bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4167: MUC3A promotes lung cancer progress via activating NFκB pathway and attenuates radiosensitivity
Authors: Sun Yingming , You Chengcheng , Ma Shijing , Luo Yuan , Gong Yan , Xiao Yu , Zhang Junhong , Xie Conghua
Published: August 2018

MUC3A is highly expressed in 40% of lung adenocarcinoma, but its functions and effects on clinical outcomes are not well understood. Tissue microarray of 92 patients' tumor samples from Chinese National Human Genetic Resources Sharing Service Platform indicated that highly expression of MUC3A was associated with poor prognosis, advanced staging and low differentiation. IP-MS and co-IP results revealed that MUC3A interacted with RELA and activated the NFκB pathway via promoting RELA phosphorylation and interfering the binding of RELA to IκB. MUC3A knockdown significantly suppressed cell proliferation and induced G1 arrest via down-regulating cell cycle checkpoints such as CDK2/4/6 and Cyclin D1. MUC3A deficiency increased γ-H2AX phosphorylation and increased radiation-induced DNA double strain breaks. MUC3A knockdown inhibited the BRCA-1/RAD51 pathway and nuclear translocation of P53 and XCRR6, suggesting that MUC3A promote DNA damage repair and attenuate radiation sensitivity. Moreover, MUC3A deficiency induced autophagy in lung cancer cells and increased the protein levels of LC3 II and Beclin-1. MUC3A knockdown significantly suppressed tumor growth in H1975 xenograft model and had a synergistic effect with radiation. Less nuclear translocation of RELA and P53 was also observed in tumor tissue in vivo. Our studies indicated that MUC3A was a potential oncogene and its highly expression was associated with unfavorable clinical outcomes in patients with lung adenocarcinoma, who should be more frequently follow-up, and might benefit less from radiotherapy.

Citation Format: Yingming Sun, Chengcheng You, Shijing Ma, Yuan Luo, Yan Gong, Yu Xiao, Junhong Zhang, Conghua Xie. MUC3A promotes lung cancer progress via activating NFκB pathway and attenuates radiosensitivity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4167.
Abstract 4179: A novel approach for antimetastatic therapies against TNBC utilizing a physiologic suppressor
Authors: Yesilkanal Ali Ekrem , Rabe Daniel C. , Tiwari Payal , Frankenberger Casey , Johnson Gary L. , Rosner Marsha
Published: August 2018

Metastatic progression of tumors is the major cause of death in patients with triple-negative breast cancer (TNBC). However, since metastasis is a multistep process, unraveling its complexity is a major challenge. One effective way of tackling this question is to study natural blockers of the metastatic process, metastasis suppressors, and identify the mechanisms by which they regulate metastasis. Raf kinase inhibitory protein (RKIP), a protein that regulates kinase activity, is a suppressor of TNBC metastasis. Although RKIP inhibits the activity of key kinases such as Raf-1, GRK2, NIK/IKK in cultured cells, the kinase targets of RKIP in tumors are not known. To address this question, we used a mass spectrometry approach involving inhibitor-conjugated beads to identify kinases that are downregulated by RKIP in human TNBC xenograft tumors. Our results identified a network of stress kinases targeted by RKIP, including kinases that have not been previously reported as RKIP targets. In order to unravel the effect of this stress network on metastatic gene expression, we investigated genes that correlate with RKIP expression in TCGA breast cancer patient data set. We identified prometastatic genes such as APC and DOCK4 as novel RKIP targets in in vitro and in vivo models of TNBC. We also demonstrated these genes are downstream of the RKIP-stress network. Finally, by using a high-throughput invasion assay, we developed a low-dose multidrug cocktail of small-molecule kinase inhibitors that mimic RKIP's antimetastatic role in TNBCs. Elucidating RKIP function at a systems level reveals the interplay between key metastatic signaling cascades, particularly in relation to cell motility and invasion. Our findings suggest that the low-dose multidrug combination that targets a network of stress kinases is a viable antimetastatic therapy for TNBC patients.

Citation Format: Ali Ekrem Yesilkanal, Daniel C. Rabe, Payal Tiwari, Casey Frankenberger, Gary L. Johnson, Marsha Rosner. A novel approach for antimetastatic therapies against TNBC utilizing a physiologic suppressor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4179.
Abstract 4183: Gold nanorods-assisted photothermal therapy inhibits metastasis by decreasing the mammary tumors bleeding in canine and felines
Authors: Ali Moustafa Ragab Khalil
Published: August 2018

Metastasis enables cancer cells to migration, which is responsible for most cancer-related deaths. It usually begins with local invasion to the surrounding tissues, followed by intravasation into the lymph and blood microvasculature before the cancer cells finally colonize within the microenvironment of other locations in the patient's body. Recently, we discovered that gold nanorods assisted photothermal therapy (AuNRs-PPTT) inhibits cancer cell migration and prevent metastasis. AuNRs-PPTT is a therapy in which AuNRs are injected to a tumor before near-infrared light is transiently applied to the tumor producing localized heat. However, AuNRs-PPTT has great potential in replacing the current ineffective anti-metastasis treatments but most of the studies has been performed in vitro. The objectives of this study to understand the AuNRs-PPTT impacting blood and blood vessels in naturally occurring mammary glands tumor in cats and dogs. Our histopathology results showed AuNRs-PPTT caused infiltration of neoplastic cells into lymphatic vessels. Furthermore, we observed that AuNRs-PPTT significantly cause blood coagulation around the tumor, which could be incorporated in the surgery to decrease the bleeding and potentially avoiding the risk of metastasis caused by the surgery. This observation might explain why AuNRs-PPTT inhibited metastasis for mammary gland metastasis upon AuNRs-PPTT. After 24 months, the optimized doses of 2.5 nm of AuNRs irradiated by near-Infrared laser with 0.5 w/cm2 intensity for 2 minutes, have shown no any toxicity signs in liver and kidney functions.

Citation Format: Moustafa Ragab Khalil Ali. Gold nanorods-assisted photothermal therapy inhibits metastasis by decreasing the mammary tumors bleeding in canine and felines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4183.
Abstract 4186: Monensin is selectively cytotoxic to cancer cells in an EMT-like state
Authors: Vanneste Marion , Qin Huang , Moose Devon , Li Mengshi , Schultz Michael , Wu Meng , Henry Michael
Published: August 2018

Metastatic, drug-resistant cancer is lethal. Epithelial-to-mesenchymal transition (EMT) is a type of phenotypic plasticity that has been implicated in cancer metastasis and drug resistance. One potential therapeutic approach is to specifically target cancer cells in an EMT-like state. In this study, we have developed a cell-based high-throughput screening (HTS) protocol using the high content Operetta imaging platform to identify EMT cytotoxic compounds. This screen was performed on epithelial (PC-3E) and mesenchymal-like (TEM 4-18) cell lines, both isolated from the parental PC-3 prostate cancer cell line based on their differential ability to invade an endothelial monolayer. A library of 2,640 compounds was screened on co-cultured PC-3E GFP cells and TEM 4-18 mCherry cells. After 72h exposure to compounds, relative numbers of GFP- and mCherry-positive cells were quantitated. Dose-response curves were established for each compound exhibiting a greater toxicity against EMT-like cells. The mechanisms of action of one of the most potent and selective compound against EMT-like cells, monensin, were further evaluated. Among the 2,640 compounds tested, salinomycin and monensin, both monovalent cation ionophores, displayed a potent and selective cytotoxic effect against EMT-like cells. A closely related compound absent from the compound library, nigericin, was also evaluated and appeared to be the most potent of the three compounds tested. Monensin (10nM) induced apoptosis, cell cycle arrest, and an increase in ROS production in TEM 4-18 cells. In addition, monensin rapidly induced swelling of Golgi apparatus, a previously known effect of monensin, in multiple cell lines most likely resulting in a blockage of intracellular protein trafficking and cell death. We then evaluated the toxicity of monensin in 24 human cancer cell lines and classified them as resistant or sensitive based on IC50 cutoff of 100nM. Supporting these findings, Gene Set Enrichment Analysis identified EMT as the top of the gene sets enriched in the sensitive group. Increased monensin sensitivity in EMT-like cells is associated with elevated uptake of H3-monensin compared to resistant cells. In conclusion, using a high-throughput screening approach, we identified monensin as a potent and specific inhibitor of cancer cells in an EMT-like state where it rapidly disrupts Golgi function. At least part of selectivity of monensin for EMT-like cells is due to increased uptake of this compound.

Citation Format: Marion Vanneste, Huang Qin, Devon Moose, Mengshi Li, Michael Schultz, Meng Wu, Michael Henry. Monensin is selectively cytotoxic to cancer cells in an EMT-like state [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4186.
Abstract 4206: Pretreatment markers of cellular-mediated inflammation and association with survival vary significantly among cancers
Authors: Howard Rachel , Egan Kathleen , Kanetsky Peter
Published: August 2018

Background.

The neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) are established markers of systemic inflammation, and they are believed to have prognostic value in various diseases including many common cancers. These indicators of the cellular-mediated inflammatory response are easily obtained from patient blood samples and hold promise as simple and inexpensive tools for risk stratification.

Methods.

In the present study, 4509 patients spanning multiple cancer types (breast N=979; colorectal N=1024; esophageal N=594; hepatocellular N=287; melanoma N=349 and pancreatic N=1276) treated at Moffitt Cancer Center and with valid hematology lab values, demographic information, clinical disease characteristics, and outcome data were identified. We compared marker counts and ratios across all cancer types to identify disease-specific patterns in pre-treatment host immune response and evaluated the similarities with other established measures of disease-specific immunogenicity. An initial evaluation of the association between pre-treatment NLR, PLR (and corresponding absolute counts of lymphocytes (L), neutrophils (N) and platelets (P)) and disease-specific survival was conducted, controlling for age, sex, race, disease stage, treatment modality, and additionally for primary site and histological and molecular subtypes as appropriate.

Results.

Mean levels of N, L, P, NLR, and PLR all demonstrated significant differences across cancer types. Pre-treatment NLR was significantly associated with disease-specific death in four of our six cancer sites (colorectal: hazard ratio (HR) = 1.47, 95% confidence interval (CI) = 1.21-1.79; esophageal: HR = 1.38, 95% CI = 1.05-1.82; melanoma: HR = 1.87, 95% CI = 1.18-2.95; pancreatic: HR = 1.69, 95% CI = 1.43-1.99). Pre-treatment PLR was significantly associated with disease-specific death in two sites (colorectal: HR = 1.34, 95% CI = 1.10-1.64; pancreatic: HR = 1.53, 95% CI = 1.30-1.79). This suggests that the utilization of markers of the cellular-mediated inflammatory response for clinical prognosis and decision-making may require disease-specific risk classification criteria.

Citation Format: Rachel Howard, Kathleen Egan, Peter Kanetsky. Pretreatment markers of cellular-mediated inflammation and association with survival vary significantly among cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4206.
Abstract 4212: PD-L1 expression, EGFR and KRAS mutations in unresectable stage III non-small cell lung cancer (NSCLC) patients
Authors: Cronin-Fenton Deirdre , Dalvi Tapashi , Hedgeman Elizabeth , Norgaard Mette , Pedersen Lars , Hansen Hanh , Fryzek Jon , Walker Jill , Mellemgaard Anders , Rasmussen Torben , Shire Norah , Riggas James , Potter Danielle , Hamilton-Dutoit Stephen , Sørensen Henrik
Published: August 2018

Background: Anti-PD-L1 therapy may improve prognosis in advanced NSCLC. We examined the relation of PD-L1 expression, KRAS and EGFR mutations, with survival in unresectable stage III NSCLC patients.

Methods: We obtained data on unresectable stage III NSCLC patients (defined via TNM AJCC staging and without surgery up to 120 days after diagnosis) diagnosed 2001-2012. We retrieved medical data from Danish population-based registries and paraffin-embedded tumor tissue from pathology archives. We assessed PD-L1 expression using the Ventana IHC (SP263) validated assay. We genotyped KRAS and EGFR using PCR-based kits. Follow-up began at NSCLC diagnosis and continued to death, emigration, or 31/12/2014. We used Cox regression to compute hazard ratios (HRs) and associated 95% confidence intervals (95%CI) for PD-L1, EGFR, and KRAS.

Results: Among 305 patients, 183 (60%) were men, 167 (55%) were aged >65 years at diagnosis and none used immunotherapy; 148 (49%) had adenocarcinoma, 117 (38%) squamous histology, 96 (31.5%) had PD-L1 positive tumors (>=25%), 6 (2%) had EGFR mutations, and 69 (23%) had KRAS mutations. Among PD-L1 positive tumors, 55% had stage IIIA, 45% IIIB disease; 1% had EGFR and 34% had KRAS mutations. Among PD-L1 negative tumors, 54% had stage IIIA and 46% IIIB; 3% had EGFR and 16% had KRAS mutations. Median survival was similar in patients with KRAS wild-type and KRAS mutations (Hazards ratio (HR)=1.07; 95% CI=0.76-1.51). Patients with an EGFR mutation had a lower non-statistically significant risk of death (HR=0.75; 95% CI=0.28-2.06). Tumor cell positivity for PD-L1 (>=25% versus <25%) yielded an HR=0.80 (95%CI=0.60-1.07). Immune cell positivity for PD-L1 >=1% and >=25% yielded HRs of 0.50 (95%CI=0.39-0.66) and 0.45 (95%CI=0.30-0.67), respectively. Tumor infiltration by immune cells with PD-L1 measured as a continuous variable yielded an HR=0.96 (95%CI=0.93-0.99).

Conclusion: Our findings suggest that PD-L1 expression and EGFR mutations, but not KRAS mutations, are associated with survival in this real-world Danish study of unresectable Stage III NSCLC patients.

Citation Format: Deirdre Cronin-Fenton, Tapashi Dalvi, Elizabeth Hedgeman, Mette Norgaard, Lars Pedersen, Hanh Hansen, Jon Fryzek, Jill Walker, Anders Mellemgaard, Torben Rasmussen, Norah Shire, James Riggas, Danielle Potter, Stephen Hamilton-Dutoit, Henrik Sørensen. PD-L1 expression, EGFR and KRAS mutations in unresectable stage III non-small cell lung cancer (NSCLC) patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4212.
Abstract 4218: Breast cancer survival by age and subtype (ER/PR/HER2) in a nationwide population-based cohort
Authors: Johansson Anna L. , Trewin Cassia B. , Hjerkind Kirsti V. , Ellingjord-Dale Merete , Johannesen Tom B. , Sorlie Therese , Ursin Giske
Published: August 2018

Purpose: We assessed the effect of breast cancer subtype, as defined by estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2) status, on breast cancer survival among young (20-39y), middle-aged (40-49y), screen-aged (50-69y) and elderly (70-89y) women, to elucidate the role of tumor biology for differences in survival across age. Material and methods: A population-based cohort of 21,385 women with a breast cancer diagnosis at ages 20 to 89 between 2005 and 2015 was identified in the Cancer Register of Norway. Subtype was defined as luminal A-like (ER+ PR+ HER2-), luminal B-like HER2-negative (ER+ PR- HER2-), luminal B-like HER2-positive (ER+ PR+/PR- HER2+), HER2-positive (ER- PR- HER2+) and triple-negative (TRN) (ER- PR- HER2-). Cox regression models estimated hazard ratios (HR) for the association between age at diagnosis, subtype and breast cancer specific mortality, while adjusting for year, grade and TNM stage. Results: Young women had higher rates of HER2-positive and TRN tumors compared to middle-aged, screen-aged and elderly women who more often had luminal A-like tumors. Compared to women aged 50-59y, young women had doubled mortality rate (20-39y: HR=2.3 [95% CI 1.8-2.8]), while elderly had two to five times higher mortality rate (70-79y: HR=2.3 [1.9-2.7]; 80-89y: HR=5.2 [4.2-6.4]). After adjustment for subtype, grade and stage the association was reduced among young women (20-39y: HR=1.3 [1.1-1.6]) but less so among the elderly (70-79y: HR=2.1 [1.7-2.5]; 80-89y: HR=3.9 [3.2-4.9]). Among young women, luminal A-like and luminal B-like HER2-negative subtypes were still associated with increased mortality after adjustment for grade and stage. Among the elderly, all subtypes were associated with increased mortality after adjustment for grade and stage, with stronger effects for TRN, HER2-positive and luminal B-like HER2-positive subtypes. Conclusion: Tumor-associated factors, such as subtype, grade and stage, may explain a large part of the poorer survival among young patients, whereas comorbidities and less intensive treatment may explain the persisting poorer survival across subtypes among the elderly.

Citation Format: Anna L. Johansson, Cassia B. Trewin, Kirsti V. Hjerkind, Merete Ellingjord-Dale, Tom B. Johannesen, Therese Sorlie, Giske Ursin. Breast cancer survival by age and subtype (ER/PR/HER2) in a nationwide population-based cohort [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4218.
Abstract 4219: Breast cancer distribution and survival among Buddhist and Muslim women in southern Thailand
Authors: Defever Kali , Rentschler Katie M. , Khazan Ana , Pinkerton Elizabeth , Virani Shama , Sriplung Hutcha , Pang Judy , Kleer Celina G. , Leon Carlos F. Mendes de , Colacino Justin A. , Rozek Laura S.
Published: August 2018

Objective: Thailand is undergoing a period of rapid economic growth, which has led to an epidemiologic transition from infectious to chronic diseases such as cancer. Preliminary research shows a difference in rates of breast cancer incidence and mortality between Buddhist and Muslim women in southern Thailand. This study examines differences in breast cancer and potential explanations for this disparity. Methods: Demographic, diagnostic, and outcome data from breast cancer patients diagnosed from 2001-2015 were collected from a population-based cancer registry in southern Thailand and matched with formalin-fixed paraffin-embedded blocks from Songklanagarind Hospital. This region was selected due to the relatively high proportion of Muslim women. Of 424 cases selected, 369 were Buddhist and 55 were Muslim. Formalin-fixed paraffin-embedded blocks were sent to Michigan Medicine and histological and subtype analyses were performed by two pathologists. Statistical analysis was performed in RStudio using chi-square tests of independence, logistic regression, and Cox proportional hazards models. Results: Muslim women were generally diagnosed at a younger age than Buddhist women (Muslim mean: 46.6 years, Buddhist mean: 52.7 years) and with later stage cancers (Muslim: 36% stage 3 and 14% stage 4, Buddhist: 20% stage 3 and 8% stage 4). Buddhist and Muslim women had similar distributions of Luminal A and B subtypes, but Muslim women were more likely to be diagnosed with Triple Negative breast cancer (Muslim: 30%, Buddhist: 18%), the histological subtype with the worst prognosis. Invasive ductal carcinoma was most common in both groups, but Buddhists had more heterogeneity in subtypes. There were no significant differences in tumor histology or subtype by religion. Conclusions: These analyses show differences in the distribution of breast cancer between Buddhist and Muslim women. Muslim women are diagnosed younger with later stage breast cancers, and with histological differences, which generally lead to lower survival rates. Lack of statistical significance may be due to small sample size, necessitating further studies.

Citation Format: Kali Defever, Katie M. Rentschler, Ana Khazan, Elizabeth Pinkerton, Shama Virani, Hutcha Sriplung, Judy Pang, Celina G. Kleer, Carlos F. Mendes de Leon, Justin A. Colacino, Laura S. Rozek. Breast cancer distribution and survival among Buddhist and Muslim women in southern Thailand [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4219.
Abstract 422: Single-stranded library preparation enables unbiased sequencing of damaged, FFPE-derived DNA for both targeted gene capture and WGS applications
Authors: Vilborg Anna
Published: August 2018

Next Generation Sequencing is increasingly used in translational cancer research and as a diagnostic test. Most tumor specimens available for testing are formalin-fixed, paraffin-embedded (FFPE) blocks. FFPE-derived DNA is typically damaged, causing difficulties for standard library preparation methods. Frayed ends prevent blunt-ended double-stranded adapter ligation, used for whole genome sequencing (WGS) and targeted bait hybridization library preparation. Fragmented DNA and modified bases interfere with PCR, which underlies amplification based targeted sequencing.

We present a single-stranded library preparation method especially forgiving for low quality FFPE-derived DNA. By excising damaged bases and using single-stranded adapter ligation, we omit repair aimed at generating blunt-ended double-stranded DNA, and eliminate the need for whole genome PCR. After ligation of the first adapter, libraries can either undergo second adapter ligation to generate WGS libraries, or be used as input to oligo-selective sequencing (OS-Seq) target capture.

We show that our FFPE-derived PCR-free WGS libraries exhibit coverage depth and uniformity highly similar to double-stranded PCR-free libraries of matched cell line (non-FFPE) materials. Additionally, we present performance of our WGS library preparation on clinical FFEP samples.

We further demonstrate reproducible high and uniform coverage for reference standards and clinical FFPE samples in targeted capture. We show a lack of correlation between DNA quality and sequencing metrics such as on-target rate (R2=0.005), uniformity (R2=0.0002), and coverage (R2=0.06), with successful removal of C>T FFPE artifacts comparable to standard repair methods. We demonstrate sensitive copy number alteration detection through analysis of coverage depth, feasible due to the absence of pre-capture PCR.

In conclusion, our single-stranded library preparation method is forgiving for sample quality and provides uniform and high coverage as the basis for somatic variant calling.

Citation Format: Anna Vilborg. Single-stranded library preparation enables unbiased sequencing of damaged, FFPE-derived DNA for both targeted gene capture and WGS applications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 422.
Abstract 4221: Association between SOX9 expression in Mexican patients with early colon cancer stage
Authors: Ruiz-Garcia Erika , Galicia Tatiana , Figueroa Edith Fernandez , Lino-Silva Saul , Lopez-Camarillo Cesar , Marchat Laurence , Calderillo German , Zinser Juan , Meneses-Garcia Abelardo , Vega Horacio Astudillo-de la
Published: August 2018

Introduction. Colon cancer is the fourth leading cause of mortality worldwide. Between 30-40% of patients are diagnosed at early stage (I or II), sadly 20% will relapse. It is necessary to have a biomarker that identifies patients at high risk. SOX 9 is a transcription factor required for differentiation of different cells and is important for cell proliferation, senescence and lineage commitment. The exact role of SOX9 in carcinogenesis and cancer progression is controversial because could have oncogenic and tumor-suppressing functions. Reports show that strong levels of SOX 9 in colon cancer stage II are linked to low risk of relapse. Objective. The aim of this study was to investigate if the protein expression of SOX9 was associated with the stage, clinical characteristics and relapse of Mexican colon cancer patients. Methods. We obtained 97 samples embedded in paraffin. A pathologist blinded to the clinical information determined the immunoreactivity of SOX9 into 2 groups: low and high expression (by evaluating the percentage of positive nucleus and the tissue staining intensity). All statistical analyses were conducted with SPSS v.22 Statistics. Results. We include stage I (N= 34) and stage II (N=63) patients. The median follow-up period was 42 months. We found statistical difference between SOX9 expression and age (p=0.003), tumor localization (p=0.048) and stage (p<0.001) for whole patients group. Twelve patients (12.3%) relapsed, 7 (at locally level) and 5 with distant metastasis: liver (N=3) and retroperitoneal nodes (N=2), all had low SOX9 expression; one patient with local relapse had died (because of surgical complications). In the relapse group, we found a significant correlation between SOX9 expression and stage (p=0.038) but not with relapse free survival (RFS). Conclusion. We found interesting data even though this is a retrospective study with limitations. This study could not associated SOX9 and RFS, because there are few events. Nevertheless, we observe that 41% patients had a systemic relapse. In the other hand, the youngest patients (<40 y) and the right colon had the highest SOX9 expression. With this result, we have decided to increase the sample size before any assumption, and perform NGS to the five systemic relapses.

Citation Format: Erika Ruiz-Garcia, Tatiana Galicia, Edith Fernandez Figueroa, Saul Lino-Silva, Cesar Lopez-Camarillo, Laurence Marchat, German Calderillo, Juan Zinser, Abelardo Meneses-Garcia, Horacio Astudillo-de la Vega. Association between SOX9 expression in Mexican patients with early colon cancer stage [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4221.
Abstract 4237: Differences in the frequencies of tumor VHL mutation and HIF-2α expression between black and white patients with clear cell renal carcinoma
Authors: Callahan Catherine L. , Moore Lee E. , Lenz Petra , Schwartz Kendra , Ruterbusch Julie , Davis Faith , Chow Wong-Ho , Linehan W. Marston , Merino Maria J. , Hewitt Stephen M. , Rothman Nathaniel , Hofmann Jonathan N. , Nickerson Michael L. , Purdue Mark P.
Published: August 2018

Background: Black Americans have a poorer prognosis for clear cell renal cell carcinoma (ccRCC) than white Americans, potentially due in part to differences in tumor biology. In a recent analysis of The Cancer Genome Atlas (TCGA), tumors from black ccRCC patients had a lower rate of mutation in the VHL tumor suppressor gene and lower expression of hypoxia inducible factors (HIF) than tumors from white ccRCC patients. However, as this study was based on a small number of black patients (N=19) and had limited information on patients' medical histories and risk factors profiles, further investigation is needed.

Objective: We evaluated differences in the frequencies of somatic VHL gene mutations and HIF-1α and -2α protein expression between tumors from black and white ccRCC patients.

Methods: The investigation utilized formalin-fixed tissue and data collected from patients participating in a case-control study conducted in Chicago and Detroit. We sequenced VHL using the Ion Torrent platform for tumors from 69 black and 98 white patients, and measured tumor HIF-1α and -2α protein expression for 88 black and 240 white patients using immunohistochemistry.

Results: Black patients' tumors had a lower frequency of VHL mutation than those of white patients (32% vs. 49%; P = 0.03) as well as a lower frequency of above-median HIF-2α expression (33% vs. 56%; P=0.002). HIF-1α expression did not differ by race (P=0.14). These racial differences persisted after multivariable model adjustment for age, sex, hypertension, chronic kidney disease, body mass index, smoking status, stage, grade, and tumor size [VHL mutation: odds ratio (OR) = 0.44, 95% confidence interval (CI) = 0.19, 0.98; HIF-2α expression: OR = 0.33, 95% CI = 0.18, 0.61].

Conclusions: Our observation that VHL mutation and high HIF-2α expression are less frequent in ccRCC tumors of black vs. white patients confirms the earlier TCGA finding. These findings suggest that ccRCC in black patients is a fundamentally different disease than ccRCC in white patients.

Citation Format: Catherine L. Callahan, Lee E. Moore, Petra Lenz, Kendra Schwartz, Julie Ruterbusch, Faith Davis, Wong-Ho Chow, W. Marston Linehan, Maria J. Merino, Stephen M. Hewitt, Nathaniel Rothman, Jonathan N. Hofmann, Michael L. Nickerson, Mark P. Purdue. Differences in the frequencies of tumor VHL mutation and HIF-2α expression between black and white patients with clear cell renal carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4237.
Abstract 4239: Infection, inflammation and cancer: Understanding Alaska Native cancer health disparities
Authors: Martinson Holly , Alberts Steven , Olnes Matthew
Published: August 2018

Gastric cancer is a leading cancer health disparity among the Alaska Native (AN) people, occurring at a 3-fold higher incidence and 4-fold higher mortality rate in comparison to U.S. Non-Hispanic whites (NHW). AN gastric cancer patients have significant differences in tumor location and appearance compared to NHW patients. In addition, AN patients are younger at the time of diagnosis, 60 versus 69 years and have a lower 5-year survival rate of 10% compared to 22% of NHW gastric cancer patients. The purpose of this research was to understand the role of gene mutations, inflammation, and infection as possible factors in the promotion of gastric cancer in the AN population. In this study, we examined previously obtained tissue samples from AN gastric cancer patients diagnosed between 2006-2014 at the Alaska Native Medical Center. Using next-generation sequencing, immunohistochemistry and in situ hybridization, we evaluated for 50 cancer related gene mutations, the presence of the virus, Epstein-Barr virus (EBV), the bacterium, Helicobacter pylori (H. pylori), and inflammatory factors. Cancer related gene mutations were observed in 69% of gastric tumors from AN patients. The most commonly mutated genes were TP53 (30%), PIK3CA (13%), STK11 (6%), KRAS (5%), and PTEN (5%). Of particular interest, gene mutations were associated with patients who were younger at time of diagnosis (less than 55 years old) and had a history of chronic gastritis. Additionally, EBV is associated with 23% of AN gastric cancers, which is significantly higher than the 10% of EBV associated gastric cancer cases observed in other populations. EBV associated AN gastric cancer patients were more likely to have a history of chronic gastritis, prior or current H. pylori infection, and tobacco use. Notably, aberrant overexpression of the inflammatory factor cyclooxygenase 2 (COX-2) and the glycoprotein Mucin 1 (MUC1) in gastric cancer cells was significantly associated with a poorer prognosis among AN gastric cancer patients. Collectively, these findings indicate infection and inflammation are potential driving factors in the pathogenesis of gastric cancer among the AN people, which may have important clinical implications.

Citation Format: Holly Martinson, Steven Alberts, Matthew Olnes. Infection, inflammation and cancer: Understanding Alaska Native cancer health disparities [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4239.
Abstract 425: Linked Target Capture: Rapid and high-performance NGS target enrichment for clinical sequencing applications
Authors: Pel Joel , Choi Wendy , Despotovic Milenko , Gelinas Laura , Leung Amy , Ung Lloyd , Marziali Andre
Published: August 2018

With the continued decrease of DNA sequencing costs, targeted next-generation sequencing (NGS) is seeing broad adoption in many research, commercial and clinical settings. However, current target capture methods typically have long, multiday workflows that can limit their clinical utility. In addition, small panels for applications such as liquid biopsy typically have high off-target rates or low uniformity, resulting in an increased cost of sequencing required to reach the desired coverage for variant detection. We have developed a novel library preparation and enrichment method named “Linked Target Capture” that replaces typical multiday "PCR-capture-PCR" workflows with a single, linked "PCR/capture" step. This approach, which uses physically linked capture probes and universal PCR primers, enables users to work from extracted DNA to loaded sequencer in less than a single day with minimal hands-on time. The linked PCR and capture step is cycled multiple times to reduce off-target DNA and increase uniformity, ultimately reducing the cost of sequencing. Additionally, the universal primers and captures probes can be combined to enable detection of DNA fusions with unknown partners. Using this method, we evaluated the ability to detect multiple mutation types from both tissue and cell free DNA, as a function of sequencing usage. Unique Molecular Identifiers (UMIs) were integrated and enabled the detection of variants below 0.1%, represented on both senses of the starting DNA (duplex sequencing). Fusion detection was also demonstrated without a priori knowledge of the fusion partner. Using a 30-gene pan-cancer panel, on-target fraction was measured to be above 95%, and the fraction of the panel covered at greater than 25% of the mean depth was greater than 99%. In summary, we have developed a method that enables rapid and cost-effective detection of clinically relevant cancer variants, such as SNVs and gene fusions. This method holds promise for many NGS areas, including clinical applications requiring rapid and simple workflows, or groups new to NGS where simple workflows and repeatable performance help remove barriers to technology adoption.

Citation Format: Joel Pel, Wendy Choi, Milenko Despotovic, Laura Gelinas, Amy Leung, Lloyd Ung, Andre Marziali. Linked Target Capture: Rapid and high-performance NGS target enrichment for clinical sequencing applications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 425.
Abstract 4258: Magnesium intake and mortality due to liver cancer and other liver diseases: Results from the Third National Health and Nutrition Examination Survey Cohort
Authors: Xiangzhu Zhu , Wu Lijun , Fan Lei , Kabagambe Edmond K , Song Yiqing , Tao Menghua , Zhong Xiaosong , Hou Lifang , Shrubsole Martha J. , Liu Jie , Dai Qi
Published: August 2018

People with fatty liver disease are at high risk of magnesium deficiency. Meanwhile, low magnesium status is linked to both chronic inflammation and insulin resistance. However, no study has investigated the association between intake of magnesium and risk of mortality due to liver cancer and other liver diseases. We evaluated the association between total magnesium intake and mortality due to liver cancer and other liver diseases in the Third National Health and Nutrition Examination Study (NHANES III) cohort, which included 13,504 participants who completed liver ultrasound examination for hepatic steatosis. Overall magnesium intake was associated with a reduced risk of mortality due to liver cancer and other liver disease at borderline significance (P=0.05). In multi-variable adjusted models, every 100 mg increase in intake of magnesium was associated with a 49% reduction in the risk for mortality due to liver cancer and other liver diseases. Although interactions between magnesium intake and alcohol use and hepatic steatosis at baseline were not significant (P>0.05), inverse associations between magnesium intake with liver cancer and other liver disease mortality were stronger among alcohol drinkers and those with hepatic steatosis. Our novel findings suggest higher intakes of magnesium may be associated with a reduced risk of mortality due to liver cancer and other liver disease particularly among alcohol drinkers and those with hepatic steatosis. Further studies are warranted to confirm the findings.

Citation Format: Zhu Xiangzhu, Lijun Wu, Lei Fan, Edmond K Kabagambe, Yiqing Song, Menghua Tao, Xiaosong Zhong, Lifang Hou, Martha J. Shrubsole, Jie Liu, Qi Dai. Magnesium intake and mortality due to liver cancer and other liver diseases: Results from the Third National Health and Nutrition Examination Survey Cohort [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4258.
Abstract 4264: Mathematical modeling of differential effects of sunitinib on primary tumor and metastatic growth
Authors: Nicolò Chiara , Mastri Michalis , Tracz Amanda , Ebos John M. , Benzekry Sébastien
Published: August 2018

Sunitinib is a drug with anti-angiogenic activity used in the treatment of patients with metastases from renal cell carcinoma or gastrointestinal tumors. However, despite clear efficacy in reducing established tumor growth, recent preclinical studies have shown limited, or even opposing, efficacies in preventing metastatic spread.

In this work, we evaluated a mathematical metastatic model to describe primary tumor and metastatic dynamics in response to sunitinib in a clinically relevant mouse model of spontaneous metastatic breast cancer that develops after surgical removal of an orthotopically implanted primary tumor. Mice received either vehicle or sunitinib in the neoadjuvant (presurgical) setting according to different schedules. The experimental dataset comprises measurements of primary tumor kinetics, metastatic burden and pre-surgical molecular and cellular biomarkers, including vascular cell Ki67 and CD31 expression, circulating tumor cells (CTCs) and myeloid derived suppressor cells (MDSCs). Estimation of the model's parameters was performed using a mixed-effects population approach. To describe tumor growth under sunitinib treatment, a simple ordinary differential equation model of tumor growth inhibition was used.

Population fits obtained modeling the effect of treatment only on primary tumor growth described well the experimental data of all the treated groups considered. On the contrary, simulations of treatment also on metastasis could not reproduce the behavior of the data. By inserting in the model the available biomarkers as covariates, through a Wald-test, measurements of Ki67+/CD31+, CTCs and granulocytic MDSCs were found significantly correlated with the model parameter expressing the metastatic aggressiveness of the tumor.

Together, these mathematical models confirm a differential effect of sunitinib on primary (localized) tumors compared to secondary (metastatic) disease. Our results suggest that Ki67+/CD31+, CTCs and MDSCs measurements might help in predicting metastatic potential and thus aid in predicting benefit in overall survival for preoperative antiangiogenic treatments.

Citation Format: Chiara Nicolò, Michalis Mastri, Amanda Tracz, John M. Ebos, Sébastien Benzekry. Mathematical modeling of differential effects of sunitinib on primary tumor and metastatic growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4264.
Abstract 4276: Analysis of sensitivity of genomic signatures of therapeutic responses of non-small cell lung cancer in patient-derived xenograft models
Authors: Tavassoly Iman , Iyengar Ravi
Published: August 2018

Genomic alterations are important characteristics of therapeutic responses and therapeutic-resistance phenotype in cancer. These genomic alterations are complex and are determinants of aberrations in signaling pathways and their dynamics. A genomic signature includes a set of genomic alterations like gene expressions, mutations, copy number variations, etc. These genomic signatures are used as biomarkers for assigning treatment to individuals benefiting from a specific treatment plan and are validated using preclinical models such as patient-derived xenograft models (PDX models). We have proposed a methodology to optimize these genomic signatures in silico and evaluate their accuracy in vivo using PDX models of non-small cell lung cancer (NSCLC). Our integrative analysis has shown that different sizes and complexities of gene sets provide different layers of information applicable in designing therapeutic regimens. To eliminate sloppy signatures, it is possible to find optimized and sensitive genomic signatures for precision oncology.

Citation Format: Iman Tavassoly, Ravi Iyengar. Analysis of sensitivity of genomic signatures of therapeutic responses of non-small cell lung cancer in patient-derived xenograft models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4276.
Abstract 4278: Somatic MAPK pathway mutations are associated with high mutational burden and good survival in head and neck squamous cell carcinoma (HNSCC)
Authors: Ngan Hoi-Lam , Fong Andrew Y. , Chan Sharon , Yu Shing Chun , Ip Laura R. H. , Grandis Jennifer R. , Lui Vivian
Published: August 2018

Somatic mutations of the MAPK pathway occur in ~14% of head and neck squamous cell carcinoma (HNSCC; TCGA Provisional; www.cbioportal.org). Notably, mutations found in MAPK signaling components are apparent hotspot or activating mutations, potentially driving activation of the MAPK pathway. These mutations include HRAS p.G12V/D/A/C/S & p.G13V/R, MAPK1 p.E322K/*, BRAF p.D594N & p.V600E mutations. We found that this MAPK pathway mutated subset of HNSCC tumors have a higher mutational burden than MAPK-wildtype (WT) tumors. The average rate of non-synonymous mutations in MAPK pathway mutated tumors is 265.1±42.84 mutation/tumor vs 143.5±5.83 mutation/tumor in WT tumors in the TCGA cohort (P=0.0005). MAPK pathway mutations are not associated with HPV positivity (P=0.5815). Subsequent analysis shows that this subset of MAPK pathway-mutated tumors is unexpectedly associated with TP53 wildtype status (P=0.005584), as well as CASP8 mutations [29.3%; 27/92 cases vs. a 6.5% rate (27/418 cases) in the MAPK pathway WT group; P=9.91 x10-9]. Based on the current survival data of the TCGA Provisional cohort, it appears that patients whose tumors bearing HRAS, BRAF, MAPK1, MAP2K1, and RPS6KA1 mutations have a long median survival of 7.94 years (95.3 months; P=0.0165) vs. patients without these somatic mutations. Though TP53 WT status is a well-recognized biomarker for good prognosis in HNSCC, it only predicts with a median survival of ~45.8 months in this very same cohort. Thus, our findings suggest that MAPK pathway mutations may serve as potential genomic biomarkers for good prognosis in HNSCC. Recently, both HRAS and MAPK1 hotspot mutations have been shown to serve as potential neo-antigens in cervical cancer. Further investigation is needed to determine if these somatic MAPK pathway mutations are capable of mounting an anti-cancer immunity (via hotspot neo-antigens or neo-antigens due to higher mutational burden per se) in these patients, which may contribute to their improved survival. Acknowledgements: VWYL received funding supports from the Research Grant Council, Hong Kong (General Research Fund: #1711484, #17121616; Theme-based Research: T12-401/13-R) and the Hong Kong Cancer Fund, Hong Kong.

Citation Format: Hoi-Lam Ngan, Andrew Y. Fong, Sharon Chan, Shing Chun Yu, Laura R. H. Ip, Jennifer R. Grandis, Vivian Lui. Somatic MAPK pathway mutations are associated with high mutational burden and good survival in head and neck squamous cell carcinoma (HNSCC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4278.
Abstract 4281: A family-wide computational analysis of the catalytic domains of the Never In Mitosis A-like kinase (NEK) proteins
Authors: Durmus Carline A. , Singh Shaneen
Published: August 2018

Members of the Never In Mitosis A-like kinase (NEK) proteins are overexpressed in leukemia, breast, ovarian, prostate, and cervical cancers. Overexpression of particular NEK proteins is also implicated in the increased resistance of certain cancer cells to premature senescence due to various cancer treatments. Depending on the cancer cell type, there are NEK members that, when inhibited, either increase the cancer cells' susceptibility to specific drugs or increase their resistance. Structural information and model of action of NEKs is limited to only two members of the family, even though the different members play an important role in human metabolism. The goal of this research is to perform a comprehensive computational analysis of the 11 members of the human NEK protein family. To provide detailed annotations of the NEK family members, the three-dimensional structures of the catalytic domains was modeled using various approaches including template-based modeling, threading, and ab inito techniques. The information gathered from the models was integrated with information obtained from sequence analysis, biophysical characterization including surface electrostatic profiles, and predicted molecular interactions involving NEK members and other proteins/ macromolecules to establish structure-function correlations. Here we present a detailed analysis of the catalytic domains of the 11 NEK proteins and propose interaction and binding partners for each of the individual members of the family. The role of NEKs in the cell cycle, numerous medical disorders, and as potential chemotherapeutic targets underscores the importance of understanding the structure-function relationship of this family of proteins and establishing their mechanism of action, including delineating the differences among the different members of the family, and our study is a step in that direction.

Citation Format: Carline A. Durmus, Shaneen Singh. A family-wide computational analysis of the catalytic domains of the Never In Mitosis A-like kinase (NEK) proteins [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4281.