including DHFR, TYMS, ATIC, GART, AHCY, MTHFD1, SLC19A1, and multiple other genes were positively correlated with each other, suggesting their co-regulation. In contrast, NNMT expression was negatively correlated with expression of several other OCM genes. Further studies could investigate whether correlations of expression levels of individual OCM genes with drug response are related to specific metabolic roles of these genes or whether such associations may be due to the general increase in cellular growth and proliferation and tumor progression, which may affect sensitivity to cancer treatment.

Citation Format: Julia Krushkal, Suleyman Vural, Dong-Joon Min. Association of transcriptional levels of folate-mediated one-carbon metabolism related genes in cancer cell lines with drug treatment response [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 4246.
Abstract 4254: Integrated analysis with MVisAGe identifies concordant and discordant genomic alterations of driver genes
Authors: Walter Vonn , Du Ying , Danilova Ludmila , Hayward Michele , Hayes D. Neil
Published: August 2019

Integrated analyses of multiple genomic datatypes are now common in cancer profiling studies. Such data present opportunities for numerous computational experiments, yet analytic pipelines are limited. Tools such as the cBioPortal and Regulome Explorer, while useful, are not easy to access programmatically or implement locally. The MVisAGe R package allows users to quantify gene-level associations between two genomic datatypes in order to investigate the effect of genomic alterations (e.g. DNA copy number changes on gene expression). Visualizing Pearson/Spearman correlation coefficients according to the genomic positions of the underlying genes provides a powerful yet novel tool for conducting exploratory analyses. We demonstrate its utility by analyzing three publicly available datasets from squamous tumors. Our approach highlights canonical oncogenes in chr11q13 that displayed the strongest associations between expression and copy number, including CCND1 and CTTN, genes not identified by copy number analysis in the primary reports. We demonstrate highly concordant usage of shared oncogenes on chr3q, yet strikingly diverse oncogene usage on chr11q as a function of HPV infection status. Regions of chr19 that display remarkable associations between methylation and gene expression were identified, as were previously unreported miRNA-gene expression associations that may contribute to the epithelial-to-mesenchymal transition.

Citation Format: Vonn Walter, Ying Du, Ludmila Danilova, Michele Hayward, D. Neil Hayes. Integrated analysis with MVisAGe identifies concordant and discordant genomic alterations of driver genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4254.
Abstract 4260: Novel insights into immunotherapy by deep mining of big cancer genomic data
Authors: Liang Han
Published: August 2019

Immunotherapy has revolutionized patient care and cancer research. To gain novel insights into immunotherapy, we performed the pan-cancer analyses of >11,000 tumor samples of 33 cancer types from The Cancer Genome Atlas and CPTAC as well as large amounts of in-house immunotherapy related data. Through the mining on these large-scale cancer genomics and proteomics data, I will discuss three novel ideas that would challenge the current paradigm for developing effective immunotherapy. (I) Checkpoint inhibition: antibody is NOT the only approach. I will discuss the role of enhancers in regulating immune checkpoint. (II) Neoantigen: Somatic mutations are NOT the only source. I will discuss the contribution of RNA editing to proteomics diversity and neoantigen in cancer. (III) Predictive markers: gene-based markers is NOT the only option. I will discuss the utility of a global energy index for predicting the response to anti-PD1 treatment. Collectively, these results suggest novel directions for future immunotherapy development.

Citation Format: Han Liang. Novel insights into immunotherapy by deep mining of big cancer genomic data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4260.
Abstract 4265: Transient versus permanent autophagy inhibition in pancreatic ductal adenocarcinoma
Authors: Pearce Jane B. , O'Flanagan Ciara H. , Hursting Stephen D.
Published: August 2019

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers worldwide, with a 5- year survival rate of less than 5 percent. KRAS-driven PDACs often exhibit increased dependence on autophagy, a process by which cells degrade internal components to mobilize energy stores. When faced with cellular stress, such as nutrient deprivation, tumor growth may initially slow in response to decreasing supplies of growth factors and cytokines. Under these conditions, the induction of autophagy can enable continued tumor growth even in the presence of nutrient stress. Therefore, we posited that nutrient restriction in combination with autophagy inhibition would synergistically disrupt aberrant metabolic pathways and more effectively stunt PDAC tumor progression.

To determine the impact of transient autophagy inhibition, cells were treated with 10 μM of the pharmaceutical agent chloroquine (CQ) for 48 hours. To modulate growth factor/cytokine signaling as well as nutrient sensing signaling serum and glucose restriction were used in vitro. Next, permanent autophagy ablation was achieved through CRISPR/Cas9 technology, autophagy related 5 (Atg5) was deleted in Panc02 cells generating an autophagy-deficient (Atg-/-) PDAC cell line. Growth kinetics were determined in a range of culture matrixes to determine the proliferation rate, invasiveness, and anchorage independence of cells.

The combination of CQ and nutrient stress elicited an additive effect on cellular proliferation in both murine and human-derived KRAS mutant PDAC cells (Panc02 and MIA PaCa-2 respectively). In contrast, Atg5-/- Panc02 cells did not display any alteration in cellular proliferation in vitro. Atg5 deletion resulted in decreased expression of mesenchymal markers N-Cadherin and Snail as well as decreased invasiveness and anchorage independent colony formation. Upon intrapancreatic injection in a syngeneic model, Atg-/- cells exhibited reduced tumor growth relative to control Atg5+/+cells, indicating the compensatory mechanisms effective in vitro failed to protect these cells in vivo. Thus, our findings reveal a potential synergism between autophagy inhibition and nutrient stress in PDAC.

Citation Format: Jane B. Pearce, Ciara H. O'Flanagan, Stephen D. Hursting. Transient versus permanent autophagy inhibition in pancreatic ductal 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 4265.
Abstract 4267: mTORC1-dependent tumors have innate vulnerability to autophagic cell death by HDAC inhibitors
Authors: Yang Fuchun , Wang Chenran , Sun Shaogang , Haas Michael , Yeo Syn , Guan Jun-Lin
Published: August 2019

mTORC1 plays a significant role in the development and progression of many different types of cancers. Although mTORC1 inhibitors, such as Rapamycin, have anti-tumor effects on some specific cancers, their efficacy is still largely limited to anti-proliferative effects. Histone deacetylase (HDAC) inhibitors have been proven to be effective in cancer treatment including some solid cancers. We have previously established a vascular tumor cell line, Tsc1Δ EC, which was derived from Tsc1 deletion in mouse endothelial cells leading to constitutive activation of mTORC1. Here, we found that a pan-HDAC inhibitor, SAHA, caused Tsc1Δ EC cell death and growth arrest in vitro and in vivo. Our data showed that a selective Class I HDAC inhibitor CI994 treatment also caused Tsc1Δ EC cell death. Unlike mTORC1 inhibitors, the anti-tumor activity of SAHA was dependent on mTORC1 activation but it had little effect on mTORC1 activity in mTORC1 activated tumor cells. We found that Z-VAD-FMK, a pan-caspase inhibitor, had no inhibitory effect on SAHA treatment. Cell death pathway array analysis revealed that SAHA treatment in Tsc1ΔEC upregulated autophagy-related genes. Further experiments revealed that both autophagy gene Fip200 deletion and autophagy inhibition by spautin-1 in Tsc1Δ EC impaired tumor cell death by SAHA treatment. We further found that SAHA could play a role by increasing reactive oxygen species (ROS) via autophagy. Fip200 deletion caused Nrf2 activation through p62 accumulation, which can lead to antioxidation effect through p62-Keap1-Nrf2 pathway. We showed that inhibition of p62 expression re-sensitized Fip200 deleted Tsc1Δ EC to SAHA treatment. Taken together, HDAC inhibitors treatment provides an alternative promising therapeutic strategy for mTORC1-dependent cancers.

Note: This abstract was not presented at the meeting.

Citation Format: Fuchun Yang, Chenran Wang, Shaogang Sun, Michael Haas, Syn Yeo, Jun-Lin Guan. mTORC1-dependent tumors have innate vulnerability to autophagic cell death by HDAC 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 4267.
Abstract 4272: Suppression of epigenetic regulator NURF leads to autophagy mediated chemo-and immune sensitization of triple negative breast cancer
Authors: Tyutyunyk Liliya , Gewirtz David A. , Landry Joseph , Dao Nga
Published: August 2019

Dysregulation of the epigenome is implicated in initiation and progression of variety of cancers and their acquired resistance to chemotherapy. As such, targeting epigenetic regulators has the potential to modulate tumor cell biology and reestablish tumor cell sensitivity to chemotherapy and/or radiation. Our studies demonstrate that silencing of the epigenetic regulator Nucleosome Remodeling Factor (NURF) sensitizes breast tumor cells to chemotherapy and enhances the anti-tumor immune response. Compared to controls, NURF KD 4T1 breast tumor cells exposed to doxorubicin (Dox) show increased DNA damage (gamma H2AX staining) and autophagy (acridine orange staining) in vitro and enhanced growth inhibition both in vitro and in vivo. NURF KD also sensitizes 4T1 cells to doxorubicin stimulated Natural Killer (NK) cell antitumor activity ex vivo, which is associated with a cytokine/chemokine secreted by doxorubicin exposed NURF KD cells; potential candidates are CCL5, TNFa and CCL2. The importance of NK cells for the enhanced growth control of doxorubicin treated NURF KD cells was confirmed using a mAb depletion approach. Autophagy may be instrumental in NK cell activation and elimination of tumor cell targets by mediating cytokine secretion. Sensitization of NURF KD 4T1 cells to doxorubicin, both increased autophagy and enhanced NK cell activity, were also observed using a small molecule inhibitor of NURF, suggesting that NURF can also be targeted pharmacologically. Our studies suggest that enhanced doxorubicin induced DNA damage and autophagy (cell autonomous effects) and NK cell cytotoxic activity (cell non-autonomous affects) may be primary contributors to immune sensitization in NURF KD cells. Increased cell autonomous antitumor effects by doxorubicin in concert with increased cell non-autonomous immunogenicity could help to achieve tumor regression, reduce metastasis, and possibly promote long term remission in breast cancer.

Citation Format: Liliya Tyutyunyk, David A. Gewirtz, Joseph Landry, Nga Dao. Suppression of epigenetic regulator NURF leads to autophagy mediated chemo-and immune sensitization of triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4272.
Abstract 4280: The cycloartane triterpenoid ADCX impairs autophagic degradation through Akt overactivation and promotes apoptotic cell death in multidrug-resistant HepG2/ADM cells
Authors: YAO NAN , Sun Haiyan , Huang Maohua , Ye Wencai , Chen SiBao , Zhang Dong-Mei
Published: August 2019

Multidrug resistance is the main obstacle in cancer chemotherapy. Emerging evidence has demonstrated the important role of autophagy in cancer cell resistance to chemotherapy. Therefore, autophagy inhibition may be a promising strategy for conquering drug resistance in liver cancer cells.

Methods: HepG2/ADM cells were treated with ADCX in the presence or absence of relevant inhibitors, apoptosis was measured by flow-cytometry and expression of autophagy and apoptosis related proteins was detected by western blotting. Confocal microscope was used for GFP-LC3 assay, tandem mRFP-GFP-LC3 assay, DQ-BSA method and colocalization of GFP-LC3 and LAMP1. Celluar ultrastructure was observed by transmission electronic microscopy.

Results: ADCX, a natural cycloartane triterpenoid extracted from the traditional Chinese medicine (TCM) source Cimicifugae Rhizoma (Shengma), inhibited autophagic degradation by impairing the maturation of lysosomal cathepsins in multidrug resistant liver cancer HepG2/ADM cells, thereby leading to autophagic flux inhibition. Interestingly, Akt was over-activated by ADCX treatment, which was associated with impairment of cathepsin maturation. Moreover, impairing autophagic degradation promoted ADCX-induced apoptotic cell death in HepG2/ADM cells.

Conclusions: Our study indicates that impairing autophagic degradation may be an effective approach for overcoming resistance and also suggests a novel role for Akt in autophagic degradation.

Citation Format: NAN YAO, Haiyan Sun, Maohua Huang, Wencai Ye, SiBao Chen, Dong-Mei Zhang. The cycloartane triterpenoid ADCX impairs autophagic degradation through Akt overactivation and promotes apoptotic cell death in multidrug-resistant HepG2/ADM cells [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 4280.
Abstract 4286: TGFβ induced SMAD4 dependent apoptosis proceeded by EMT in colorectal cancer
Authors: Poyil Pratheeshkumar , Siraj Abdul K. , Padmaja Divya Sasidharan , Parvathareddy Sandeep Kumar , Bu Rong , Masoodi Tariq , Kong Yan , Thangavel Saravanan , Ahmed Saeeda Omer , Al-Sanea Nasser , Ashari Luai H. , Abduljabbar Alaa , Alhomoud Samar , Al-Dayel Fouad , Al-Kuraya Khawla S.
Published: August 2019

Colorectal cancer (CRC) is one of the leading cause of cancer-related deaths Worldwide. In Saudi Arabia, CRC is more aggressive and presents at younger age, warranting new treatment strategies. Role of TGFβ/Smad4 signaling pathway in initiation and progression of CRC is well documented. Current study examined the role of TGFβ/Smad4 signaling pathway in a large cohort of Saudi CRC, followed by in vitro analysis to dissect the dual role of TGFβ on inducing epithelial to mesenchymal transition (EMT) and apoptosis. In this study, we investigated Smad4 alterations and their association with clinicopathological outcomes in a large cohort of CRC samples using targeted capture sequencing, Fluorescent in-situ hybridisation and immunohistochemistry. Our study demonstrated high frequency of Smad4 alterations with low expression of Smad4 protein identifying a sub-group of aggressive CRC to be an independent marker for poor prognosis. Functional studies using CRC cells show that TGFβ induces Smad4 dependent EMT followed by apoptosis. Induction of mesenchymal transcriptional factors, Snail1 and Zeb1 was essential for TGFβ-induced apoptosis. Our results indicate that KLF5 acts as an oncogene in CRC cells regardless of Smad4 expression and inhibition of KLF5 is requisite for TGFβ-induced apoptosis. Furthermore, TGFβ/Smad4 signal inhibits the transcription of KLF5 that in turn switches Sox4 from tumor promoter to suppressor. A high incidence of Smad4 alterations were found in the Saudi CRC patients. Functional study results indicate that TGFβ induces Smad4 dependent EMT followed by apoptosis in CRC cells.

Citation Format: Pratheeshkumar Poyil, Abdul K. Siraj, Divya Sasidharan Padmaja, Sandeep Kumar Parvathareddy, Rong Bu, Tariq Masoodi, Yan Kong, Saravanan Thangavel, Saeeda Omer Ahmed, Nasser Al-Sanea, Luai H. Ashari, Alaa Abduljabbar, Samar Alhomoud, Fouad Al-Dayel, Khawla S. Al-Kuraya. TGFβ induced SMAD4 dependent apoptosis proceeded by EMT 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 4286.
Abstract 4288: Race specific differences in G-protein decoupling from CCR9 in prostate cancer cells contribute to the differences in docetaxel response
Authors: Kapur Neeraj , Mir Hina , Singh Shailesh
Published: August 2019

Current treatment approaches have failed to reduce racial disparity in treatment outcome of prostate cancer (PCa) primarily due to the race-specific difference in the biology of PCa. Therefore, identification of race-specific molecular differences is needed to address the disparity in treatment outcome. In this study, we have determined the race-specific differences in CCR9 signaling. Phospho-proteomic profile of key pro-survival molecules following CCL25 treatment in African American (AA) and European American (EA) PCa cells was determined using antibody microarray and validated by western blot analyses. Coupling and decoupling of G-protein(s) with CCR9 in response to CCL25, which determines downstream signaling of CCR9 was ascertained by immunoprecipitation assay (IPA). Cell viability and apoptosis in response to a taxane drug docetaxel (DTX), with/without CCL25 stimulation and CCR9-blockade, were examined using MTT and flow cytometry, respectively. Levels of pro-apoptotic proteins were determined by western blot analyses. Our data show differential G-protein(s) decoupling from CCR9 in AA and EA cells. CCR9-activation dissociated Gαi2/3/Gαq/ Gα13/Gβ1γ7 –proteins in AA cells compared to Gαs/Gβ2γ9 and Gα13/Gαs/G β1/β3γ7 in EA cells, respectively, contribute to different molecular mechanisms supporting cell survival in cell lines derived from two races. Race-specific G-protein signaling in PCa cells, following CCL25 stimulation, is reflected into hyper-activation of molecules involved in PI3K/Akt and MEK/Erk1/2 signaling, which are associated with PCa aggressiveness in AA cells compared to EA counterparts. Further, activation of CCR9-CCL25 axis significantly influences the therapeutic response of PCa cells against DTX, which is highly compromised in AA cells compared to EA cells following CCL25 stimulation. However, this protective effect of CCL25 was abrogated after CCR9 blockade. Inhibition of MEK/Erk1/2 axis significantly improved DTX-induced cell death in AA cells, suggesting the importance of this axis in reducing drug response. Further, stimulation with CCL25, exclusively downregulated cleaved caspase-7, 8 and Bim in response to DTX in AA cells. In all, differential decoupling of G-proteins from CCR9 controls the downstream signaling and therefore determines disparity associated with PCa outcome and offer novel race-specific therapeutic targets for PCa.

Citation Format: Neeraj Kapur, Hina Mir, Shailesh Singh. Race specific differences in G-protein decoupling from CCR9 in prostate cancer cells contribute to the differences in docetaxel response [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 4288.
Abstract 4292: Molecular mechanism of APIO-EE-7 suppresses cell metastasis by targeting Aurora B in osteosarcoma
Authors: Jin Guoguo , Li Jitian , Guo Zhiping , Teng Junyan , Li Xiaoling , Zhao Zhenjiang
Published: August 2019

Osteosarcoma is one of the most prevalent malignant bone tumors in children and adolescents and has the characteristics of early metastasis, rapid progression and poor prognosis. Although with the advancement in techniques and treatment increasing the survival rates up to 60%, the prognosis remains poor for most patients with metastatic or recurrent osteosarcoma. Identifying the molecular mechanism and developing therapeutic agents for metastasis is urgent. Aurora B kinase play a key role in mitosis and have been reported to be associated with cancer metastasis. However, the role of Aurora kinase in osteosarcoma is still unclear. In this study, we identified a novel compound, referred to as APIO-EE-7, which inhibits growth and colony formation and induces apoptosis in osteosarcoma. Using computer modeling, we found that APIO-EE-7 can interact with Aurora B at ATP-binding pocket. Treatment with APIO-EE-7 can increase EMT marker expression level of E-cadherin and decrease N-cadherin, vimentin and survivin expression. Importantly, APIO-EE-7 dramatically attenuated tumor incidence and volume in osteosarcoma metastasis mouse model. Our findings suggest that APIO-EE-7 is a potential therapeutic agent against osteosarcoma metastasis by targeting Aurora B, which provides hope for rapid clinic translation.

Citation Format: Guoguo Jin, Jitian Li, Zhiping Guo, Junyan Teng, Xiaoling Li, Zhenjiang Zhao. Molecular mechanism of APIO-EE-7 suppresses cell metastasis by targeting Aurora B in osteosarcoma [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 4292.
Abstract 4293: Analyzing the redox/fyn/c-Cbl pathway in glioblastoma multiforme: A mechanistic approach
Authors: Shah Neal , Stripay Jennifer
Published: August 2019

Glioblastoma multiforme (GBM) is the most common aggressive tumor of the central nervous system (CNS) with 10,000 newly diagnosed cases annually, and an incidence rate of 3 in 100,000 individuals in the United States. Unfortunately, the current standard of care of radiotherapy with concomitant Temozolomide (TMZ) has not been effective in consistently controlling tumor growth, as the median age of survival for patients is 14.6 months after treatment, with inevitable recurrence beyond this time. One of the difficulties that emerge when treating GBM is tumor heterogeneity. For example, GBM cells upregulate different receptor tyrosine kinases (RTKs). Signaling through RTKs enables these cells to maintain their proliferative status to ensure their survival. The E3 ubiquitin ligase c-Cbl is a negative regulator of RTKs, and our lab has found it to be physically sequestered by ARGHEF7 (Cool-1) in GBM. We identified a combination of drugs, a c-Cbl restorative agent (CRA01) and an oxidizing agent (Tamoxifen [TMX]), that decreased c-Cbl/Cool-1 complex formation and activated c-Cbl through the Redox/Fyn/c-Cbl pathway (RFC) in GBM cells. Treatment with CRA01+TMX led to degradation of RTKs. Little is known about the RFC pathway in cancer regulation or its ability to prevent cell growth in TMZ resistant GBM cells. Here, we examine ways to regulate c-Cbl in GBM cells and seek to identify the mechanism(s) resulting in c-Cbl/Cool-1 complex formation. Furthermore, we aim to use a mouse model of TMZ resistance to determine the effects of CRA01+TMX in vivo. These results will provide important knowledge on the RFC pathway that can help properly identify patients with GBM and different cancers with c-Cbl dysregulation for whom this treatment could prove beneficial.

Citation Format: Neal Shah, Jennifer Stripay. Analyzing the redox/fyn/c-Cbl pathway in glioblastoma multiforme: A mechanistic approach [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 4293.