bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3837: Super-enhancers define breast cancer subclasses and identify novel tumor cell vulnerabilities
Authors: Collins Cindy , Chen Mei Wei , Eaton Matthew , Orlando David , McKeown Michael , Fritz Christian , Olson Eric , Guenther Matthew
Published: August 2015

Breast cancer cell state is driven by genomic mutational events, aberrant signaling cascades and transcriptional misregulation. The profound clinical impact of ER-modulatory drugs underscores the importance of understanding and targeting the transcriptional dependencies of breast cancer cells in an effort to create new therapeutics. Recently, large clusters of cis-acting enhancers, termed Super-enhancers, have emerged as dominant transcriptional regulators of oncogenes and other key tumor drivers in cancer cells, indicating that these elements control and maintain breast tumor cell state. Mapping these elements and the genes they control in patient tumors can provide insight into breast cancer classification and identify therapeutic targets.

We have discovered Super-enhancers in breast cancer patient tissue and have characterized their roles in enforcing tumor cell state. We find that Super-enhancers define known clinical subgroups in invasive ductal carcinoma and pinpoint the putative transcriptional drivers of each subgroup. Super-enhancer-associated genes encode both known and novel therapeutic targets including kinases, phosphatases, chromatin regulators and transmembrane proteins, including key drivers such as ERRB2 in HER2+ patient samples, ESR1 in estrogen receptor positive samples, and CCND1 in samples of luminal subtype. shRNA knockdown confirms that Super-enhancer regulated genes are indeed essential for tumor cell survival and that Super-enhancer analysis in primary patient samples can be used to define new subtype specific cancer vulnerabilities.

In sum, we describe the biological and disease relevance of Super-enhancer-associated genes in the context of tumor cell state, genome mutational landscape and drug target discovery.

Citation Format: Cindy Collins, Mei Wei Chen, Matthew Eaton, David Orlando, Michael McKeown, Christian Fritz, Eric Olson, Matthew Guenther. Super-enhancers define breast cancer subclasses and identify novel tumor cell vulnerabilities. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3837. doi:10.1158/1538-7445.AM2015-3837
Abstract 3842: Expression analysis of SMYD5 in breast cancer and normal tissues
Authors: Matos Neto João Nunes de , Araujo Maíra de Azevedo Feitosa , Rabello Doralina do Amaral , Motoyama Andrea Barretto , Oliveira Diego Madureira de , Pittella Silva Fabio
Published: August 2015

Lysine methyltransferases are a group of enzymes that carry a SET domain, which catalyzes the addition of methyl groups to specific lysine residues. Several lysine methyltransferases have been described to be involved in human carcinogenesis. The SMYD family of methyltransferases constitutes a group of five genes that encodes proteins bearing a SET and a MYND domain, whose activity have not yet been completely characterized. Although deregulation of SMYD family members has been reported to contribute to cancer progression through several different mechanisms, to date a clear relationship of SMYD5 with breast cancer, the second most frequent cancer worldwide and the most common among women, was not determined. In the present study we investigated the expression profile of SMYD5 in breast tumors and adjacent non-tumor samples, in breast cancer cell lines and in several normal tissues. qPCR revealed SMYD5 mRNA expression level was downregulated in 7 breast cancer cell lines when compared to normal breast tissues. Relative expression of SMYD5 in breast tumors and normal breast samples revealed a significant (p<0.001) reduction of SMYD5 expression in tumors comparing to the non-cancerous breast samples. These findings led us to investigate the role of SMYD5 in cell proliferation. We observed that reduction of SMYD5 expression by shRNA in HEK293 cells induced acceleration in culture growth. Moreover, the generation of MDA-MB-231 tumor sublines expressing varying levels of SMYD5 revealed different proliferative profiles. SMYD5 expression inversely correlated with growth rate in highly proliferative cultures. However, slow proliferating cells (i.e. long doubling time) do not seem to be affected by SMYD5 levels. This observation indicates that specific subgroup of highly proliferative cells may depend on SMYD5 downregulation to exhibit this phenotype. In addition, we found that SMYD5 has a sub-cellular distribution similar to other SMYD family proteins suggesting it may exert enzymatic activity in both cytosolic and nuclear substrates. Taken together, our data indicates a possible role for SMYD5 in modulating breast carcinogenesis through epigenetic alterations, probably acting as tumor suppressor.

Note: This abstract was not presented at the meeting.

Citation Format: João Nunes de Matos Neto, Maíra de Azevedo Feitosa Araujo, Doralina do Amaral Rabello, Andrea Barretto Motoyama, Diego Madureira de Oliveira, Fabio Pittella Silva. Expression analysis of SMYD5 in breast cancer and normal tissues. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3842. doi:10.1158/1538-7445.AM2015-3842
Abstract 3843: Nrf2-keap1 axis: uncovers molecular profile in lung carcinoids
Authors: Sparaneo Angelo , la Torre Annamaria , Trombetta Domenico , Di Candia Leonarda , Copetti Massimiliano , Balsamo Teresa , Maiello Evaristo , Graziano Paolo , Fazio Vito M. , Muscarella Lucia A. , Sanchez-Cespedes Montse
Published: August 2015

Introduction. The Keap1/Nrf2 pathway is a master regulator of antioxidants and cellular stress re-sponses implicated in resistance of tumour cells against chemotherapeutic drugs. Recent data suggest that genetic and epigenetic mechanisms may play a pivotal role in the regulation of KEAP1 expression in Non Small Cell Lung Cancer. At present, the data concerning the mechanism of alteration of Nrf2-Keap1 pathway in the Carcinoids of the lung remain almost incomplete.

Materials and methods. Here we report a comprehensive molecular characterization of Keap1/Nrf2 axis in cell lines and 48 tissues from Lung Carcinoid affected patients by integrating data from altera-tions at DNA, transcript and protein levels.

Results. An hypermethylation of the CpGs island located into the P1 promoter region of the KEAP1 was detected in 16 out of the 32 Typical Carcinoids (50%) and 8 out of the 16 Atypical Carcinoids (50%). No somatic mutations were detected both in the kelch-repeats region of the KEAP1 gene and in the Nhe2 domain of NFE2L2 gene, whereas LOH at the KEAP1 locus (19p13.2) was found in more than 50% of cases, suggesting that biallelic inactivation of KEAP1 in lung cancer is a common event in lung carcinoids. Decreased of the KEAP1 expression in methylated cancer cells induced greater nuclear accumulation of Nrf2, causing enhanced transcriptional xenobiotic metabolism enzymes.

Conclusions. This is the first study to our knowledge that provides new insights into the mechanism of deregulation of Nrf2/Keap1 detoxification pathway in lung carcinoids. Loss of KEAP1 function leading to constitutive activation of Nrf2-mediated gene expression in cancer suggests that deregulation of the Keap1/Nrf2 system could play a pivotal role in the pathogenesis of carcinoids.

Citation Format: Angelo Sparaneo, Annamaria la Torre, Domenico Trombetta, Leonarda Di Candia, Massimiliano Copetti, Teresa Balsamo, Evaristo Maiello, Paolo Graziano, Vito M. Fazio, Lucia A. Muscarella, Montse Sanchez-Cespedes. Nrf2-keap1 axis: uncovers molecular profile in lung carcinoids. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3843. doi:10.1158/1538-7445.AM2015-3843
Abstract 3847: MSI status frequency, MSI-target genes mutation profile and ancestry proportions in Brazilian colorectal carcinoma patients
Authors: Berardinelli Gustavo N. , Scapulatempo-Neto Cristovam , Duraes Ronilson , Peixoto-Guimaraes Denise , Melani Armando , Pereira Rui , Reis Rui
Published: August 2015

Introduction: Colorectal cancer (CRC) is the fourth in incidence and in mortality worldwide for both sexes. There are three pathways in the pathogenesis of CRC: chromosome instability (CIN), microsatellite instability (MSI) and CpG island methylator phenotype (CIMP). These pathways are closely related and some tumors may harbor alterations in multiple pathways. The MSI is the less common and is more frequently related with HNPCC Syndrome. In Brazil, CRC incidence is increasing and the frequency of MSI and its biological and clinical impact are largely unexplored. Furthermore, the literature has reported the influence of ancestry factors on the incidence and prognosis in this tumor type. Goals: to assess the frequency of MSI status in Brazil CRC tumors; to analyze the mutation profile of MSI target genes in MSI-positive tumors and to determine the patients ancestry by molecular markers. Materials and Methods: 1013 CRC patients were enrolled in the study. The MSI evaluation was performed using a multiplex PCR comprising 5 markers (NR27, NR21, NR24, BAT25, and BAT26). The MSI-H tumors were also assessed for mutations in a panel of 25 MSI-target genes, and their genetic ancestry will be evaluated using a panel of 46 AIMs (Ancestry-Informative Markers). Results: MSS status was observed in 86.0%, MSI-L in 4.0% and MSI-H in 10.0% of cases. The analysis of 25 MSI-target genes in 101 MSI-H cases showed distinct mutations frequencies, with the highest mutated genes been ATM (83.0%), EGFR (80.0%) and MRE11 (78.0%) and the lowest mutated genes been BLM (3.0%), WISP3 (2.0%) and TRBP2 (1.0%). No alterations were observed in BRCA1, BRCA2, XRCC2, PTEN and XPO5. We showed that the average ancestry proportions for MSS+MSI-L group were 74.1% of European, 12.3% of African, 6.6% of Native Americans, and 7.0% of East Asian, while for MSI-H group were 73.7% of European, 14.3% of African, 6.8% of Native Americans, and 5.2% of East Asian. So, no statistical difference was observed between distinct MSI status groups. Conclusion: The MSI frequencies identified in Brazilian CRC patients are in agreement with the international literature. We identify altered MSI-target genes in MSI-H tumors samples with potential clinical impact. For while, the ancestry proportions not showed an important factor for MSI status in Brazilian CRC patients.

Citation Format: Gustavo N. Berardinelli, Cristovam Scapulatempo-Neto, Ronilson Duraes, Denise Peixoto-Guimaraes, Armando Melani, Rui Pereira, Rui Reis. MSI status frequency, MSI-target genes mutation profile and ancestry proportions in Brazilian colorectal carcinoma patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3847. doi:10.1158/1538-7445.AM2015-3847
Abstract 3848: Subtype-specific DNA damage dependent and independent functions of damage repair proteins confer chemo-resistance to leukemia
Authors: Salunkhe Sameer , Kaur Ekjot , Ramaswamy Ashwin , Patkar Ketaki , Dutt Shilpee
Published: August 2015

Resistance to chemotherapy is a major challenge in the field of leukemia. Since, cancer cells can acquire resistance to DNA damage based therapy by modulating DNA Damage Repair (DDR) pathways, an in-depth understanding of DDR is important for novel drug discoveries. Hence, to understand relation between DDR and resistance we used doxorubicin resistant sub-line (K562-R) of K562 and Mitoxantrone resistant sub-line (HL60/MX) of HL60 as a model system.

We show that lethal doses of Mitoxantrone to HL60 and HL60/MX do not induce DNA DSBs (double strand breaks) and accordingly there is no activation of Chk2, although there is equal uptake of drug in both, sensitive and resistant cell types. Since Mitoxantrone produce DSBs by targeting TOP2B, we checked the expression of TOPB2 and found significant decrease in the levels of topoisomerase 2 B (TOP2B). Moreover, negative regulator of TOPB2, mir 21-5P is upregulation in untreated HL60/MX explaining the absence of DSBs in HL-60/MX with Mitoxantrone treatment. Surprisingly, although there are no DSBs induced, we find high levels of DNA-PKcs, MRE11 and Rad50 in HL-60/MX. Furthermore, inhibition of DNA-PKcs re-sensitizes HL-60/MX cells to Mitoxantrone, suggesting a DNA damage independent role for DNA-PK in HL-60/MX cells. Recently DNA-PKcs is shown to play key role in fat metabolism. Indeed we find significant differences in the metabolism of HL60 and HL-60/MX where HL-60 cells use glucose but HL-60/MX cells show reduced glucose and glutamine metabolism and an over expression of fatty acid synthase. However link between DNA-PKcs over expression and differential metabolism in these cells still need to be explored. Interestingly, in contrast to HL60 model, Doxorubicin does induce equal DSBs in K562 and K562-R cells. However K562-R cells hyperactivate ATM and Chk2 to repair their DNA and survive. Importantly, we show that K562 start to show elevated activation of ATM and Chk-2 as early as two rounds of drug treatment. Accordingly, ATM inhibition leads to induction of apoptosis in resistant K562 cells.

In conclusion, we show that K562 and HL60 cells use the DNA double strand break repair proteins in DNA damage dependent and independent pathways to acquire resistance to DSB inducing chemo therapeutics. Our data also highlight the importance of considering subtype specific therapeutics in leukemia.

Note: This abstract was not presented at the meeting.

Citation Format: Sameer Salunkhe, Ekjot Kaur, Ashwin Ramaswamy, Ketaki Patkar, Shilpee Dutt. Subtype-specific DNA damage dependent and independent functions of damage repair proteins confer chemo-resistance to leukemia. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3848. doi:10.1158/1538-7445.AM2015-3848
Abstract 3854: Inhibition of uracil DNA glycosylase (UDG) sensitizes cancer cells to thymidylate synthase inhibitors
Authors: Yan Yan , Condie Allison , Gerson Stanton
Published: August 2015

Thymidylate synthase (TS) is responsible for the de novo synthesis of thymine nucleotides that are used as building blocks for DNA synthesis. Two classes of therapeutic agents inhibit TS including fluropyrimidines (eg, 5-FU, 5-FdU) and antifolates (eg, pemetrexed), which lead to depletion of deoxythymidine triphosphate (dTTP) and expansion of deoxyuridine triphosphate (dUTP). Fluropyrimidines are also metabolized to 5-fluorouridine triphosphate (5FdUTP). As a result, both elevated dUTP and 5FdUTP are incorporated into DNA. Uracil DNA N-glycosylase (UDG or UNG) is the primary DNA repair enzyme to remove uracil and 5-FU bases from DNA and creates abasic (AP) sites, thus initiating base excision repair (BER) pathway. However, whether the cytotoxic effects of TS inhibitors are dependent on UDG activity still remains controversial. Previously, our lab has shown that in DLD1 colon cancer cells, knockout of UDG hypersensitized cells to pemetrexed treatment and the cell death was accompanied by remarkable S phase arrest and stalled replication fork. In this study, we examined the cytotoxicity of both pemetrexed and 5-FdU in SW480, HCT116, DLD1, and HEC1A cancer cell lines after performing stable UDG knockdown (KD) by shRNA. We hypothesized that loss of UDG would sensitize cancer cells to TS inhibitors treatment with accumulation of a large amount of uracil and 5-FU bases in DNA and ultimately lead to replication folk collapse. Results showed that reduced UDG protein and activity levels enhanced the cell killing effect, increased the sub-G1 populations, and delayed cell cycle recovery following TS inhibitors treatment. In response to 5-FdU treatment, cells with UDG shRNA were mainly arrested at late G1 and early S phase by 24 hours of treatment. After releasing cells in drug free medium, loss of UDG displayed delayed recovery from cell cycle arrest in comparison to shRNA scramble control cells. We have also detected a significant induction of the amount of AP sites after incubation of extracted DNA from UDG shRNA KD cells with purified UDG protein following 5-FdU treatment, indicating the accumulation of uracil and 5-FU in DNA as a consequence of 5-FdU treatment. Now, further studies are undergoing to determine the actual levels of uracil and 5-FU incorporation into DNA and the replication status after TS inhibitors treatment. These studies confirm that uracil and 5-FU incorporation due to loss of UDG accelerates stall of replication, collapse of the replication fork, and increased cytotoxicity of TS inhibitors.

Citation Format: Yan Yan, Allison Condie, Stanton Gerson. Inhibition of uracil DNA glycosylase (UDG) sensitizes cancer cells to thymidylate synthase inhibitors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3854. doi:10.1158/1538-7445.AM2015-3854
Abstract 3857: The polymorphisms of XRCC1 Arg194Trp and the XRCC1Arg399Gln affect the clinical features and the prognosis of MDS
Authors: Norjmaa Batchimeg , Saitoh Takayuki , Kasamatsu Tetsuhiro , Minato Yusuke , Sunaga Noriaki , Murakami Hirokazu
Published: August 2015

Background: X-ray repair cross-complementing group 1 (XRCC1) is involved an important role in base excision repair (BER) system of DNA repair. Polymorphism in DNA repair genes may be modified of DNA repair capacity. However, it is unclear that the polymorphisms of XRCC1alter the clinical features of MDS patients. Our study was performed to evaluate the effect of the XRCC1Arg194Trp and the XRCC1Arg399Gln with the susceptibility and clinical features of MDS.

Methods: We genotyped the polymorphisms by using polymerase chain reaction -restriction fragment-length polymorphism (PCR-RFLP) analysis in 119 patients with MDS [median 67.9 years, range 17.1-86.5 years; male/female 81/38; RCUD (n = 40), RARS (n = 6), RCMD (n = 21), MDS-U (n = 13), RAEB-1(n = 14), RAEB-2 (n = 12), others (n = 13)] and 202-health controls.

Results: In the allele and genotype frequencies of the XRCC1Arg194Trp and the XRCC1Arg399Gln were not statistically significant difference in patients and the controls. However, Arg/Arg genotypes of XRCC1 194 and the XRCC1 399 were significantly associated with lower Hb. In addition, XRCC1 399 non Arg/Arg genotype was significantly associated with previous history of radiotherapy and multiple cancers. Furthermore, XRCC1Arg194Trp non Arg/Arg genotype and XRCC1Arg399Gln Arg/Arg genotype were significantly associated with poor prognosis of MDS patients.

Conclusion: We found that the polymorphisms of XRCC1 may be affected the clinical features and the prognosis of MDS.

Citation Format: Batchimeg Norjmaa, Takayuki Saitoh, Tetsuhiro Kasamatsu, Yusuke Minato, Noriaki Sunaga, Hirokazu Murakami. The polymorphisms of XRCC1 Arg194Trp and the XRCC1Arg399Gln affect the clinical features and the prognosis of MDS. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3857. doi:10.1158/1538-7445.AM2015-3857
Abstract 3861: Prognostic impact of KRAS copy number amplification in esophagogastric junction adenocarcinoma
Authors: Nakamura Kenichi , Imamura Yu , Tokunaga Ryuma , Ohuchi Mayuko , Kiyozumi Yuki , Kosumi Keisuke , Izumi Daisuke , Harada Kazuto , Kurashige Junji , Karashima Ryuichi , Hiyoshi Yukiharu , Iwagami Shiro , Baba Yoshifumi , Sakamoto Yasuo , Miyamoto Yuji , Yoshida Naoya , Saeki Hiroshi , Oki Eiji , Maehara Yoshihiko , Baba Hideo
Published: August 2015

Background: The incidence of esophageal adenocarcinoma (EAC) or esophagogastric junction adenocarcinoma (EGJA) has been dramatically increasing. KRAS oncogenic alterations activate multiple pathways in various types of cancer. A recent comprehensive genetic study has reported that around 20% of EAC harbor KRAS copy number gain (Dulak AM et al, 2012, Nat Genet). However, the prognostic role KRAS amplification has not been well examined in EAC/EGJA.

Methods: DNA was extracted from formalin-fixed paraffin-embedded tissue of 145 EGJA (Siewert types I-III). KRAS copy number was detected by real-time quantitative PCR, and KRAS copy number gain was defined as KRAS/RNase P (as a reference) ratio ≥ 2.5. The impact of KRAS amplification was analyzed in relation to clinicopathological factors, and patient outcomes [disease free survival (DFS), and overall survival (OS)]. Multivariate cox proportional hazards model was performed adjusting clinicopathological factors.

Results: KRAS amplification was observed in 40 (33.1%) cases. KRAS amplification was significantly associated with the lymph node metastasis (P = 0.0145), and was significantly associated with poorer patient outcome (P = 0.0355 in DFS, and P = 0.0067 in OS). In multivariate analysis, KRAS amplification was an independent prognostic factor for OS [multivatiate hazard ratio (HR) = 2.53; 95% confidence interval (CI), 1.22-5.25, P = 0.014] and DFS [multivatiate hazard ratio (HR) = 1.94; 95% confidence interval (CI), 1.04-3.56, P = 0.0382].

Conclusions: KRAS copy number gain may be a useful prognostic marker in EGJA.

Citation Format: Kenichi Nakamura, Yu Imamura, Ryuma Tokunaga, Mayuko Ohuchi, Yuki Kiyozumi, Keisuke Kosumi, Daisuke Izumi, Kazuto Harada, Junji Kurashige, Ryuichi Karashima, Yukiharu Hiyoshi, Shiro Iwagami, Yoshifumi Baba, Yasuo Sakamoto, Yuji Miyamoto, Naoya Yoshida, Hiroshi Saeki, Eiji Oki, Yoshihiko Maehara, Hideo Baba. Prognostic impact of KRAS copy number amplification in esophagogastric junction adenocarcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3861. doi:10.1158/1538-7445.AM2015-3861
Abstract 3869: Exploration of mechanisms for chromothripsis by irradiation
Authors: Morishita Maki , Muramatsu Tomoki , Hayashi Shin , Hirai Momoki , Suto Yumiko , Konishi Teruaki , Moriyama Keiji , Inazawa Johji
Published: August 2015

Chromothripsis is the massive but highly localized chromosome rearrangements within a one-step catastrophic event rather than a series of subsequent and random alterations. Chromothripsis occurs commonly in various human cancers and it is thought to be associated with increasing malignancy and oncogenesis. However the causes and consequences of chromothripsis remain unclear. Therefore, to explore mechanisms of chromothripsis, we investigated whether chromothripsis was artificially induced by irradiation. We elicited DNA double-strand breaks in the oral cancer cell line HOC313, or its highly metastatic subline HOC313-LM by The Single Particle Irradiation system to Cell (SPICE), a focused vertical micro-beam system designed to irradiate the nuclei of adhesive cells. We established irradiated monoclonal sublines and analyzed the copy number variations (CNVs) and SNPs using SNP array. Chromosomal alterations, induced by irradiation including CNVs, were detected in some monoclonal sublines. Interestingly SNP array analysis showed that one subline named LM200-#25 had multiple chromosomal alterations which happened locally in chromosome 7. Moreover, we detected several chromosomal alterations such as t(12;7;11) translocation in LM200-#25 subline by Multi-Color FISH analysis. These results suggested that chromothripsis might be induced by irradiation in LM200-#25 subline.

Citation Format: Maki Morishita, Tomoki Muramatsu, Shin Hayashi, Momoki Hirai, Yumiko Suto, Teruaki Konishi, Keiji Moriyama, Johji Inazawa. Exploration of mechanisms for chromothripsis by irradiation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3869. doi:10.1158/1538-7445.AM2015-3869
Abstract 3873: Improving the effectiveness of chemotherapy by combining compounds that suppress drug-induced microsatellite instability
Authors: Chang Christina L. , Huang Li-Yan , Wu Chang-Lin , Chi Jhih-Ying
Published: August 2015

Many chemotherapeutic agents damage DNA and induce DNA damage response (DDR) signaling, resulting in growth arrest or apoptosis. DNA mismatch repair (MMR) system not only maintains genomic stability but also participates in DDR signaling. MMR deficiency leads to genetic hypermutability, manifested as microsatellite instability (MSI), and contributes to cancer pathogenesis and drug resistance. MSI has been linked to chemotherapy and therapy-related secondary cancer. Therefore, it is important to prevent drug-induced MSI to increase the effectiveness of chemotherapy while reducing cancer mortality. The purpose of this study is to characterize the MSI-inducing ability of individual chemotherapeutic agents and identify small compounds that suppress drug-induced MSI. In a human colorectal cancer cell model, all tested drugs individually induced the instability of reporter and endogenous microsatellites while reducing steady-state levels of certain MMR proteins. Relatively, oxaliplatin induced a higher MSI frequency than many tested drugs such as 5-FU. It is known that MMR-deficient tumors are resistant to 5-FU and not oxaliplatin. We then screened a commercially available library for small compounds that suppress oxaliplatin-induced MSI using a dual-fluorescent MSI reporter. We found that the majority of compounds were capable of reducing oxaliplatin-induced MSI. However, they also undesirably decreased the cytotoxicity of oxaliplatin. On the other hand, a small number of compounds such as I-6 and II-13 suppressed oxaliplatin-induced MSI with or without an improvement of drug cytotoxicity. Relative to oxaliplatin alone, co-treatment of 1 μM oxaliplatin with 6-10 μM compound II-13 decreased drug-induced MSI frequency by 45-70% without significantly affecting the cytotoxicity of oxaliplatin. Co-treatment of oxaliplatin with 4-10 μM compound I-6, however, decreased both drug-induced MSI and cell numbers by 50-78% in a dose-dependent manner. To our surprise, compounds such as II-13 suppressed MSI induced by oxaliplatin but not by 5-FU. In conclusion, individual drugs displayed different MSI-inducing abilities whereas MSI-suppressing compounds appear to be drug-specific. Further identification and validation of MSI-suppressing compounds specific for 5-FU or leucovorin, for example, would improve the effectiveness of combination chemotherapy such as FOLFOX.

Citation Format: Christina L. Chang, Li-Yan Huang, Chang-Lin Wu, Jhih-Ying Chi. Improving the effectiveness of chemotherapy by combining compounds that suppress drug-induced microsatellite instability. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3873. doi:10.1158/1538-7445.AM2015-3873
Abstract 3874: Mutational landscapes of oral tongue squamous cell carcinoma reveal recurrent mutations in genes of therapeutic and prognostic relevance
Authors: Vettore Andre L. , Ramnarayanan Kalpana , Ong Choon Kiat , Leong Hui Sun , Lim Weng Khong , Cutcutache Ioana , Mcpherson John R. , Zhang Shenli , Skanthakumar Thankshayeni , Tan Daniel SW , Teh Bin Tean , Rozen Steve , Tan Patrick , Iyer N Gopalakrishna
Published: August 2015

Carcinoma of the oral tongue (OTSCC) is the most common malignancy of the oral cavity, characterized by frequent recurrence and poor survival. The last three decades has witnessed a change in the OTSCC epidemiological profile, with increasing incidence in younger patients, females and never-smokers. This study aims to characterize the OTSCC genomic landscape and to determine factors that may delineate the genetic basis of this disease, inform prognosis and identify targets for therapeutic intervention. Seventy-eight Asian OTSCC cases were subjected to whole-exome and targeted deep sequencing. While the most common mutation seen was in TP53, the OTSCC genetic landscape differed from previously described cohorts of patients with head and neck squamous cell cancers: OTSCCs demonstrated frequent mutations in DST, FSIP2 and RNF213 while alterations in CDKN2A and NOTCH1 were significantly less frequent than previously reported. Despite a lack of previously-known NOTCH1 mutations, integrated analysis showed enrichments of alterations affecting Notch signaling, more commonly seen in women. Importantly, Notch pathway alterations were prognostic on uni- and multivariate analyses. Furthermore, a high proportion of OTSCCs presented with alterations in drug targetable genes and chromatin remodeling genes. Mutations in these groups were also prognostic, where patients harboring mutations in these actionable pathways more likely to succumb from recurrent disease compared to those who did not, suggesting that these patients should indeed be considered for treatment with targeted compounds in future trial designs. In conclusion, these findings define the mutational landscape of OTSCC, highlight the key role of the Notch signaling pathway in oral tongue tumorigenesis and uncover somatic mutations in therapeutically relevant genes which may represent candidate drug targets.

Citation Format: Andre L. Vettore, Kalpana Ramnarayanan, Choon Kiat Ong, Hui Sun Leong, Weng Khong Lim, Ioana Cutcutache, John R. Mcpherson, Shenli Zhang, Thankshayeni Skanthakumar, Daniel SW Tan, Bin Tean Teh, Steve Rozen, Patrick Tan, N Gopalakrishna Iyer. Mutational landscapes of oral tongue squamous cell carcinoma reveal recurrent mutations in genes of therapeutic and prognostic relevance. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3874. doi:10.1158/1538-7445.AM2015-3874
Abstract 3877: The mutational burdens and evolutionary ages of early gastric cancers are comparable to those of advanced gastric cancers
Authors: Jung Seung-Hyun , Kim Min Sung , Choi Youn Jin , Kim Shinn Young , Shin Sun , Yoo Nam Jin , Chung Yeun-Jun , Lee Sug Hyung
Published: August 2015

Early gastric cancers (EGCs) precede advanced gastric cancers (AGCs), with a favourable prognosis compared to AGC. To understand the progression mechanism of EGC to AGC, it is required to disclose EGC and AGC genomes in mutational and evolutionary perspectives. We performed whole-exome sequencing and copy number profiling of nine microsatellite (MS)-unstable (MSI-H) (five EGCs and four AGCs) and eight MS-stable (MSS) gastric cancers (four EGCs and four AGCs). In the cancers, we observed well-known driver mutations (TP53, APC, PIK3CA, ARID1A, and KRAS) that were enriched in cancer-related pathways, including chromatin remodelling and tyrosine kinase activity. The MSI-H genomes harboured ten times more mutations, but were largely depleted of copy number alterations (CNAs) compared to the MSS cancers. Interestingly, EGC genomes showed a comparable level of mutations to AGC in terms of the number, sequence composition, and functional consequences (potential driver mutations and affected pathways) of mutations. Furthermore, the CNAs between EGC and AGC genomes were not significantly different in either MSI-H and MSS. Evolutionary analyses using somatic mutations and MSI as molecular clocks further identified that EGC genomes were as old as AGC genomes in both MSS and MSI-H cancers. Our results suggest that the genetic makeup for gastric cancer may already be achieved in EGC genomes and that the time required for transition to AGC may be relatively short. Also, the data suggest a possibility that the mutational profiles obtained from early biopsies may be useful in the clinical settings for the molecular diagnosis and therapeutics of gastric cancer patients.

Citation Format: Seung-Hyun Jung, Min Sung Kim, Youn Jin Choi, Shinn Young Kim, Sun Shin, Nam Jin Yoo, Yeun-Jun Chung, Sug Hyung Lee. The mutational burdens and evolutionary ages of early gastric cancers are comparable to those of advanced gastric cancers. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3877. doi:10.1158/1538-7445.AM2015-3877
Abstract 3893: Whole-exome sequencing analysis of primary central nervous system lymphoma reveals recurrent MYD88 and PIM1 mutations
Authors: Nagane Motoo , Fukumura Kazutaka , Ueno Toshihide , Lee Jeunghun , Shishido-Hara Yukiko , Shirahata Mitsuaki , Mishima Kazuhiko , Ichimura Koichi , Mukasa Akitake , Narita Yoshitaka , Nishikawa Ryo , Mano Hiroyuki
Published: August 2015

Primary central nervous system lymphoma (PCNSL) is defined as diffuse large B-cell lymphoma (DLBCL) confined to the central nervous system. Although PCNSL cannot be histologically distinguished from extracerebral DLBCL, its prognosis is quite poor. To gain insights into the transforming mechanism of PCNSL, we conducted whole-exome sequencing for 44 PCNSL specimens.

Genomic DNA was extracted from tumors and their matched normal samples. Exome fragments were captured by using SureSelectXT Human All ExonV5+lncRNA, and subjected to deep sequencing with the HiSeq 2000 system.

There were 8 cases with germinal center B-cell-like (GCB) subtype and 34 cases with non-GCB subtype. Whole-exome sequencing of tumor and paired normal yielded sequencing data with a mean coverage of 156X and 80X, with 98% and 99% of the targeted bases covered by ≥20 independent reads, respectively. Of 17,832 somatic mutations identified in the PCNSL specimens, 11,611 (65%) were nonsynonymous single nucleotide variations. Predominant nucleotide substitution was a C>T transition (57%) especially in the context of the sequence GCG. We also identified 798 insertions/deletions. Interestingly, MYD88 mutations were detected in 35 of 44 patients (79.5%), and PIM1 mutations were detected in 42 patients (95.5%). Also, a number of genetic aberrations were shown to activate the NF-κB pathway.

These results suggest that MYD88 and PIM1 mutations have important roles in the development of PCNSL and could be the therapeutic targets of this intractable disorder.

Citation Format: Motoo Nagane, Kazutaka Fukumura, Toshihide Ueno, Jeunghun Lee, Yukiko Shishido-Hara, Mitsuaki Shirahata, Kazuhiko Mishima, Koichi Ichimura, Akitake Mukasa, Yoshitaka Narita, Ryo Nishikawa, Hiroyuki Mano. Whole-exome sequencing analysis of primary central nervous system lymphoma reveals recurrent MYD88 and PIM1 mutations. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3893. doi:10.1158/1538-7445.AM2015-3893
Abstract 3895: Genomic alterations modify ubiquitination pathways in pulmonary carcinoid tumors
Authors: Asiedu Michael K. , Thomas Charles L. , Dong Jie , Khadka Prasidda , Sun Zhifu , Kosari Farhad , Jen Jin , Molina Julian , Vasmatzis George , Aubry Marie Christine , Yang Ping , Wigle Dennis
Published: August 2015

Introduction: Pulmonary carcinoid tumors account for up to 5% of all lung malignancies in adults, and comprise 30% of all carcinoid malignancies. They are defined histologically as typical carcinoid (TC) and atypical carcinoid (AC) tumors, and are characterized by neuroendocrine differentiation and the potential to metastasize.

Method: We characterized genomic alterations in pulmonary carcinoid tumors using whole genome and exome sequencing in addition to mRNA expression and SNP genotyping from specimens of normal lung, typical and atypical carcinoid, and SCLC.

Results: Analysis of the sequencing data identified novel mutations in the pulmonary neuroendocrine tumor spectrum, including KRAS, ABCA9, GALNT10, HSFX1, PTHLH, RANBP2, BRIP1, FXR1, BACE2, NCOR2, DGKI, HERC1, HERC5 and GLI3. Pathway analysis found 45% of the cases to harbor a mutation in genes that are involved in protein-protein interaction with ubiquitin c (UBC) and may therefore play a role in ubiquitin protein degradation pathway. We also identified genes differentially expressed in corresponding regions of copy number variation, 52 of which were linked to ubiquitination pathways in 88% of the samples genotyped. Genes amplified in 15 to 23% of the cases included ITM2A, MAOA, EGR2, HAGH, TSC22D3, NBEA, TCEAL2, and TSPYL2 whereas deleted regions in 15% of the cases implicated CFD, GDI1, IFITM1 and IFITM2.

Conclusion: These results suggest that in addition to previously identified pathways, dysregulation of the ubiquitin pathway may contribute to lung carcinoid tumorigenesis and could be exploited for therapeutic purposes.

Citation Format: Michael K. Asiedu, Charles L. Thomas, Jie Dong, Prasidda Khadka, Zhifu Sun, Farhad Kosari, Jin Jen, Julian Molina, George Vasmatzis, Marie Christine Aubry, Ping Yang, Dennis Wigle. Genomic alterations modify ubiquitination pathways in pulmonary carcinoid tumors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3895. doi:10.1158/1538-7445.AM2015-3895
Abstract 3896: Recurrent TERT promoter mutations in primary central nervous system lymphoma
Authors: Bruno Aurélie , Daniau Mailys , Mokhtari Karima , Rahimian Amithys , Polivka Marc , Jouvet Anne , Adam Clovis , Figarella-Branger Dominique , Miquel Catherine , Eimer Sandrine , Houillier Caroline , Soussain Carole , Alentorn Agusti , Hoang-Xuan Khê
Published: August 2015

Primary central nervous system lymphoma (PCNSL) is a rare extranodal diffuse large B-cell lymphoma (DLBCL) restricted to the CNS and associated with a poor prognosis. Despite a notable effort contributing to better characterize the genomic basis of these tumors, few molecular abnormalities were proposed as predictive or prognostic biomarkers. Recently, two hotspot mutations, C228T and C250T, and the polymorphism rs2853669, located within TERT core promoter region have known a growing interest due to their prognostic value in a wide range of tumors, including melanoma, hepatocellular carcinoma or glioblastoma.

Forty-one PCNSL tumor samples of newly diagnosed PCNSL were sequenced for C228T and C250T TERT somatic mutations. TERT promoter mutations status was correlated with clinical outcome and rs2853669 genotype.

We identified C228T and C250T mutations and rs2853669 genotype in 20%, 9.4% and 50%, respectively. No case with co-occurrence of C228T and C250T mutations was identified. C228T mutations, but not C250T, were significantly associated with shorter overall survival (OS) (median OS = 4.5 months vs 33 months for non-mutated, p = 0.0048) and progression free survival (PFS) (median PFS = 3 months vs 11.5 months for non-mutated, p = 0.0260). We found no association between TERT promoter mutations and the rs2853669 genotype.

To our knowledge, we showed the presence of TERT promoter mutations in PCNSL for the first time. In addition, C228T promoter mutation was associated with a poor outcome. Considering that these mutations are known to confer enhanced TERT promoter activity, we speculate that an increased telomerase activity could play a role in PCNSL aggressiveness.

This work was granted by the LOC study group network (réseau national de centres experts des lymphomes primitifs du SNC, INCa), the Ligue contre le Cancer (Comité du Val d’Oise), the Fondation pour la Recherche Médicale (FDT20140930968), the APHP-CRIC 2013 (assistance publique - hôpitaux de Paris), and the Association pour la Recherche sur les Tumeurs Cérébrales.

Citation Format: Aurélie Bruno, Mailys Daniau, Karima Mokhtari, Amithys Rahimian, Marc Polivka, Anne Jouvet, Clovis Adam, Dominique Figarella-Branger, Catherine Miquel, Sandrine Eimer, Caroline Houillier, Carole Soussain, Agusti Alentorn, Khê Hoang-Xuan. Recurrent TERT promoter mutations in primary central nervous system lymphoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3896. doi:10.1158/1538-7445.AM2015-3896
Abstract 3897: High-throughput profiling of actionable mutations in salivary duct carcinoma
Authors: Ku Bo Mi , Bae Yeon-Hee , Jung Hyun Ae , Sun Jong-Mu , Ko Young Hyeh , Jeong Han-Sin , Son Young-Ik , Baek Chung-Hwan , Park Keunchil , Ahn Myung-Ju
Published: August 2015

Salivary duct carcinoma (SDC) is a highly aggressive subtype of salivary gland cancers and there is no established standard therapy for this disease. Thus, development of molecular markers for SDC will be important to guide the diagnosis and therapy of this aggressive tumor. We performed next-generation sequencing using the Ion Torrent AmpliSeq cancer panel, which explores the mutational status of hotspot regions in 50 cancer-associated genes, and we analyzed copy number variations (CNVs) of 21 genes by NanoString nCounter for 37 patients with SDC. Fluorescent in situ hybridization was also conducted to confirm ERBB2 gene amplification. Clinical records and tumor histopathology of the patients were retrospectively reviewed. Genetic alterations were detected in 29 of 37 (78.3%) tumors, including mutations in PIK3CA (N = 9, 24.3%), ERBB2 (N = 4, 10.8%), and EGFR (N = 4, 10.8%). To our knowledge, this is the first time that ERBB2 mutations have been reported in this tumor type. Both PIK3CA and ERBB2 mutation status were associated with poor overall survival, but without statistical significance. ERBB2 amplification was strong and common in SDC and almost all cases also exhibited EGFR and ERBB3 amplifications. This study reports the largest and most comprehensive analysis of DNA aberrations in SDC. Our results show that PIK3CA and/or ERBB2 alterations in the development of SDC might be a useful diagnostic tool and could serve as a potential therapeutic target.

Key words: Salivary duct carcinoma, next-generation sequencing, molecular markers, PIK3CA, ERBB2, EGFR

Citation Format: Bo Mi Ku, Yeon-Hee Bae, Hyun Ae Jung, Jong-Mu Sun, Young Hyeh Ko, Han-Sin Jeong, Young-Ik Son, Chung-Hwan Baek, Keunchil Park, Myung-Ju Ahn. High-throughput profiling of actionable mutations in salivary duct carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3897. doi:10.1158/1538-7445.AM2015-3897
Abstract 39: Fibroblast growth factor induces neoplastic cell transformation through a non-canonical signaling pathway
Authors: Yoo Sun-Mi , Lee Cheol-Jung , Lee Mee-Hyun , Cho Yong-Yeon
Published: August 2015

Induction of cell proliferation is closely related with the cellular signaling pathway activation by stimulation of diverse growth factors such as epidermal growth factor (EGF) and fibroblast growth factor. The stimulation of growth factors induces activation of extracellular signal-regulated kinases (ERKs)/p90 ribosomal S6 kinases (p90RSK), resulting in induction of cell proliferation and cell transformation. Although fibroblast growth factor (FGF) is a well-known growth factor and acts as a ligand of FGF receptor (FGFR), a receptor tyrosine kinase, in cytoplasmic membrane, the tumor promoter potential has not been clearly understood. Here, we provided the evidences that FGF acted as a tumor promoter. We found that FGF-induced cell proliferation and anchorage-independent cell transformation were correlated with the induction of G1/S cell cycle transition. Importantly, we found that kaempferol targeted and inhibited FGFR phosphorylation by in vitro and ex vivo. Interestingly, FGF stimulation utilized a non-canonical signaling pathway to activate RSK2 and ATF-1, which was not transduced by EGF stimulation. We confirmed that kaempferol inhibited tyrosine phosphorylation of FGFR, resulted in nuclear accumulation of phospho-ATF-1 at Ser63. Importantly, kaempferol, PKC412, PD98059 and U0126 inhibited EGF-induced anchorage-independent cell transformation in JB6 Cl41 cells. In contrast, FGF-induced cell transformation in soft agar was not inhibited by PD98059 and U0126. Taken together, these results demonstrate that FGF acts as a tumor promoter and dual inhibition of kaempferol on the kinase activities of FGFR and RSK2 suppresses the FGF-induced neoplastic cell transformation through a non-canonical signaling pathway which is not utilized by EGF stimulation.

Citation Format: Sun-Mi Yoo, Cheol-Jung Lee, Mee-Hyun Lee, Yong-Yeon Cho. Fibroblast growth factor induces neoplastic cell transformation through a non-canonical signaling pathway. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 39. doi:10.1158/1538-7445.AM2015-39
Abstract 3902: MSS HNPCC frequently contain CNVs in chromatin regulators
Authors: Chen WeiXiang , sheng Xia , Ding Jun
Published: August 2015

BACKGROUND & AIMS: Approximately half of hereditary non-polyposis colorectal cancers (HNPCCs) don't display evidence of mismatch repair defects. The pathogenesis of microsatellite-stable (MSS) HNPCCs, and their effects on patients’ prognoses and responses to treatment, differ from those of other colorectal cancers (CRCs). We sought to identify genetic somatic alterations associated with MSS HNPCCs. METHODS: We examined genomic DNA samples from 95 primary HNPCCs and adjacent normal appearing mucosae from patients undergoing surgery. We performed the copy number variation (CNV) of the entire genome using the Cytoscan HD Array in 20 MSS and 4 MSI HNPCC tumors and their adjacent normal tissues. Extensive comparison with somatic alterations in MSI HNPCCs allowed segregation of MSS HNPCC-exclusive alterations. RESULTS: We found that copy number of genes that regulate chromatin was altered in MSS HNPCCs; the most frequent CNV were observed in CHD6, CHD7 and CHD8, which encode members of the chromodomain helicase/adenosine triphosphate dependent chromatin remodeling family. Somatic genetic alterations in these 3 genes were detected in 13/10/5 of 20 MSS HNPCCs. Genes altered in patients with CHARGE syndrome (congenital malformations involving the central nervous system, eye, ear, nose, and mediastinal organs) who had CHD7 mutations were also altered in CRCs with copy number amplification in CHD7. CONCLUSIONS: Genetic aberrations in chromatin remodeling could contribute to the development of MSS HNPCCs.

Note: This abstract was not presented at the meeting.

Citation Format: WeiXiang Chen, Xia sheng, Jun Ding. MSS HNPCC frequently contain CNVs in chromatin regulators. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3902. doi:10.1158/1538-7445.AM2015-3902