bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4321: TNF receptor 2 is essential for RIP1-dependent cell death in refractory leukemia
Authors: Aguadé-Gorgorio Julia , McComb Scott , Eckert Cornelia , Dobay Maria Pamela , Cario Gunnar , Mezzatesta Caterina , Stackelberg Arend Von , Stanulla Martin , Martin Schrappe , Bourquin Jean-Pierre , Bornhauser Beat C.
Published: July 2017

The identification of molecular determinants that regulate sensitivity to specific agents is essential for the development of new therapeutic approaches in cancer. We have earlier shown that a subset of refractory acute lymphoblastic leukaemia (ALL) samples respond to SMAC-mimetic (SM) induced IAP depletion by concurrently inducing RIP1-dependent apoptosis and necroptosis. Comparative gene expression profiling indicated a correlation of sensitivity to SM with the expression of TNF receptor 2 (TNFR2) in primary ALL. Using an independent cohort of primary chemotherapy-resistant ALL samples, we found that presence of high TNFR2 expression identified by qPCR predicted ex vivo-sensitivity to SM. High TNFR2 levels also correlated with higher expression of TNFR1. Deletion of either TNFR1 or TNFR2 using CRISPR/Cas9 in primary ALL conferred resistance to treatment with SM, indicating that TNFR1 and 2 are both functionally required for cell death. Concomitant with an important role for TNFR2 in the response to SM, the overexpression of TNFR2 leads to increased sensitivity to TNF through increased activation of the TNFR1/RIP1 death axis. On the mechanistic level, SM induced recruitment of RIP1 to TNFR1, which was abolished in cells deficient for TNFR2. Taken together, our data reveal a novel function of TNFR2 in cell death signalling, as TNFR2 predicts sensitivity to SMAC mimetics and plays a key role in modulating a switch from RIP1-controlled cell survival to cell death.

Citation Format: Julia Aguadé-Gorgorio, Scott McComb, Cornelia Eckert, Maria Pamela Dobay, Gunnar Cario, Caterina Mezzatesta, Arend Von Stackelberg, Martin Stanulla, Schrappe Martin, Jean-Pierre Bourquin, Beat C. Bornhauser. TNF receptor 2 is essential for RIP1-dependent cell death in refractory leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4321. doi:10.1158/1538-7445.AM2017-4321
Abstract 433: Glycogen accumulation in aggressive breast cancers during hypoxic exposure
Authors: Altemus Megan , Yates Joel , Wu ZhiFen , Bao LiWei , Merajver Sofia
Published: July 2017

Isolation of specific metabolic alterations in aggressive triple negative and inflammatory breast cancers represents a compelling avenue for the development of treatments for these diseases. The ability of cancer to utilize diverse metabolic pathways to modulate increased survival and proliferation is well established. Indeed, we have previously described a series of metabolic adaptations in the triple negative inflammatory breast cancer cell line SUM149 and demonstrated a role for the small GTPase RhoC in the metabolic phenotype of the cell line.

In this work we seek to describe a survival mechanism for cancer cells that are subjected to hypoxic environments. Hypoxic survival or growth is often necessitated at the center of a growing tumor mass or if the tumor is growing in the lymphatic system, as is often the case for inflammatory breast cancers. Here we investigate the regulation of glycogen levels in breast cancer and normal-like cell lines in atmospheric and 1% oxygen environments. Reserves of glucose are typically stored in liver and muscle cells as the polysaccharide glycogen. Elevated levels of glycogen have previously been observed in various cancers, and recent studies have implicated the importance of glycogen metabolism in promoting cancer cell survival. We hypothesize that aggressive breast cancers utilize modifications of the glycogen synthesis and degradation pathways to provide nutritional flexibility as they proliferate and invade into diverse environments. MCF10A, SUM149, and SUM190 cell lines demonstrate a greater than 10-fold increase in glycogen accumulation when subjected to hypoxic growth conditions. MDA-MB-231 cells also increase glycogen storage, though at levels on the order of 2-3 times higher in hypoxia when compared to normoxic growth. Conditioned media for all cell lines in normoxic and hypoxic conditions were analyzed for glucose and lactate levels to determine changes in metabolite consumption.

The data presented indicate an unexpected accumulation of glycogen in response to hypoxic conditions. Studies to determine the mechanisms through which these changes occur and why they are important for continued survival and growth of the cancer cells are ongoing and will be presented.

Citation Format: Megan Altemus, Joel Yates, ZhiFen Wu, LiWei Bao, Sofia Merajver. Glycogen accumulation in aggressive breast cancers during hypoxic exposure [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 433. doi:10.1158/1538-7445.AM2017-433
Abstract 4331: Novel Wnt-SCD-LRP5/6 pathway linking liver fibrosis to cancer
Authors: Lai Keane , Kweon Soo-Mi , Chi Feng , Hwang Edward , Wu Raymond , Kabe Yasuaki , Murali Ramachandran , Mishra Lopa , Ntambi James , Tsukamoto Hidekazu
Published: July 2017

Activated hepatic stellate cells (HSCs) are primarily responsible for the genesis of liver fibrosis which promotes liver tumor development. Stearoyl-CoA desaturase (SCD) which synthesizes monounsaturated fatty acid (MUFA such as oleic acid or palmitoleic acid), is implicated in metabolic syndrome, tumorigenesis and stemness. Indeed, we demonstrate SCD upregulation in both HSCs and liver tumor cells in patients. Further, SCD correlates with the advancing grade of HCC and mortality in patients. However, its causality in tumorigenesis and mesenchyme-tumor crosstalk, and underlying mechanisms, are unknown. The present study aimed to determine whether and how SCD promotes and links liver fibrosis and cancer. In both HSCs and liver tumor-initiating stem cell-like cells (TIC), we reveal that the Wnt effector β-catenin is a potent co-activator for SREBP-1-dependent Scd transcription as demonstrated by promoter-reporter assay and re-ChIP analysis. We also discover β-catenin which drives SCD expression is in turn stabilized by SCD-derived MUFA. To identify molecular targets of MUFA mediating this SCD-β-catenin positive loop, we performed MUFA-nano-beads pull-down assay with TIC lysate, ESI-MS based identification of MUFA interacting proteins, computational docking analysis, co-IP and ribonucleoprotein-IP. These analyses reveal that MUFA is essential for LRP5/6 expression: MUFA interferes Transportin-1 and Ran-1 interaction, resulting in suppressed nuclear import of the mRNA binding protein HuR, HuR cytoplasmic accumulation, and increased HuR binding to and stabilization of Wnt co-receptor Lrp5/6 mRNA. As such, genetic or pharmacologic SCD inhibition reduces cytosolic HuR, LRP5/6 expression, β-catenin stabilization, HSC activation and TIC self-renewal and attenuates liver fibrosis and tumorigenesis in mice. Moreover, conditional genetic ablation of Scd2 in HSCs not only abrogates HSC-mediated promotion of TIC-derived tumorigenesis in a xenograft mouse model but also inhibits DEN-induced liver tumor development in Col1a1-Cre; Scd2flox/flox mice (tumor volume reduced to 21.5 + 7.9 vs. 360.9 + 193 mm3 in Scd2flox/flox mice; tumor multiplicity decreased to 18 + 5.4 vs. 45 + 8.4 in Scd2flox/flox mice, both p<0.05). Collectively, our findings support that a newly disclosed Wnt-SCD-LRP5/6 loop may serve as a novel therapeutic target for liver cancer and underlies a known crosstalk between liver mesenchyme and liver tumor development.

Citation Format: Keane Lai, Soo-Mi Kweon, Feng Chi, Edward Hwang, Raymond Wu, Yasuaki Kabe, Ramachandran Murali, Lopa Mishra, James Ntambi, Hidekazu Tsukamoto. Novel Wnt-SCD-LRP5/6 pathway linking liver fibrosis to cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4331. doi:10.1158/1538-7445.AM2017-4331
Abstract 4336: Human mesodermal-derived CNS metastasis-associated stromal cells induce a fibrotic response to limit tumor growth
Authors: Legendre Christophe , Gooden Gerald C. , Johnson Kyle N. , Martinez Rae Anne , Bernstein Mark , Glen Jennifer , Kiefer Jeffrey , Hinek Aleksander , Toms Steven A. , Salhia Bodour
Published: July 2017

Metastasis to the central nervous system (CNS) remains a major cause of mortality and morbidity in patients with systemic cancer. However, the mechanistic interactions of the neural niche with disseminated tumors cells in CNS metastases (CM) are still poorly understood. To better understand the cross-talk between the neural niche and metastatic tumors, we generated five different patient-derived cell lines (PDCs) originating from surgically resected CM. To assess the genetic and epigenetic characteristics of each PDC, DNA and RNA sequencing, and DNA methylation analysis was performed. Non-tumoral PDCs revealed normal copy number profiles, and retention of germline mutations as seen in patient-matched germline DNA. In contrast, one PDC (CM04) resembled its patient tumor, showing numerous copy number and somatic alterations. RNA-seq and DNA methylation analysis demonstrated that non-tumoral PDCs highly resembled each other, suggestive of a common cell of origin. Additionally, PDCs revealed gene expression signatures associated with cancer associated fibroblasts, epithelial to mesenchymal transition, and mesenchymal stem cells. Further in vivo studies demonstrated that CM04 cells were tumorigenic, whereas non-tumoral PDC (CM08) cells were unable to form tumors in mice. However, CM04:CM08 mixed tumors were significantly smaller than CM04 only tumors and revealed induction of a fibrotic response by immunohistochemistry. These data offer the first evidence that CNS metastasis-associated stromal cells (cMASCs) produce a collagen and fibronectin-rich extracellular matrix constituting a protective host response, which impedes growth of tumor cells. The therapeutic potential of these cells merits further exploration.

Citation Format: Christophe Legendre, Gerald C. Gooden, Kyle N. Johnson, Rae Anne Martinez, Mark Bernstein, Jennifer Glen, Jeffrey Kiefer, Aleksander Hinek, Steven A. Toms, Bodour Salhia. Human mesodermal-derived CNS metastasis-associated stromal cells induce a fibrotic response to limit tumor growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4336. doi:10.1158/1538-7445.AM2017-4336
Abstract 4348: Methylation analysis of uveal melanoma reveals definitive patterns in tumors harboring BAP1 mutations
Authors: Durante Michael , Field Matthew , Kurtenbach Stefan , Bussies Parker , Decatur Christina , Harbour J. William
Published: July 2017

Introduction: Uveal melanoma (UM) is the most common primary intraocular malignancy and can be classified by gene expression profiling into two distinct molecular classes that correspond to metastatic risk: Class 1 (low risk) and Class 2 (high risk). The less aggressive Class 1 UMs express a more differentiated phenotype and exhibit numerous characteristics of normal uveal melanocytes, while the metastasizing Class 2 UMs display loss of melanocytic differentiation and have acquired a primitive, stem-like phenotype. The majority of Class 2 UMs harbor loss of chromosome 3 in addition to inactivating mutations of the tumor suppressor BAP1, which also catalyzes ubiquitin removal from histone H2A and modulates gene expression. Histone modifications have been shown to be associated with DNA methylation and this study investigates the global methylation and gene expression changes in BAP1 mutant tumors.

Methods: RNA-Sequencing data and Illumina Human Methyl 450K BeadChip Array data obtained from 92 primary uveal melanoma tumors was analyzed using optimized pipelines.

Results: This analysis revealed that the more aggressive Class 2 tumors exhibit a distinct pattern of hypermethylation and silencing of developmental genes involved in neural crest migration and differentiation. Chromosomal regions that were significantly enriched for hypermethylated genes with decreased gene expression in Class 2 tumors included chromosome 3p14-26, 3q12-29 and 8p12-22, whereas the only significantly enriched region for genes that were hypomethylated with increased gene expression in Class 2 tumors was chromosome 8q22-24. Additionally, BAP1 itself was differentially hypermethylated in Class 2 UMs, suggesting that it may regulate its own transcription.

Conclusions: Class 2 UMs harboring BAP1 mutations displayed distinct regions of differential hypermethylation in comparison to Class 1 UMs. In these tumors, the most significantly hypermethylated regions occurred on chromosome 3 and in regions that were enriched for genes encoding neural crest guidance cue proteins that regulate homing, migration and invasion. These findings suggest that BAP1 mutations are associated with marked reorganization of the DNA methylome, providing new insights into the pathophysiology of UM and suggesting that methylation may serve as a diagnostic to further stratify metastatic risk. Furthermore, these findings may open new opportunities for targeted therapy of Class 2 UMs.

Citation Format: Michael Durante, Matthew Field, Stefan Kurtenbach, Parker Bussies, Christina Decatur, J. William Harbour. Methylation analysis of uveal melanoma reveals definitive patterns in tumors harboring BAP1 mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4348. doi:10.1158/1538-7445.AM2017-4348
Abstract 4352: Identification of ZFP42/REX1 as a regulator of cancer stemness in CD133+ liver cancer stem cells by genome-wide DNA methylation analysis
Authors: Luk Steve Tin-Chi , Tong Man , Ng Kai Yu , Yip Kevin Yuk-Lap , Guan Xin Yuan , Ma Stephanie
Published: July 2017

The existence of a cancer stem cell (CSCs) subset is well established in hepatocellular carcinoma (HCC). This subset can be characterized by its CD133 expression. Since the discovery of this marker, studies have revealed deregulated pathways and epigenetic alterations associated with this subset, but few have focused on changes in DNA methylation. This study aims to fill this research gap by discovering aberrant DNA methylation patterns governing CD133+ CSC-driven HCC. Results from Infinium HumanMethylation450 BeadChip (HuMet450 BeadChip) have led to the discovery of differential methylation patterns between CD133+ liver CSCs and matched CD133- differentiated samples. ZFP42/REX1 is one of the top-ranking differentially methylated candidates. Probes corresponding to its promoter are extensively hypermethylated in the CD133+ samples. To explore the hypothesis that promoter DNA hypermethylation modulates REX1 expression, REX1 mRNA levels were first validated to be down regulated in sorted CD133+ HCC cell lines (n=2) and HCC samples (n=46, p<0.05) by RT-qPCR. Upon 5-AZA treatment, only low-REX1-expressing cells re-expressed REX1. By in silico prediction, a CpG island of interest located in the REX1 promoter region was selected for further investigation. Results of pyrosequencing of this CpG island show that REX1 expression appears to be negatively correlated with the degree of DNA methylation in HCC cell lines (n=3); and that HCC samples (n=13) exhibit a predominantly hypermethylated state compared to the matched non-tumor samples. To add onto the clinical relevance of REX1, two HuMet450 BeadChip datasets of HCC sample cohorts (GSE54503 and GSE60753) were obtained from Gene Expression Omnibus (GEO). In these cohorts, the CpG probes corresponding to the REX1 promoter region are significantly hypermethylated (p<0.01) in HCC samples compared to the adjacent non-tumor tissues. Lentiviral-based approaches were adopted to establish stable REX1 overexpressing and knockdown cells in HCC cell lines. REX1 expression appears to be negatively correlated with the cells’ abilities to migrate, invade, and form foci in vitro; and tumorigenicity in vivo. ChIP-seq has been adopted to study the DNA-binding property of REX1 in HCC cells. These findings suggest that REX1 may play a part in mediating various cancer properties in HCC.

Citation Format: Steve Tin-Chi Luk, Man Tong, Kai Yu Ng, Kevin Yuk-Lap Yip, Xin Yuan Guan, Stephanie Ma. Identification of ZFP42/REX1 as a regulator of cancer stemness in CD133+ liver cancer stem cells by genome-wide DNA methylation analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4352. doi:10.1158/1538-7445.AM2017-4352
Abstract 4363: Bisulfite DNA sequencing analyses to detect methylation patterns in the p73 gene promoter in prostate cancer cell lines
Authors: Braganca Nicholas E. , Carastro L. Michael , Schabort Johannes J. , Park Jong Y.
Published: July 2017

Transcription is regulated through a variety of different mechanisms. One facet of transcriptional regulation is epigenetics, which is the regulation of gene expression without altering the nucleotide sequence of the genome, but rather reversible modifications, e.g. CpG methylation. The CpG islands in tumor suppressor gene promoters are often hypermethylated, thus down regulating their expression. The p73 gene is a member of the p53 tumor suppressor family of proteins, and like p53, has a bifurcated promoter. The p73 P1 promoter transcribes a full-length mRNA, which then translates into the transcriptionally active p73. The p73 P2 promoter transcribes a truncated mRNA, which translated into transcriptionally inactive ΔNp73. The ΔNp73 product lacks the N-terminal trans-activation domain that TAp73 possesses. This study sought to analyze the extent of DNA methylation in the CpG islands in the p73 P1 promoter of three prostate cancer (PCa) cell lines (LNCaP, PC-3, and DU145), and primary prostate cells. We hypothesized that the p73 P1 promoter would be hypermethylated in prostate cancer cell lines and hypomethylated in primary prostate cells. The methylation status of the p73 P1 promoter in all four prostate cell lines was analyzed by using bisulfite sequencing PCR (BSP). Our analyses revealed that a CpG island in the p73 P1 was hypermethylated in LNCaP, PC-3, and DU145 cells compared to primary prostate cells. Furthermore, among the three PCa cell lines evaluated, the p73 P1 promoter was the most methylated in DU145 cells, and the least methylated in LNCaP cells. The P1 region sequenced contained 28 CpG islands, and among them, only five were methylated in the primary prostate cells (18% methylated), 23 were methylated in LNCaP cells (82% methylated), 26 in PC-3 cells (93% methylated), and 28 in DU145 cells (100% methylated). Furthermore, of the 28 CpG sites, 14 of them were differentially methylated in the primary prostate cell line versus the three PCa cell lines evaluated in this study. These data are consistent with the PCa tumor-derived cell lines (LNCaP, PC-3, and DU145) having hypermethylated CpG sites in the p73 P1 promoter compared to the primary prostate cell line.

Citation Format: Nicholas E. Braganca, L. Michael Carastro, Johannes J. Schabort, Jong Y. Park. Bisulfite DNA sequencing analyses to detect methylation patterns in the p73 gene promoter in prostate cancer cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4363. doi:10.1158/1538-7445.AM2017-4363
Abstract 437: Stromal support of pancreatic tumor metabolism
Authors: Lyssiotis Costas A.
Published: July 2017

Pancreatic Ductal Adenocarcinoma (PDAC) is an aggressive disease characterized by a prominent desmoplastic stromal reaction and deregulated metabolism. The role of stroma in PDAC biology is complex and has been shown to play critical roles that may differ depending on the biological context. The intense stromal reaction also impacts the vasculature, leading to a highly hypoxic and nutrient poor environment. As such, these tumors must adapt how nutrients are captured and utilized to support their metabolic needs. In this talk, I will describe how stromal-associated pancreatic stellate cells (PSCs) are critical for PDAC metabolism through the secretion of non-essential amino acids (NEAA). Specifically, we uncovered an undescribed role for alanine, which outcompetes glucose and glutamine-derived carbon in PDAC to fuel the tricarboxylic acid (TCA) cycle, and thus NEAA and lipid biosynthesis. This shift in fuel sources decreases the dependence on glucose and serum-derived nutrients, which are limiting in the pancreatic tumor microenvironment. Moreover, we demonstrated that PSC alanine secretion is dependent on PSC autophagy, a process stimulated by the cancer cells. Thus, our results demonstrate a novel metabolic crosstalk between PSCs and cancer cells, with PSC-derived alanine as an alternative carbon source, and highlight a previously unappreciated metabolic network within pancreatic tumors where diverse fuel sources are utilized to promote growth in an austere tumor microenvironment.

Citation Format: Costas A. Lyssiotis. Stromal support of pancreatic tumor metabolism [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 437. doi:10.1158/1538-7445.AM2017-437
Abstract 4370: ASNS and other significant mutations in head and neck squamous cell carcinomas: mutational landscape in a South Asian population
Authors: Rehmani Sadiq , Razzak Safina Abdul , Madhani Sarosh , Azim M Kamran , Ahmed Rashdia , Khan Mumtaz , Ghias Kulsoom
Published: July 2017

Head and neck cancers are the sixth most common cancer type globally and contribute significantly to the burden of disease in South Asia. Specifically in Pakistan, they are the most commonly diagnosed cancer in males and the second most common in females. The increasing burden of head and neck squamous cell carcinoma (HNSCC) in the region along with a unique set of risk factors merited a deeper investigation of the disease at the genomic level. Whole exome sequencing of HPV-negative HNSCC samples and matched normal genomic DNA (n = 7) was performed. Smoking, oral tobacco use and alcohol were identified risk factors in the study cohort. Significant somatic single nucleotide variants (SNVs) were identified and pathway analysis performed to determine most frequently affected signaling pathways. Significant, novel recurrent mutation in ASNS (asparagine synthetase) and driver mutations in previously reported genes, including TP53, PIK3CA, FGFR2, ARID2, MLL3, MYC and ALK, were identified. Using the IntOGen platform, we identified MAP kinase, cell cycle, actin cytoskeleton regulation, PI3K-Akt signaling and other pathways in cancer as among the most commonly affected pathways in all the samples. This data is the first of its kind from the Pakistani population. The results of this study can guide a better mechanistic understanding of HNSCC in the population, ultimately contributing new, rational therapeutic targets for the treatment of the disease.

Citation Format: Sadiq Rehmani, Safina Abdul Razzak, Sarosh Madhani, M Kamran Azim, Rashdia Ahmed, Mumtaz Khan, Kulsoom Ghias. ASNS and other significant mutations in head and neck squamous cell carcinomas: mutational landscape in a South Asian population [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4370. doi:10.1158/1538-7445.AM2017-4370
Abstract 4379: Somatic exomic landscape of small intestinal adenocarcinomas
Authors: Hänninen Ulrika A. , Katainen Riku , Hamberg Jiri , Mecklin Jukka-Pekka , Forsström Linda , Pitkänen Esa , Mäkinen Netta , Aaltonen Lauri A.
Published: July 2017

The small intestine makes up 75% of the length of the alimentary tract, however, small intestinal tumors constitute less than 5% of gastrointestinal tumors. Of small intestinal tumors, around one third are aggressive adenocarcinomas with poor outcome (5-year survival rate is approximately 30%). Reasons for their rarity are still unclear. Predisposing factors include Crohn´s disease, celiac disease, hereditary genetic syndromes such as familial adenomatous polyposis (FAP) and hereditary nonpolyposis colorectal cancer (HNPCC), and dietary factors. Due to the low incidence of small intestinal adenocarcinomas (SIAs), the number of genetic studies remains insufficient. Since there are limited data available to guide the therapeutic decisions, our aim is to characterize the somatic mutational landscape of SIAs in a population-based material using exome sequencing.

We collected information on all patients diagnosed with SIA in Finland between the years 2004-2011 utilizing the Finnish Cancer Registry. This registry maintains a nation-wide database on all cancer cases diagnosed in Finland since 1953. From these we selected all cases with 1) confirmed small intestinal primary tumor, 2) available tumor material, and 3) the tumor content of at least 50%. In order to focus solely on small intestinal tumors, we excluded tumors of the papillary region since they might also have arisen from the pancreas or the biliary tract. Altogether 107 tumors representing all three parts of the small intestine were selected for exome sequencing. The tumor data was filtered against the ExAC and SISU databases to remove germline variations. In addition, Sanger sequencing of the corresponding normal tissue will be used to verify the somatic origin of the most interesting observed mutations. The data analysis is ongoing. The average number of mutations in a tumor was 358 (range 40 - 4,166). Preliminary results show that the most frequently mutated known cancer genes were TP53 (42%) and KRAS (31%). We will identify all the most frequently mutated genes, compare the mutational patterns between the three different sections of the small intestine, and further characterize their similarities to gastric and colorectal adenocarcinomas. We will also analyze the association between the discovered mutations and patients’ survival time. This comprehensive characterization of the molecular basis of SIAs will provide better insight on how these tumors arise and possibly how they should be treated.

Citation Format: Ulrika A. Hänninen, Riku Katainen, Jiri Hamberg, Jukka-Pekka Mecklin, Linda Forsström, Esa Pitkänen, Netta Mäkinen, Lauri A. Aaltonen. Somatic exomic landscape of small intestinal adenocarcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4379. doi:10.1158/1538-7445.AM2017-4379
Abstract 4382: Genomic events associated with metastasis of colorectal cancer by whole-genome sequencing
Authors: Pan Yi , Tong Joanna , Kwan Johnny , Lo Kwok Wai , Chan Anthony , To Ka Fai
Published: July 2017

Background: The diversity of the genomic landscape in colorectal cancer (CRC) is under active investigation. Concordance in molecular events between primary CRC and metastatic tumors is a subject of debate. Understanding the genetic background of metastatic CRC facilitates personalized therapies that target specific molecular events associated with the tumor.

Methods: We performed whole genome sequencing in matched primary, metastasis and normal tissues from 3 patients with RAS/NRAS/BRAF wild types and microsatellite stable CRC. We implemented an analysis pipeline that integrated the genetic lesions to characterize somatic single nucleotide variations (SNVs), short insertions and deletions (indels), structural variations including fusions and copy number alterations.

Results: Both primary and metastatic tumors showed a predominant mutational signature of C: G →T: A transition. A total of 282 non-silent mutations were identified in 3 pairs of CRC (median 63 per tumor, range 42 to 98). There were 148 (52.5%) variants shared in matched primary and metastatic tumors, 63 (22.3%) were found unique to primary and 71 (25.2%) were unique to the metastases. Only common well known genes (APC and TP53) and TTN mutations were found to be recurrent in the 3 patients. A total of 609 (range 33-171 per tumor) structural variants were discovered with 44.1% concordance between primary and metastasis pairs. We also identified 6 novel candidate fusions shared in primary and metastases and 2 private to the primary tumors. Consistent with the result of previous studies, copy loss at chromosome 17p and 18, and gain at chromosome 5, 8 and 13 were the common events both in the primary and metastatic tumor.

Discussion and conclusions: Our data demonstrated a considerable difference in mutational landscape between primary CRCs and their matching metastatic tumors. The result suggested that the metastasis might originate from a distinct subclone from a heterogeneous primary tumor, or additional gain or loss of function via mutation to permit tumor invasion and spreading is necessary to facilitate metastasis. Each of the two models is complicated by the possibility of tumor heterogeneity within the primary tumor. In conclusion, comprehensive analysis and assessment for the genomic events is a powerful approach to delve deeper into the internal relations and contradictions between primary and paired metastases, helping to identify novel genomic events associated with metastasis of CRC.

Citation Format: Yi Pan, Joanna Tong, Johnny Kwan, Kwok Wai Lo, Anthony Chan, Ka Fai To. Genomic events associated with metastasis of colorectal cancer by whole-genome sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4382. doi:10.1158/1538-7445.AM2017-4382
Abstract 4386: Identification of clinically relevant colon cancer genes predictve of improved relapse free survival
Authors: Parsons Marie J.
Published: July 2017

Colorectal cancer (CRC) is the third most common cancer worldwide, affecting over 15,000 individuals in Australia each year. While CRC is often detected at a stage where resection of the primary tumour is possible, approximately 50% will relapse and die from metastatic disease. Prognostication is mainly determined by tumour depth (T), lymph node stage (N) and the extent of cancer spread (M). However, clinical outcomes of patients with the same TNM stage can be heterogeneous. Therefore, there is a need to identify markers to better predict prognosis and stratify patients for treatment regimes.

A panel of 113 candidate CRC genes were identified as significantly mutated in whole genome and whole exome sequencing studies from 361 MSS colon cancers and 63 CRC cell lines. Custom amplicon panels for target enrichment were designed for use with the HaloPlexTM target enrichment system. Sample libraries were prepared for 274 patients with stage II/III CRC using the automated Bravo liquid handling platform followed by next-generation sequencing (NGS) on the Illumina Next-Seq 500.

Analysis of the 113 candidate genes identified 31 genes recurrently mutated above 10 percent in our discovery cohort. We identified 4 genes previously reported as colon cancer genes (APC 68%, TP53 60%, KRAS 30% and PIK3CA 20%), confirming APC, TP53 and KRAS as the most frequently mutated genes in CRC. To identify novel and clinically relevant genes, the 31 genes in our discovery cohort were tested for association with clinical features of CRC. In the discovery cohort, 24/31 genes were significantly associated with right sided CRC, 10/31 with mucinous CRC, 9/31 with stage II CRC and 7/31 with improved relapse free survival (RFS). Of these significantly associated genes, 10/24 genes were validated as significantly associated with right sided colon cancer, 3/9 with stage II and 3/10 with mucinous CRC in the validation cohort. Five of these genes were selected for further investigation as they were significantly associated with improved RFS, together with one or more clinical feature of CRC.

Identification of novel recurrently mutated genes is key to a better understanding of the molecular mechanisms of CRC and development of novel therapeutics.

Citation Format: Marie J. Parsons. Identification of clinically relevant colon cancer genes predictve of improved relapse free survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4386. doi:10.1158/1538-7445.AM2017-4386
Abstract 4389: TSC1/2 mutations define a molecular subset of HCC with aggressive behavior and treatment implication
Authors: Ho Daniel Wai , Chan Lo Kong , Chiu Yung Tuen , Xu Iris Ming , Poon Ronnie , Cheung Tan To , Tang Chung Ngai , Tang Victor , Lo Irene , Lam Polly , Yau Derek , Li Miao Xin , Wong Chun Ming , Ng Irene O. L.
Published: July 2017

We investigated the mutational landscape of mTOR signaling cascade in hepatocellular carcinomas (HCCs) with chronic hepatitis B (HBV) background, aiming to evaluate and delineate mutation-dependent mechanism of mTOR hyper-activation in hepatocarcinogenesis. We performed next-generation sequencing on human HCC samples and cell line panel. Systematic mutational screening of mTOR pathway-related genes was undertaken and mutant genes were evaluated based on their recurrence. Protein expressions of TSC1, TSC2 and pRPS6 were assessed by immunohistochemistry in human HCC samples. Rapamycin sensitivity was estimated by colony formation assay in HCC cell lines and the treatment was further tested using our patient derived tumor xenograft (PDTX) models. Results: We identified and confirmed multiple mTOR components as recurrently mutated in HBV-associated HCCs. Of significance, we detected frequent (16.2%, n = 18/111) mutations of TSC1 and TSC2 genes in the HCC samples. The spectrum of TSC1/2 mutations likely disrupts the endogenous gene functions in suppressing the downstream mTOR activity through different mechanisms and leading to more aggressive tumor behavior. Mutational disruption of TSC1 and TSC2 was also observed in HCC cell lines and our PDTX models. TSC-mutant cells exhibited reduced colony forming ability upon Rapamycin treatment. With the use of the biologically relevant TSC2-mutant PDTXs, we demonstrated the therapeutic benefits of the hyper-sensitivity towards Rapamycin treatment. Taken together, our findings suggest the significance of previously undocumented mutation-dependent mTOR hyper-activation and frequent TSC1/2 mutations in HBV-associated HCCs. They define a molecular subset of HCC having genetic aberrations in mTOR signaling, with potential significance of effective specific drug therapy.

Citation Format: Daniel Wai Ho, Lo Kong Chan, Yung Tuen Chiu, Iris Ming Xu, Ronnie Poon, Tan To Cheung, Chung Ngai Tang, Victor Tang, Irene Lo, Polly Lam, Derek Yau, Miao Xin Li, Chun Ming Wong, Irene O. L. Ng. TSC1/2 mutations define a molecular subset of HCC with aggressive behavior and treatment implication [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4389. doi:10.1158/1538-7445.AM2017-4389
Abstract 4401: Role of estrogen signaling in colon microenvironment during obesity
Authors: Archer Amena , Pettersson Linnea , González-Granillo Marcela , Savva Christina , Korach-André Marion , Williams Cecilia
Published: July 2017

Recent epidemiological studies highlight the strong association between high body mass index (BMI) and enhanced risk of colon cancer. This association appears stronger in men than in women, indicating a possible protective role of estrogens in this context. The biological action of the estrogens is mediated by specific transcription factors, the estrogen receptors (ERs). ERβ is the main ER in the intestine; and it is expressed in both epithelial cells and immune cells. Anti-inflammatory and anti-tumorigenic effects of ERβ in colitis-associated neoplasia have been demonstrated. Several rodent models for obesity show an impaired intestinal epithelial barrier function and an increase of pro-inflammatory markers in the colon. Moreover, in murine colitis models, high fat diet (HFD) exacerbates colonic inflammation. However, the specific molecular mechanisms linking obesity to increased colon cancer development, where estrogen signaling may be involved, is not clear.

We hypothesize that ERβ-selective agonists can oppose the HFD-mediated inflammatory pro-tumorigenic colonic signalling in a gender-specific manner during obesity, and thereby protect against colorectal cancer. Our study is focused on the initiation of colon inflammation during obesity and aims to investigate the impact of ERβ activation in this context. To address this question, male and female mice were fed a HFD for 26 weeks and treated with a ERβ-selective agonist for 3 weeks prior sacrifice. Stool pellets were regularly collected. Animals were sacrificed; colon samples and caecal contents were collected for further analysis. We show that the expression pattern of inflammatory genes in colon is modified by the ERβ-selective agonist in HFD fed mice. Moreover the ERβ-selective agonist appears to induce gender-specific changes of the microbiota of HFD-fed mice. Our results show that an ERβ-selective agonist can modulate the colon microenvironment during obesity in mice and will provide a better comprehension of the molecular mechanisms leading to obesity-associated colonic inflammation.

Citation Format: Amena Archer, Linnea Pettersson, Marcela González-Granillo, Christina Savva, Marion Korach-André, Cecilia Williams. Role of estrogen signaling in colon microenvironment during obesity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4401. doi:10.1158/1538-7445.AM2017-4401
Abstract 4402: CHTM1, a novel protein linked to cellular metabolism and human malignancy
Authors: Babbar Mansi , Huang Ying , Sheikh M Saeed
Published: July 2017

Several lines of emerging evidence indicate that alterations in metabolism are linked to pathogenesis of human malignancies. However, more studies are needed to completely understand the link between tumorigenesis and metabolism. In this context, we have characterized a novel protein named CHTM1 (Coiled-coil Helix Tumor and Metabolism 1) that appears to be associated with cancer and cellular metabolism. Per our findings, CHTM1 was present in cytosol as well as mitochondria. CHTM1 knockdown in human cancer cell lines caused oxidative stress, and decrease in cellular oxygen consumption and mitochondrial ATP levels, suggesting mitochondrial dysfunction. In view of the importance of mitochondria to nutrient stress, the effect of CHTM1 deficiency on human cancer cells in glucose-deprived conditions was also analyzed. The results indicated that CHTM1-deficient cells became more sensitive to glucose deprivation and exhibited altered cellular metabolism involving down regulation of PKC-CREB-PGC1 alpha signaling events. CHTM1 expression was also found to be increased in patient samples representing breast, colon and lung cancers when compared to their respective matching normal tissues. Based on our findings, we propose CHTM1 to be a valuable tumor marker that can also be developed as a target for novel therapeutics particularly those that exploit cellular metabolism to mediate their effects.

Citation Format: Mansi Babbar, Ying Huang, M Saeed Sheikh. CHTM1, a novel protein linked to cellular metabolism and human malignancy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4402. doi:10.1158/1538-7445.AM2017-4402
Abstract 4409: Cholesterol pathway determines ovarian cancer drug resistance through transcription factor SREBP2
Authors: Karashchuk Galina , Karashchuk Nataliya , Caksa Signe , Smith Tyler S. , Brodsky Alexander S.
Published: July 2017

Ovarian cancer is the most common cause of gynecological cancer death in women in United States. Up to 70% of all ovarian cancer cases are high-grade serous carcinomas with 5-year survival rates less than 30%. Recent studies have suggested the importance of the cholesterol pathway in multiple cancers including gynecological malignancies. Here we demonstrate that genetic or pharmacological disturbance of cholesterol pathway in high-grade serous ovarian carcinoma cell lines results in significant changes in survival rate after drug treatment, and in protein and RNA expression patterns.

SREBP2 is a transcription factor encoded by SREBF2 gene that regulates expression of sterol-regulated genes and thus maintains cholesterol homeostasis. To assess the role of SREBP2 in ovarian cancer we have created a stable OVCAR8 cell line with SREBF2 disrupted using CRISPR technology. This SREBF2-KD line has reduced SREBF2 mRNA and protein expression level that indicates an effective gene knockdown. Activation of SREBF2 is dependent on the cholesterol status of the cell. We observed that expression of the SREBP2 precursor form is significantly reduced in SREBF2-KD line when cells are maintained under low serum conditions. Mutant cells treated with paclitaxel in low, but not high serum or in presence of statin, revealed significantly lower cell viability. SREBF2-KD cells do not survive long-term, high concentrations of paclitaxel, nor do they grow back as efficiently as control cells. RNA expression and proteomic analysis revealed the critical regulators mediating SREBP2 activity in stressed cells. Together, these observations suggest that the cholesterol pathway is critical for ovarian cancer cells not only to resist stresses, such as chemotherapy, but also to return to a high proliferation state upon recurrence. Further studies will provide important targets for developing new drugs for treatment of ovarian cancer.

Citation Format: Galina Karashchuk, Nataliya Karashchuk, Signe Caksa, Tyler S. Smith, Alexander S. Brodsky. Cholesterol pathway determines ovarian cancer drug resistance through transcription factor SREBP2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4409. doi:10.1158/1538-7445.AM2017-4409
Abstract 4413: Targeting glutamine metabolism in MUC1 expressing triple negative breast cancer
Authors: Goode Gennifer D. , Gunda Venugopal , Singh Pankaj
Published: July 2017

Breast cancer, the second leading cause of cancer deaths in women, accounts for nearly 1 in 3 cancer cases diagnosed in the U.S. women. Triple negative breast cancer (TNBC) accounts for approximately 15-25% of all breast cancer cases and has an increased incidence of metastasis, high recurrence within 1-3 years and a high mortality rate. Therefore, identifying factors that facilitate tumor growth and metastasis have the potential to serve as novel molecular targets for breast cancer therapy. Mucin1 (MUC1), a glycoprotein associated with chemoresistance, is aberrantly overexpressed in TNBC and facilitates growth and metastasis of TNBC cells. Recent studies suggest a role for MUC1 in modulating cancer cell metabolism to support tumor growth. In the present study we examined the role that MUC1 plays in TNBC tumor metabolism; thus facilitating tumor growth. Our results indicate that MUC1 expression facilitates glutamine metabolism. A correlation between MUC1 expression, glutamine dependency, and amino-oxyacetate (AOA) sensitivity was established. These alterations can be attributed in part to alterations in the expression of genes regulating glutamine metabolism. Collectively, these findings suggest that MUC1 serves as a metabolic regulator in TNBC, facilitating metabolic reprogramming of glutamine that influences growth of TNBC. Additionally, the findings with AOA’s effectiveness provide evidence for potential therapeutic utility, particularly for MUC1 overexpressing TNBC.

Citation Format: Gennifer D. Goode, Venugopal Gunda, Pankaj Singh. Targeting glutamine metabolism in MUC1 expressing triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4413. doi:10.1158/1538-7445.AM2017-4413
Abstract 4416: Studies on role of acyl-CoA cholesterol acyltransferase (ACAT) expression in ovarian/endometrial cancer progression - An invitro study
Authors: Ayyagari Vijayalakshmi N. , Wang Xinjia , Brard Laurent
Published: July 2017

INTRODUCTION: Cancer progression and tumorigenesis have been linked to alterations in cellular metabolic pathways of lipid and cholesterol synthesis in many cancers. Increased levels of cholesterol esters (CE) have been reported in breast cancer, leukemia, glioma and prostate cancer, but not exploited in detail in ovarian and endometrial cancers. Inside cells, excess free cholesterol is esterified by acyl-CoA cholesterol acyltransferase (ACAT) and stored as cholesteryl ester (CE) in lipid droplets (LDs). Cholesteryl ester accumulation may be a consequence of loss of tumor suppressor PTEN and subsequent activation of PI3K/AKT pathway as observed in pancreatic cancer. In the present study, we focused on the role of ACAT and cholesterol esters in altered cholesterol metabolism in ovarian/endometrial cancer cell lines.

METHODS: We studied the effect of abrogation of cholesterol esterification either by an ACAT-1 inhibitor/shRNA knockdown or via inhibition of PI3K/AKT/mTOR pathways and subsequent effect on ovarian/endometrial cancer cells proliferation, invasion, cell migration and tumorigenesis. The expression of ACAT was studied at the protein and mRNA levels in a panel of ovarian/ endometrial cancer cell lines and also in normal and ovarian cancer clinical samples. ACAT expression was assessed by western blotting, ELISA, quantitative RT-PCR and immunostaining techniques.

RESULTS: Our results reveal an elevated expression of ACAT-1 at both protein and mRNA levels in ovarian and endometrial cancer cell lines as compared to primary cells. Our results also provide preliminary data on involvement of ACAT and cholesterol esters in the progression and metastasis of ovarian cancer.

CONCLUSION: These studies may aid in the development of new biomarkers or treatment targets for ovarian/endometrial cancer.

Citation Format: Vijayalakshmi N. Ayyagari, Xinjia Wang, Laurent Brard. Studies on role of acyl-CoA cholesterol acyltransferase (ACAT) expression in ovarian/endometrial cancer progression - An invitro study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4416. doi:10.1158/1538-7445.AM2017-4416