bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4562: Slug knockdown suppresses malignant phenotype of nanomaterial-transformed human lung epithelial cells
Authors: Voronkova Maria , Luanpitpong Sudjit , Wang Liying , Rojanasakul Yon
Published: August 2015

Nanomaterials have increasingly become part of modern everyday life, but their long-term health effects are largely unknown. Previous studies have shown that carbon nanotubes (CNTs), one of the most widely used nanomaterials in industry, can induce or promote tumor formation in animals, but the underlying mechanisms are unclear. We previously found that chronic exposure to CNTs induced malignant transformation of human lung epithelial cells, the primary cellular target of inhaled nanomaterials. The transformed cells exhibited aggressive cancer phenotypes, including increased cell migration, invasion and anchorage-independent cell growth. We hypothesized that such increased aggressiveness may be due to epithelial-mesenchymal transition (EMT). To test this hypothesis, cultured human lung epithelial BEAS-2B cells were continuously exposed to physiologically relevant concentration (0.02 μg/cm2 surface area dose) of single-walled CNT (SWCNT) for a period of 6 months. The cells were then analyzed for EMT markers and aggressive cellular behavior. Western blot analysis of EMT markers indicated an increased expression of mesenchymal markers and decreased epithelial markers, indicating the activation of EMT in the chronic SWCNT-exposed cells. Moreover, the cells exhibited a dramatic increase in one of the EMT master regulators, a transcription factor Slug (Snail2). We hypothesized that Slug upregulation may be responsible for the aggressive phenotype of the cells. We stably downregulated the Slug expression using lentiviral shRNA particles, and examined its effect on cell migration and invasion by Transwell® assays. Our results showed that knockdown of Slug attenuated cell migration and invasion without having any effect on cell proliferation. Together, our results indicated the activation of EMT by SWCNT and demonstrated its role in aggressive cancer phenotype. Slug plays a crucial role in this process and could serve as a potential biomarker for CNT-induced malignancies.

Citation Format: Maria Voronkova, Sudjit Luanpitpong, Liying Wang, Yon Rojanasakul. Slug knockdown suppresses malignant phenotype of nanomaterial-transformed human lung epithelial cells. [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 4562. doi:10.1158/1538-7445.AM2015-4562
Abstract 4587: Genome-wide copy number analysis identified a copy number polymorphism at chromosome 8p11 associated with sporadic colorectal cancer risk in Singapore Chinese
Authors: Cheah Peh Yean , Thean Lai Fun , Teo Yik Ying , Koh Woon-Puay , Yuan Jian-Min , Chew Min Hoe , Tang Choong Leong
Published: August 2015

Colorectal cancer (CRC) is one of the most frequent cancers and leading cause of cancer mortality in the developed world. Twin study has attributed about 35% of the etiology of sporadic CRC to genes. Hitherto, more than 20 single nucleotide polymorphism (SNP) loci have been associated with CRC risk. The role of structural variant in CRC, however, remains unclear. We performed genome-wide association study (GWAS) on 2,000 ethnicity-, age-, and gender-matched Singapore Chinese CRC patients (aged 50 or more and with no dominant family history of CRC) and healthy controls. Genome-wide genotyping was performed using Affymetrix SNP 6 platform. Copy number polymorphism (CNP) was interrogated in 1830 samples that passed quality assurance tests using a multivariate segmentation algorithm. A 150 kb region at chromosome 8p11 was identified to be significantly associated (-log10 p-value = 29) with sporadic CRC risk. This CNP was preferentially amplified in the cases compared to the controls. The amplification was not gender-specific suggesting that it is not involved in gender-limiting pathway. It is now being replicated in an independent panel using digital polymerase chain reaction (dPCR) and multiplex endogenous reference technique. In silico analysis of a 1.5 Mb region encompassing the CNP reveals a candidate gene 300kb 5′ of the CNP previously implicated in cancer progression. The expression of this gene in cases with copy number and metastasis status is being interrogated.

Citation Format: Peh Yean Cheah, Lai Fun Thean, Yik Ying Teo, Woon-Puay Koh, Jian-Min Yuan, Min Hoe Chew, Choong Leong Tang. Genome-wide copy number analysis identified a copy number polymorphism at chromosome 8p11 associated with sporadic colorectal cancer risk in Singapore Chinese. [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 4587. doi:10.1158/1538-7445.AM2015-4587
Abstract 4616: Genome wide association analysis identified 15q24 as a bladder cancer susceptibility locus
Authors: Matsuda Koichi , Takahashi Atsushi , Tanikawa Chizu , Kubo Michiaki , Nakamrua Yusuke
Published: August 2015

Bladder cancer is one of the most frequent cancers, which causes ∼150 000 death per year in the world. Both environmental and genetic factors are involved in the development of bladder cancer, and tobacco smoking is known to be the most important factor to increase the risk of bladder cancer; Recent genome-wide association studies (GWASs) in European populations have identified multiple genetic factors associated with bladder cancer. However, no GWAS has yet been conducted in Asian populations. Through genome wide association analysis and an independent replication study using a total of 1,131 bladder cancer cases and 12,558 non-cancer controls of Japanese populations, here we identified a SNP rs11543198 on chromosome 15q24 as a bladder cancer susceptibility locus. Rs1154319 was associated with bladder cancer risk with odds ratio (OR) of 1.41 and P value of 4.03 × 10-9. Subgroup analysis revealed rs11543198 to have a stronger effect in male smokers with OR of 1.66. Imputational analysis in this region suggested CYP1A2, which metabolizes tobacco-derived carcinogen, as a causative gene. We also confirmed the association of previously-reported loci, SLC14A1, APOBEC3A, PSCA, and MYC, with bladder cancer. Our finding implies the crucial roles of genetic variations on the chemically-associated development of bladder cancer.

Citation Format: Koichi Matsuda, Atsushi Takahashi, Chizu Tanikawa, Michiaki Kubo, Yusuke Nakamrua. Genome wide association analysis identified 15q24 as a bladder cancer susceptibility locus. [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 4616. doi:10.1158/1538-7445.AM2015-4616
Abstract 4626: Genetic susceptibility to diffuse large B-cell lymphoma in a pooled study of three Eastern Asian populations
Authors: Rothman Nathaniel , Bassig Bryan A. , Cerhan James R. , Au Wing-Yan , Kim Hee Nam , Sangrajrang Suleeporn , Hu Wei , Tse Jovic , Berndt Sonja , Zheng Tongzhang , Zhang Heping , Pornsopone Pattarapong , Lee Je-Jung , Kim Hyeoung-Joon , Skibola Christine F. , Vijai Joseph , Burdette Laurie , Yeager Meredith , Brennan Paul , Shin Min-Ho , Liang Raymond , Chanock Stephen , Lan Qing
Published: August 2015

Diffuse large B-cell lymphoma (DLBCL) is an aggressive subtype of non-Hodgkin lymphoma (NHL) and is the most common NHL subtype diagnosed worldwide. Some epidemiologic data have indicated differences in DLBCL incidence rates and subtype distributions between Eastern Asian and Western countries. The first large-scale genome-wide association study (GWAS) of DLBCL with over 4000 cases conducted among individuals of European ancestry recently identified five independent SNPs that achieved genome-wide significance, and two SNPs that showed a suggestive association with DLBCL risk. In order to evaluate whether Eastern Asians and individuals of European ancestry share similar genetic risk factors for this disease, we attempted to replicate these GWAS findings in a pooled series of 1124 DLBCL cases and 3596 controls from Hong Kong, South Korea, and Thailand. Three of the five genome-wide significant SNPs from the DLBCL GWAS were significantly associated with DLBCL in our study population, including the top finding from the GWAS, EXOC2 rs116446171, which achieved genome-wide significance in our data (per allele OR = 2.04, 95% CI = 1.63-2.56; ptrend = 3.9 × 10-10). Additionally, we observed a significant association with PVT1 rs13255292 (per allele OR = 1.34, 95% CI = 1.19-1.52; ptrend = 2.1 × 10-6), which was the second strongest finding in the GWAS, and with HLA-B rs2523607 (per allele OR = 3.05, 95% CI = 1.32-7.05; ptrend = 0.009). Our study, which provides the first evaluation in Eastern Asians of SNPs definitively associated with DLBCL risk in individuals of European ancestry, indicates that at least some of the genetic factors associated with risk of DLBCL are similar between these populations.

Citation Format: Nathaniel Rothman, Bryan A. Bassig, James R. Cerhan, Wing-Yan Au, Hee Nam Kim, Suleeporn Sangrajrang, Wei Hu, Jovic Tse, Sonja Berndt, Tongzhang Zheng, Heping Zhang, Pattarapong Pornsopone, Je-Jung Lee, Hyeoung-Joon Kim, Christine F. Skibola, Joseph Vijai, Laurie Burdette, Meredith Yeager, Paul Brennan, Min-Ho Shin, Raymond Liang, Stephen Chanock, Qing Lan. Genetic susceptibility to diffuse large B-cell lymphoma in a pooled study of three Eastern Asian populations. [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 4626. doi:10.1158/1538-7445.AM2015-4626
Abstract 4631: AKAP12 is elevated in paclitaxel-resistant ovarian cancer cells and correlates with poor ovarian cancer patient survival
Authors: Bateman Nicholas , Jaworski Elizabeth , Wang Guisong , Dubil Elizabeth , Marcus Charlotte , Conrads Kelly , Teng Pang-ning , Hood Brian , Hamilton Chad , Maxwell Larry , Darcy Kathleen , Conrads Thomas
Published: August 2015

Objective: Although most ovarian cancer patients respond initially to the standard of care involving carboplatinum/paclitaxel-based chemotherapy, the majority will recur with chemotherapeutically resistant disease. Unfortunately, no clinical biomarker(s) for predicting or monitoring chemotherapeutic resistance are available. We sought to identify shed and/or secreted proteins from paclitaxel-resistant human ovarian cancer cells and identify whether any of these correlate with ovarian cancer patient outcome.

Methods: A proteomic analysis of secretomes from high grade serous ovarian cancer (HGSOC) cells (OV90) was compared to that from a syngeneic paclitaxel-resistant variant (OV90-TR) and a cancer cell line developed from a chemorefractory HGSOC patient. Associations between the identified candidates and patient outcome were assessed from publicly available transcript expression data (n = 545 ovarian cancer patients) and validated independently (n = 795 ovarian cancer patients).

Results: Among the 81 differentially abundant proteins identified (q<0.05) from paclitaxel-sensitive vs -resistant HGSOC cell secretomes, AKAP12 was verified to be elevated at the protein and transcript level in all models of paclitaxel-resistant HGSOC. Further, elevated AKAP12 transcript expression was found to significantly correlate with poor progression-free (Hazard Ratio = 1.487 (± 0.148), p = 0.0085 (± 0.002) and overall (Hazard Ratio = 1.22 (± 0.08), p = 0.009 (± 0.013) survival.

Conclusions: These findings suggest that elevation and efflux of AKAP12 is characteristic of paclitaxel-resistant HGSOC cells and that elevated AKAP12 expression correlates with poor ovarian cancer patient survival.

Citation Format: Nicholas Bateman, Elizabeth Jaworski, Guisong Wang, Elizabeth Dubil, Charlotte Marcus, Kelly Conrads, Pang-ning Teng, Brian Hood, Chad Hamilton, Larry Maxwell, Kathleen Darcy, Thomas Conrads. AKAP12 is elevated in paclitaxel-resistant ovarian cancer cells and correlates with poor ovarian cancer patient survival. [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 4631. doi:10.1158/1538-7445.AM2015-4631
Abstract 4644: Curcumin C3 ® prevents ultraviolet B radiation-induced acute damage in JB6 keratinocytes and mouse skin via FGF-2/mTOR/NF-KB pathway
Authors: Khandelwal Alok R. , Anandharaj Arun , Oleksandr Ekshyyan , Moore-Medlin Tara , Fleurette Abreo , Nathan Cherie-Ann O.
Published: August 2015

Background and Significance: Aggressive Cutaneous Squamous cell carcinoma (CSCC) of the face has become the second most common type of skin cancer in the USA due to ultraviolet B (UVB) exposure in tanning booths and sun exposure of our military personnel. UVB is a carcinogen and our previous studies established oral administration of Curcumin C3 complex (C3), a standardized preparation of three curcumonoids - Curcumin (76.07%), Demethoxycurcumin (20.28%) and Bisdemethoxycurcumin (3.63%), delayed UVB-induced tumor onset and multiplicity, but not tumor progression. Accordingly, we sort to determine the preventative efficacy of C3® against UVB-induced photodamage in promotion sensitive JB6 skin keratinocytes and SKH-1 hairless mouse epidermis on the early neoplastic events in the development of UVB-induced skin carcinogenesis.

Methods: SKH-1 mice were either administered vehicle or C3 (100mg/kg/b.w) complex orally for 14 days followed by a single exposure to UVB radiation (180mj/cm2). Mice were euthanized 24 hours after UVB exposure and skin tissues and serum were collected. For in vitro studies, promoter-sensitive JB6 mouse epithelial cells were pre-treated with C3® for 2 h and the effects on UVB-induced early molecular signaling events were assessed.

Results: C3® attenuated UVB-induced epidermal hyperplasia and significantly decreased epidermal and plasma levels of fibroblast growth factor-2 (FGF-2); an important mitogen implicated in proliferation and differentiation of skin keratinocytes. In vitro, C3®blocked UVB-dependent FGF-2 induction and proliferation of cultured keratinocytes via down regulation of nuclear factor kappa B (NF-KB) and Mammalian target of rapamycin (mTOR) signaling pathways.

Conclusion: Our findings suggest C3® has the ability to protect mice from UVB-induced acute damage. Further the photo-preventive effects of C3® are mediated, at least in part, via modulation of FGF-2/mTOR/NF-KB signaling.

Citation Format: Alok R. Khandelwal, Arun Anandharaj, Ekshyyan Oleksandr, Tara Moore-Medlin, Abreo Fleurette, Cherie-Ann O. Nathan. Curcumin C3 ® prevents ultraviolet B radiation-induced acute damage in JB6 keratinocytes and mouse skin via FGF-2/mTOR/NF-KB 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 4644. doi:10.1158/1538-7445.AM2015-4644
Abstract 4660: Association of longer telomere length with increased risk of chronic hepatitis B and hepatocelluar carcinoma
Authors: Ma Qiang , Cai Jiajing , Cai Yan , Xu Yuan , Chang Fan , Xu Lei , Guo Xiaolan
Published: August 2015

Telomere, which consists of small tandem nucleotide repeats (5′-TTAGGG-3′ in human), plays a critical role in the maintenance of genomic stability in eukaryotic chromosomes. More and more findings have shown that alteration in telomere length was involved in some diseases, however whether the telomere length is associated with the development and/or progression of disease remains poorly understood. Here a case-control study was employed to illustrate the correlation of relative telomere length(RTL) with chronic hepatitis B(CHB) and hepatocellular carcinoma(HCC). In this study, 115 cases of HCC patients, 212 patients with chronic hepatitis B and 184 healthy controls well matched with age and gender were recruited. Genomic DNA was extracted from the peripheral blood leukocytes and fluorescence quantitative polymerase chain reaction(FQ-PCR) was used to detect the telomere repeated numbers. We found that the RTL in HCC group was the longest, followed by CHB patients group and healthy control group was the shortest, showing significant statistical differences. When compared with age, the RTLs of individuals who aged more than 50 years old were obvious shorter than those younger ones in the control group, but not in the HCC and CHB group. Moreover, individuals who had longer RTLs indicated a significant increased risk of chronic hepatitis B (OR: 1.83, 95%CI: 1.22-2.73), and the longest RTLs showed higher incidence of HCC (OR: 3.22, 95%CI: 2.01-5.17) when the healthy control was used as the reference group. Most importantly, when the chronic hepatitis B group was used as the reference group, individuals who had longer RTL also suffered a significant increased risk of HCC(OR: 1.58, 95%CI: 1.03-2.41). Our results suggest that longer RTL is associated with the increased risk of chronic hepatitis B and HCC, which indicates that telomere length might be involved in the development or progression of HCC, also RTL might be used as a potential predicator of HBV relative chronic liver disease and HCC.

Citation Format: Qiang Ma, Jiajing Cai, Yan Cai, Yuan Xu, Fan Chang, Lei Xu, Xiaolan Guo. Association of longer telomere length with increased risk of chronic hepatitis B and hepatocelluar 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 4660. doi:10.1158/1538-7445.AM2015-4660
Abstract 4671: Identification of novel drugs for glioblastoma using chemical biology fingerprinting
Authors: Finlay Darren , Dhruv Harshil , Evers Lisa , Peng Sen , Kiefer Jeff , Kim Seungchan , Raizer Jeffrey , Berens Michael , Vuori Kristiina
Published: August 2015

Glioblastoma Multiforme (GBM) is an aggressive brain tumor with very poor prognosis and extremely limited therapeutic options. GBM is the most common malignant brain tumor and the search for novel targets and/ or the repurposing of already extant drugs to treat the disease is therefore of utmost importance. We describe here a comprehensive multidisciplinary approach to identifying said targets and ergo potential therapies. We have applied a novel analytical strategy to The Cancer Genome Atlas (TCGA) GBM expression data to stratify GBM into novel subtypes we call molecular contexts, or mCs. Subsequently, a panel of patient-derived GBM xenografts was ascribed to our novel mCs. Utilizing a technique we term Chemical Biology Fingerprinting, or CBF, short-term cultures derived from these clinically-relevant preclinical models were screened for chemosensitivity with a deeply annotated, yet clinically relevant, chemical library. Agents that were statistically more toxic to one context than another were then re-tested in true drug dose response experiments to confirm sensitivity. Preliminary data demonstrated that mC14, characterized by mutant p53 and transcriptionally similar to the GBM proneural subtype, showed distinct vulnerability to Arsenic Trioxide (ATO) as compared to mC4, enriched for NF1 mutations and with transcriptional patterns similar to the GBM mesenchymal subtype. To validate the ATO vulnerability signature in GBM, we acquired 20 treatment naïve archival patient samples, that were part of a Phase I/II clinical trial to study the efficacy of ATO and Temozolomide in combination with ionizing radiation (NCT00275067). Participants in the trial exhibited varied survival with ATO treatment (91 days to >1000 days) and the clinical samples were subtyped into our molecular contexts using RNAseq data.

In summary, we demonstrate a subclassification of GBM into novel molecular contexts (mCs) and show that these contexts are differentially sensitive to clinically relevant drugs.

Citation Format: Darren Finlay, Harshil Dhruv, Lisa Evers, Sen Peng, Jeff Kiefer, Seungchan Kim, Jeffrey Raizer, Michael Berens, Kristiina Vuori. Identification of novel drugs for glioblastoma using chemical biology fingerprinting. [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 4671. doi:10.1158/1538-7445.AM2015-4671
Abstract 4692: BGB-283, a novel RAF kinase and EGFR dual inhibitor, displays potent antitumor activity in B-RAF mutated colorectal cancers
Authors: Tang Zhiyu , Yuan Xi , Du Rong , Cheung Shing-Hu , Zhang Guoliang , Wei Jing , Zhao Yuan , Feng Yingcai , Zhang Yi , Du Yunguang , Hu Xiaoxia , Gong Wenfeng , Liu Yong , Gao Yajuan , Hao Rui , Ji Jiafu , Zhang Lianhai , Li Shuangxi , Sutton David , Wei Min , Zhou Changyou , Wang Lai , Luo Lusong
Published: August 2015

Oncogenic B-RAF, which drives cell transformation and proliferation, has been detected in approximately 70% of human malignant melanomas and 5-15% of colorectal cancers (CRC). B-RAFV600E mutation, which gives rise to constitutive MAPK signaling, accounts for at least 90% of oncogenic B-RAF mutations. Despite the remarkable clinical activities achieved by vemurafenib and dabrafenib in treating B-RAFV600E metastatic melanoma, their clinical efficacy in B-RAFV600E CRC is far less impressive. Prior studies suggested that feedback activation of EGFR and MAPK signaling upon B-RAF inhibition contributed to the intrinsic resistance of CRC to the first generation B-RAF inhibitors. This report represents the first characterization of a dual RAF kinase/EGFR inhibitor, BGB-283, which is currently under clinical investigations. BGB-283 is a potent and selective pan-RAF and EGFR inhibitor with IC50 ranging from 5 to 47 nM on RAF and EGFR kinases. In vitro, BGB-283 potently inhibits B-RAFV600E-activated ERK phosphorylation and cell proliferation. It demonstrates selective cytotoxicity and preferentially inhibits proliferation of cancer cells harbouring B-RAFV600E and EGFR mutation/amplification. In B-RAFV600E CRC cell lines, BGB-283 effectively inhibits the reactivation of EGFR and achieved sustained inhibition of MAPK pathway. In vivo, BGB-283 is highly efficacious in inhibiting tumor growth accompanied by partial and complete tumor regressions in both BRAFV600E mutant cell derived CRC xenograft models, including HT29, Colo205, WiDr, as well as two primary human CRC xenograft models. In particular, BGB-283 shows compelling efficacy and potent inhibition of EGFR/MAPK signaling in WiDr xenograft model where EGFR reactivation occurs upon B-RAF inhibition. These findings support BGB-283 as a potent antitumor drug candidate with clinical potential for treating CRC harboring B-RAFV600E mutation.

Citation Format: Zhiyu Tang, Xi Yuan, Rong Du, Shing-Hu Cheung, Guoliang Zhang, Jing Wei, Yuan Zhao, Yingcai Feng, Yi Zhang, Yunguang Du, Xiaoxia Hu, Wenfeng Gong, Yong Liu, Yajuan Gao, Rui Hao, Jiafu Ji, Lianhai Zhang, Shuangxi Li, David Sutton, Min Wei, Changyou Zhou, Lai Wang, Lusong Luo. BGB-283, a novel RAF kinase and EGFR dual inhibitor, displays potent antitumor activity in B-RAF mutated colorectal 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 4692. doi:10.1158/1538-7445.AM2015-4692
Abstract 4710: Evaluation of the glutaminase inhibitor CB-839 in non-small cell lung cancer
Authors: Boroughs Lindsey K. , Chen Pei-Hsuan , Cai Ling , Rodriguez Mirna , Zhang Winter , Huffman Kenneth E. , Byers Lauren A. , Girard Luc , Gazdar Adi F. , Heymach John V. , White Michael A. , Minna John D. , Emberley Ethan , Pan Alison , Parlati Frank , DeBerardinis Ralph J.
Published: August 2015

Glutamine is an abundant nutrient used by cancer cells to support energetic and biosynthetic pathways. Given that many cancer cells exhibit glutamine dependence, there has been interest in developing inhibitors targeting glutaminase, which catalyzes conversion of glutamine to glutamate. CB-839 is a glutaminase inhibitor with preclinical efficacy in suppressing cancer cell growth in culture and in vivo. It is now in Phase I clinical trials for solid and hematological malignancies, including non-small cell lung cancer (NSCLC).

Here we set out to identify biomarkers predicting sensitivity of NSCLC cells to CB-839, using a highly annotated panel of 81 cell lines. These lines had heterogeneous oncogenotypes and displayed about a 5-fold range in their ability to tolerate glutamine deprivation. Assessing CB-839 sensitivity in ∼40 lines revealed a 5-fold difference in growth suppression among cell lines. There was a strong correlation between CB-839 sensitivity and both glutamine dependence and glutamate secretion. In a subset of 4 representative cell lines, CB-839 suppressed [U-13C]glutamine metabolism in both sensitive and insensitive cells suggesting other mechanisms contribute to CB-839 sensitivity. To identify potential biomarkers predicting CB-839 sensitivity, the glutamine dependence and drug sensitivity phenotypes were correlated with several orthogonal high-content data sets including mutational analysis of commonly-mutated oncogenes and tumor suppressors; sensitivity to chemotherapeutic agents; gene expression arrays; and reverse phase protein arrays (RPPA). Although we did not identify a strong correlation between mutational status and CB-839 sensitivity, expression of phospho-Rb (S807/811) and Smad3 did correlate with drug sensitivity. In addition, sensitivity to glutamine withdrawal correlated with expression of c-Myc and MEK2 protein. While further work is necessary to examine the importance of these proteins in glutamine metabolism, we hypothesize that one or more of these may represent novel biomarkers predicting sensitivity to glutaminase inhibition.

Citation Format: Lindsey K. Boroughs, Pei-Hsuan Chen, Ling Cai, Mirna Rodriguez, Winter Zhang, Kenneth E. Huffman, Lauren A. Byers, Luc Girard, Adi F. Gazdar, John V. Heymach, Michael A. White, John D. Minna, Ethan Emberley, Alison Pan, Frank Parlati, Ralph J. DeBerardinis. Evaluation of the glutaminase inhibitor CB-839 in non-small cell lung cancer. [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 4710. doi:10.1158/1538-7445.AM2015-4710
Abstract 4721: Epithelial to mesenchymal transition is not required for breast to lung metastasis but contributes to chemoresistance
Authors: Fischer Kari R. , Durrans Anna , Lee Sharrell , Sheng Jianting , Choi Hyejin , Li Fuhai , Wong Stephen , Altorki Nasser K. , Mittal Vivek , Gao Dingcheng
Published: August 2015

The role of epithelial to mesenchymal transition (EMT) in metastasis is a longstanding source of controversy, largely due to an inability to monitor transient and reversible EMT phenotypes in vivo. We have established a novel and unique EMT lineage tracing system in spontaneous breast to lung metastasis models. In these models, mesenchymal-specific Cre-mediated recombination initiates permanent switch of fluorescent markers in tumor cells undergoing EMT. This allows us to track EMT tumor cells in the primary tumor, circulation and distant organs following the trail of breast to lung metastasis in vivo. We confirmed that within a predominantly epithelial primary tumor, a small portion of tumor cells undergo EMT. Strikingly, lung metastases were mainly comprised of non-EMT tumor cells maintaining their epithelial phenotype. Inhibiting EMT by overexpressing miR-200 did not impact lung metastasis development. However, EMT cells significantly contribute to recurrent lung metastasis formation after chemotherapy. These cells survived cyclophosphamide treatment due to reduced proliferation, apoptotic tolerance, and elevated expression of chemoresistance-related genes. This study suggests the potential of an EMT-targeting strategy, in conjunction with conventional chemotherapies, in the treatment of breast cancer patients.

Citation Format: Kari R. Fischer, Anna Durrans, Sharrell Lee, Jianting Sheng, Hyejin Choi, Fuhai Li, Stephen Wong, Nasser K. Altorki, Vivek Mittal, Dingcheng Gao. Epithelial to mesenchymal transition is not required for breast to lung metastasis but contributes to chemoresistance. [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 4721. doi:10.1158/1538-7445.AM2015-4721
Abstract 4762: ITPKA expression in lung and other cancers, regulated via gene body methylation, functions as an oncogene
Authors: Wang Yi-Wei , Ma Xiaotu , Zhang Yu-An , Wang Mei-Jung , Yatabe Yasushi , Lam Stephen , Girard Luc , Chen Jeou-Yuan , Gazdar Adi F.
Published: August 2015

Inositol-Trisphosphate 3-Kinase A (ITPKA), a kinase with limited tissue distribution, is involved in inositol phosphate metabolism. We identified ITPKA as up-regulated in lung and many other types of cancers. Using gain-of-function and loss-of-function approaches, we demonstrated by in vitro and in vivo assays that ITPKA functions as an oncogene to drive the development of lung cancer. We further showed that methylation level in the ITPKA gene body is significantly higher in various types of primary tumors than in corresponding non-malignant tissues, which was positively correlated with its expression. Our study revealed that DNMT3B-mediated methylation of the CpG island in ITPKA gene body regulates its expression via modulation of the binding of transcription activator SP1 to the ITPKA promoter. During the multistage pathogenesis of lung carcinoma, ITPKA gene body methylation first appeared at the in situ carcinoma stage and increased during disease progression. Thus ITPKA expression functions as an oncogene in lung and other cancers. Highly specific and sensitive expression and methylation of ITPKA was present in a wide range of tumor types, suggesting that deregulation of ITPKA may function as a universal or near universal hallmark of malignancy.

Citation Format: Yi-Wei Wang, Xiaotu Ma, Yu-An Zhang, Mei-Jung Wang, Yasushi Yatabe, Stephen Lam, Luc Girard, Jeou-Yuan Chen, Adi F. Gazdar. ITPKA expression in lung and other cancers, regulated via gene body methylation, functions as an oncogene. [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 4762. doi:10.1158/1538-7445.AM2015-4762
Abstract 4779: RUVBL1 and RUBVL2 are chromatin remodelers that represent prognostic and novel therapeutic targets for a subset of non-small cell lung cancers (NSCLCs)
Authors: Yenerall Paul M. , Kollipara Rahul , Carstens Ryan , Huffman Kenneth , Girard Luc , Rodriguez Jaime , Wistuba Ignacio , Mangelsdorf David , Minna John , Kittler Ralf
Published: August 2015

RUVBL1 and RUVBL2 (collectively referred to as RUVBL1/2) are AAA+ ATPases that function in various chromatin remodeling complexes. We found that RUVBL1/2 are overexpressed (n = 224) and prognostic of patient outcome in NSCLC patients (n = 697) who undergo surgical resection (combined TCGA, KMPlot.com, and SPORE P50CA70907 dataset analyses). To assess the importance and biological functions of RUVBL1/2 in NSCLC, we measured cell growth following depletion of RUVBL1/2 in 24 NSCLC lines, representing a spectrum of oncogenotypes and histologies, and 2 normal human bronchial epithelial cell lines (HBECs) using two independent RNAi reagents. Growth inhibitory phenotypes ranged from 19-87% and were “rescued” by exogenous expression of an RNAi-resistant cDNA construct, indicating “on-target” siRNA effects. Four of the 23 NSCLCs were very sensitive (>75% growth inhibition), while 88% of NSCLCs were more growth inhibited than HBECs, indicating a therapeutic window. To establish molecular biomarkers of RUVBL1/2 dependency, we correlated whole exome mutation status, whole transcriptome mRNA levels, and a number of other parameters to sensitivity to RUVBL1/2 depletion. Sensitivity to RUVBL1/2 knockdown did not correlate with the mutation status or expression of any genes. However, sensitivity to RUVBL1/2 depletion did correlate with doubling time. Flow cytometry analysis in NSCLC lines sensitive to RUVBL1/2 KD revealed that RUVBL1/2 depletion resulted in a G2/M arrest (but not apoptosis), and a decrease in cell cycle related transcripts, such as CDKN3, AURKA, CIT and CDC20, whereas resistant cell lines do not exhibit these changes. Initial ChIP-seq analysis suggests that RUVBL1/2 preferentially occupies cell cycle related genes and are depleted in nucleosome free regions (i.e. transcription start sites). These results, combined with results from others demonstrating the necessity of ATP hydrolysis for RUVBL1/2's function(s), indicate that the chromatin remodelers RUVBL1/2 are potential therapeutic targets in a subset of NSCLCs. (Supported by UTSW Green Center Fellowship, CPRIT RP120732, SPORE P50CA70907)

Citation Format: Paul M. Yenerall, Rahul Kollipara, Ryan Carstens, Kenneth Huffman, Luc Girard, Jaime Rodriguez, Ignacio Wistuba, David Mangelsdorf, John Minna, Ralf Kittler. RUVBL1 and RUBVL2 are chromatin remodelers that represent prognostic and novel therapeutic targets for a subset of non-small cell lung cancers (NSCLCs). [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 4779. doi:10.1158/1538-7445.AM2015-4779
Abstract 4794: Identification of FOXM1 driven gene network as a prognostic marker in breast cancer
Authors: Chu In-Sun , Kim Seon-Kyu , Roh Yun-Gil , Leem Sun-Hee
Published: August 2015

A transcription factor FOXM1 is known to play a key role in cell cycle progression where endogenous FOXM1 expression peaks at S and G2/M phases. It was previously reported that expression level of FOXM1 in breast cancer was strongly correlated with patient survival, since FOXM1 influenced endocrine therapy and chemo-response effect. The aim of this study is to estimate prognostic value of FOXM1 gene and to identify novel markers interconnected with FOXM1 to predict heterogeneous breast cancer behaviors.

Microarray gene expression profiling was performed using gene expression data obtained from 317 Korean patients with breast cancer to identify a signature associated with FOXM1. Various statistical methods, including the leave-one-out cross validation, were applied to identify a gene expression signature able to predict breast cancer outcome. The predictive value of the signature was verified in the two larger independent cohorts obtained from a public database. Unsupervised cluster analysis of gene expression data from the Korean cohort showed highly concordant subtypes of Caucasian cohort. Significant differences in overall and disease specific survival between the subgroups divided by the expression signature of FOXM1-associated genes were observed (log-rank test, each P <0.001, respectively). Multivariate Cox regression analysis revealed that the expression signature of FOXM1-associated genes was a strong predictor of breast cancer outcomes. Our findings were verified in the two independent patient cohorts and confirmed that the signature produced consistent prediction patterns. Finally, gene network analyses in the signature revealed that, FOXO1, CCNK, MYC, BRD4 and EIF4G1 could be important mediators interconnected with FOXM1 in the breast cancer behavior.

The expression signature of FOXM1 and its associated genes represents a promising diagnostic tool for the identification of breast cancer patients that have a high risk of poor clinical behavior.

Note: This abstract was not presented at the meeting.

Citation Format: In-Sun Chu, Seon-Kyu Kim, Yun-Gil Roh, Sun-Hee Leem. Identification of FOXM1 driven gene network as a prognostic marker in breast cancer. [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 4794. doi:10.1158/1538-7445.AM2015-4794
Abstract 4798: Genomic alterations in ERBB2 define a subset of pleomorphic invasive lobular breast cancer
Authors: Hirshfield Kim M. , Sanders Renee , Feld Heather K. , Barnard Nicola , Liang Li , Zhong Hua , Bhanot Gyan , Sahota Amrik S. , Brooks Andrew , Rodriguez-Rodriguez Lorna , Ganesan Shridar
Published: August 2015

Background. Pleomorphic invasive lobular carcinoma represents a unique histologic subset of breast cancer with poorer outcomes as compared with classic invasive lobular carcinoma of the breast. With the recent finding of ERBB2 alterations in recurrent invasive lobular carcinoma, the goal of this study is to define the relationship of ERBB2 alterations in the distinct subset of pleomorphic invasive lobular carcinomas.

Methods. Using the provisional invasive breast cancer data set of 962 cases in The Cancer Genome Atlas (TCGA), all breast cancers with CDH1 alterations were identified and pathologic review was performed. Independent identification of ERBB2 genomic alterations was done. The frequency and nature of genomic alterations in ERBB2, PTEN, PIK3CA, and TP53 were determined. FFPE specimens from an additional 18 cases from our own institution have been evaluated using the combination of the RainDance ThunderBolts™ Cancer Panel for validation.

Results. Of 116 TCGA breast cancers with CDH1 alterations, 86 were invasive lobular breast cancer. Within this subset, 21 pleomorphic lobular breast cancers were identified based on morphologic review. Nine ERBB2 mutations (42.9%) and three amplifications (14.3%) were found in pleomorphic invasive lobular carcinoma, but none in classic invasive lobular carcinoma (p value 1.92e-9). There were no significance differences in the frequency of TP53, PTEN or PIK3CA alterations in pleomorphic invasive lobular carcinoma as compared to classic invasive lobular carcinoma. Data from the additional 18 validation cases will be presented.

Conclusions. Genomic alterations in ERBB2 strongly associate with the finding of pleomorphic invasive lobular but not classic invasive lobular histology. The presence of ERBB2 alterations has therapeutic implications specific to this rare breast cancer subset that could impact outcomes. Comprehensive genomic profiling identifies ERBB2 mutations that are not detected with standard clinical immunohistochemistry or FISH.

Citation Format: Kim M. Hirshfield, Renee Sanders, Heather K. Feld, Nicola Barnard, Li Liang, Hua Zhong, Gyan Bhanot, Amrik S. Sahota, Andrew Brooks, Lorna Rodriguez-Rodriguez, Shridar Ganesan. Genomic alterations in ERBB2 define a subset of pleomorphic invasive lobular breast cancer. [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 4798. doi:10.1158/1538-7445.AM2015-4798
Abstract 4805: Whole genome sequencing of primary breast cancers and matched distant metastases
Authors: Tang Man-Hung , Dahlgren Malin , Brueffer Christian , Winter Christof , Chen Yilun , Olsson Eleonor , Sjöström Martin , Bendahl Pär-Ola , Niméus-Malmström Emma , Saal Lao H. , Borg Åke , Gruvberger-Saal Sofia K.
Published: August 2015

Metastatic disease is the main cause of death for breast cancer patients, but it is still unclear whether primary tumor characteristics are predictive of the metastasis phenotype. Our aim was to investigate, by analyzing chromosomal structural variation, the clonal similarities between primary breast tumors and their matched distant metastases. For 11 patients, we performed low-coverage (∼10x) whole-genome sequencing on 11 primary breast tumors and 13 matched distant metastases to enumerate chromosomal rearrangements. The tumor genomes (n = 24) harbored a median of 85 (range 18-405) chromosomal rearrangements per tumor, with a median of 82 (26-310) in primaries compared to 87 (18-405) in distant metastases. Similarity between tumors was assessed based on presence or absence of chromosomal rearrangements. Concordance between matched primaries and distant metastases from the same patient was high, with a median of 89% rearrangements being shared (range 61-100%). Nearly all of the rearrangements were patient-specific, with very little overlap when comparing all possible pairings of tumors from different patients (median 3%). The tumors exhibited different genomic patterns of rearrangements: some carried events scattered throughout the genome while other tumors had events in densely clustered foci - chromothripsis-like hotspots - at a few chromosomal locations. Irrespective of the type of rearrangement profile of the tumor genomes, the patterns were highly conserved between the primary tumor and metastasis from the same patient, although in general metastases acquired additional rearrangement events. Our study suggests that analysis of structural variation in tumor genomes could be useful for identifying tumor origin, facilitating cancer detection via measurement of rearrangements in circulating tumor DNA, and estimating degree of relatedness between primary tumors and metastases. Moreover, our finding that distant metastases have a close clonal relationship to the primary tumor at the level of chromosomal structure is most consistent with chromosomal rearrangements being early events in breast cancer progression that remain stable during the development from a primary tumor to its distant metastasis.

Citation Format: Man-Hung Tang, Malin Dahlgren, Christian Brueffer, Christof Winter, Yilun Chen, Eleonor Olsson, Martin Sjöström, Pär-Ola Bendahl, Emma Niméus-Malmström, Lao H. Saal, Åke Borg, Sofia K. Gruvberger-Saal. Whole genome sequencing of primary breast cancers and matched distant metastases. [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 4805. doi:10.1158/1538-7445.AM2015-4805
Abstract 4814: Inferring liver cancer evolution from spatial and temporal genomic heterogeneity
Authors: Gao Qiang , Wang Zhi-Chao , Xi Rui-Bin , Fan Jia
Published: August 2015

Background & Aims: The molecular pathogenesis of primary liver cancer is extremely complex and heterogeneous, which was further complicated by multiple carcinogenesis. We aimed to elucidate the pathogenesis of multifocal primary liver cancer by genomic profiling.

Methods: A patient with synchronous hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) who underwent resection and experienced post-operative intrahepatic metastases (IMs) was enrolled. Multiregion whole-exome sequencing was applied on the three primary tumors and two IMs to infer tumor clonality and evolution. The mutational and expression profiles, clinical relevance (n = 236) and functional implications of the identified potential driver gene FAT4 in HCC were investigated.

Results: In total, we identified 12, 184, 126, and 54 of protein coding mutation in the cirrhotic liver, two HCCs (designated as HCC-A and HCC-B) and one ICC respectively. The mutational data of the two HCCs and one ICC showed almost no overlaps, suggesting that they developed through an accumulation of complete different sets of genetic alterations. For each tumor, multiregion sequencing data showed varied intratumoral heterogeneity (18.1% in HCC-A, 15.7% in HCC-B, 45.6% in ICC). The mutational profile of two IMs showed obvious similarity with HCC-A (87.6% and 87.7% shared with HCC-A respectively), rather than HCC-B and ICC tumors, indicating that they originated from HCC-A. Notably, FAT4 was the only gene that mutated in both HCCs and the two IMs, but in different locations (HCC-A and two IMs have the same G to A mutation at the coding position 2530, while HCC-B genomes have the A to C mutation at the coding position 14804). Prevalence screen revealed that FAT4 was mutated in over 15% of HCC patients and also several HCC cell lines. Significant down-regulation of FAT4 mRNA and protein expression was found in HCC, and loss of FAT4 independently correlated with early recurrence in HCC patients. In HCC cell lines, knockdown of FAT4 promoted and re-expression of FAT4 reduced cell growth and invasion.

Conclusions: Spatial and temporal dissection of genomic alterations during the progression of liver cancer may help elucidate the basis for its dismal prognosis. FAT4 acts as a putative tumor suppressor that is frequently inactivated in human HCC.

Citation Format: Qiang Gao, Zhi-Chao Wang, Rui-Bin Xi, Jia Fan. Inferring liver cancer evolution from spatial and temporal genomic heterogeneity. [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 4814. doi:10.1158/1538-7445.AM2015-4814
Abstract 4816: Design, validation, and interpretation of an NGS assay for actionable variants in solid tumors
Authors: Mockus Susan M. , Ananda Guruprasad , Lundquist Micaela , Spotlow Vanessa , Simons Al , Mitchell Talia , Stafford Grace A. , Potter Christopher S. , Philip Vivek , Stearns Timothy , Srivastava Anuj , Barter Mary , Rowe Lucy , Malcolm Joan , Bult Carol , Katuturi Radha Krishna Murthy , Rasmussen Karen , Hinerfeld Douglas
Published: August 2015

The Jackson Laboratory Cancer Treatment Profile™ (JAX-CTP™) is a next generation sequencing (NGS)-based molecular diagnostic assay that detects actionable gene variants in solid tumors to inform the selection of targeted therapeutics for cancer treatment. We will describe the design of the 358- gene panel, analytical validation, and the curation and clinical reporting of actionable variants. Selection of the gene panel was based on known drug targets, casual implications in cancer, and a thorough pathway analysis. DNA is extracted from FFPE tumor samples and using hybrid capture, the genes of interest are enriched and sequenced on Illumina HiSeq 2500 or MiSeq sequencers. FASTQ files generated from Illumina's CASAVA software are submitted to the JAX Clinical Genome Analytics (CGA) data analysis pipeline to perform automated read quality assessment, alignment, and variant calling. Identified variants are then submitted for clinical curation using a combination of the in-house JAX Clinical Knowledgebase (CKB) and the external Genetic Variant Annotation (GVA) from CollabRx. Once clinically annotated, the variants are graded relative to their clinical utility for the specific tumor type and compiled into a clinical report to inform patient treatment. Extensive analytical validation, following CAP guidelines, was conducted to assess limit of detection, accuracy, precision, sensitivity, and specificity of the assay. The summarized optimized sensitivity of the assay is a minimum coverage of samples at 300X, a limit of detection of 10% for SNP’s/indels and ≥6 copies for CNV’s, and an average of 3-4 actionable variants per sample. The challenges of interpreting gene variants for clinical actionability and for establishing an analytically valid bioinformatic pipeline will be discussed in-depth.

Citation Format: Susan M. Mockus, Guruprasad Ananda, Micaela Lundquist, Vanessa Spotlow, Al Simons, Talia Mitchell, Grace A. Stafford, Christopher S. Potter, Vivek Philip, Timothy Stearns, Anuj Srivastava, Mary Barter, Lucy Rowe, Joan Malcolm, Carol Bult, Radha Krishna Murthy Katuturi, Karen Rasmussen, Douglas Hinerfeld. Design, validation, and interpretation of an NGS assay for actionable variants in solid 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 4816. doi:10.1158/1538-7445.AM2015-4816