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Background: Evasion of apoptosis is identified as one of the essential hallmarks of cancer and upregulation of inhibitor of apoptosis proteins (IAPs) is one of the mechanisms by which tumor cells evade apoptosis. An oral SMAC mimetic and antagonist of cellular IAP1 (cIAP1) and X-linked IAP (XIAP), BGB-24714, is currently investigated in a phase 1a/1b oncology trial in patients with advanced or metastatic solid tumors (NCT05381909). Here, we evaluated the anti-tumor activity of BGB-24714 as a single agent or in combination with paclitaxel in preclinical models. Results: BGB-24714 effectively inhibited cIAP1 by inducing its degradation in MDA-MB-231 cells, with an EC50 of 2.5 nM. BGB-24714 also potently antagonized the inhibitory interaction of XIAP with caspase-9 and induced caspase-9 autoactivation in MDA-MB-231 cells, with an EC50 of 23 nM. In a total of 25 breast cancer cell lines treated with TNFα, BGB-24714 potently inhibited the in vitro proliferation of 5 breast cancer cells with EC50 < 100 nM. In pharmacodynamics studies, single dose administration of BGB-24714 significantly induced degradation of cIAP1 and antagonism of the XIAP: Smac interaction in the MDA-MB-231 xenograft model in a dose dependent manner. Using the same model, BGB-24714 exhibited dose-dependent anti-tumor activities as a single agent. The tumor growth inhibition rates were 30%, 52% and 73% in low to high dosage treatment groups. Furthermore, BGB-24714 at medium dosage level demonstrated synergized anti-tumor activity in HCC1806 xenograft model when used in combination with paclitaxel. In intermittent dosing study, BGB-24714 with the intermittent dosing schedule demonstrated significant but slightly less effective anti-tumor activity than the continuous dosing schedule. In summary, BGB-24714, as a novel oral IAP antagonist, showing significant anti-tumor activities in preclinical models, which is promising and warrants the testing of the compound in human. Citation Format: Jie Li, Nan Hu, Yilu Zhang, Xiaolong Yang, Minjuan Deng, Wenfeng Gong, Longbo Yin, Yong Liu, Yajuan Gao, Wei Wei, Xing Wang, Xinyi Liang, Yanwen Ma, Xuxing Sang, Chang Liu, Jingyuan Wang, Qianqian Lu, Fengtao Song, Xi Yuan, Yibing Wang, Jing Li, Wei Jin, Xuesong Liu, Xiaomin Song. BGB-24714, a novel oral IAP antagonist, displayed significant anti-tumor activities in preclinical models as a monotherapy and in combination with paclitaxel [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6158.

High mammographic density (MD) is a strong risk factor for breast cancer; however, data on the association between MD and breast cancer subtypes has been inconsistent and most studies have been conducted using data from Western women. Studies have shown that Asian women, who in general have denser breasts compared with Western women, were more likely to develop luminal B and HER2-enriched tumors. We previously reported that higher MD, assessed using Breast Imaging Reporting and Data System (BI-RADS) categories, was associated with HER2-enriched tumors among Chinese breast cancer patients, which may at least partially explain the higher incidence of HER2-enriched tumors observed in Asian women. Since BI-RADS MD measurement is categorical and known to be subjective, in this study, we aimed to re-evaluate the MD-subtype association using an automated quantitative density metric. The analysis included 1,549 women with invasive breast cancer who were diagnosed and treated in a tertiary hospital in Beijing, China. Subtypes were defined as Luminal A (n=606): ER+ and PR+, HER2-, and low Ki-67 ( Citation Format: Xiaohong R Yang, Yuan Tian, Jennifer Guida, Hela Koka, Ariane Chan, Changyuan Guo, Erni Li, Eric Tang, Hyuna Sung, Ning Lu, Nan Hu, Gretchen Gierach, Jing Li. Association between quantitative mammographic density and breast cancer subtypes among Chinese breast cancer patients [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-08-20.

TP53 is a well-known tumor suppressor gene and mutations in TP53 are the most frequent genomic event in most cancers including breast cancer. Recent studies have shown that the frequency, spectrum, timing, and clinical implications of TP53 mutations varied in different molecular subtypes of breast cancer. For example, the frequency of TP53 mutations is the highest in basal-like subtype and lowest in luminal A tumors. However, the evaluation of TP53 protein expression, as a surrogate for TP53 mutations, in large studies in the context of tumor subtypes is limited. In addition, the etiologic relevance of TP53 expression is yet to be investigated. The goal of this study is to evaluate the association of clinical and breast cancer risk factors with TP53 expression, measured using immunohistochemistry (IHC), in breast cancer molecular subtypes. The analysis included 7,226 women with invasive breast cancer who were diagnosed and treated in a tertiary hospital in Beijing, China. Subtypes were defined as Luminal A: ER+ and PR+, HER2–, and low grade (grades 1 or 2); luminal B/HER2–: ER+ and/or PR+, HER2–, and high grade (grade 3); luminal B/HER2+: ER+ and/or PR+, HER2+ (regardless of grade); HER2-enriched: ER–, PR–, and HER2+; Triple-negative (TN): ER–, PR–, and HER2–. As expected, positive TP53 staining showed the lowest frequency in the luminal A (46%) and highest in the TN (61%) and HER2-enriched (63%) subtypes (P-value Citation Format: Yang XR, Abubakar M, Guo C, Koka H, Sung H, Guida J, Deng J, Zhou B, Hu N, Lu N. TP53 expression in relation to clinical and etiologic factors in breast cancer subtypes [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-09-12.

Introduction: Head and neck (H&N) cancers account for 5-7% of new cancer cases in the United States, and most manifest as head and neck squamous cell carcinomas (HNSCC). Fucosyltransferases (FUTs) contribute to the formation of sialofucosylated epitopes, which alter cellular signaling and mediate early steps in metastasis. However, few studies have examined the effect of FUT expression on H&N cancer survival. Here, we sought to examine the association between fucosyltransferase expression and H&N survival and investigate the mechanistic role of fucosylation in H&N cancer. Methods: FUT1-11 expression (mRNA) data was extracted from the Cancer Genome Atlas (TCGA) HNSCC dataset (n=499). Kaplan-Meier, logrank, and Cox proportional hazards tests were conducted. Levels of α1,2-fucosylated epitopes H-antigen, Lewis Y (LeY), and Lewis B (LeB) were measured in normal, dysplastic, and H&N tumor cell lines via flow cytometry, and RT-qPCR was performed to assess FUT expression. To identify fucosylated signaling and adhesion molecules, fucosylated glycopeptides were enriched from CAL27 and HSC-3 tongue squamous cell carcinoma (SCC) lysates via AAL lectin, followed by nLC-MS/MS. EGFR signaling was assessed via western blot, and parallel plate flow assays were performed to assess in vitro metastatic potential, in tumor cell lines with differential FUT expression. Results: In TCGA analyses, the median survival time (MST) of the FUT2 high expression group was 4.7 years, while low expression group MST was 2.7 years, with an adjusted hazard ratio (aHR) of 0.72 (CI = 0.54-0.95). The FUT6-high group MST was 4.7 years versus 2.9 years for low expression (aHR = 0.62, CI = 0.47-0.83). The FUT7-high group MST was 4.7 years versus 3.5 years for low expression (aHR = 0.72, CI = 0.54-0.95). Expression of the LeY epitope, with both α1,2- and α1,3-linked fucose, varied widely in tongue SCC lines, while pharyngeal SCC lines FaDu and Det-562 displayed intermediate LeY levels, via flow cytometry. EGFR, CD44, and integrins, were among the fucosylated glycoproteins identified via mass spectrometry. HSC-3 cells, sorted into low- and high-LeY populations, demonstrated differential EGFR Tyr-1086 phosphorylation, and differences in adhesion to endothelial cells under flow conditions (in vitro), with implications for tumor metastasis. Conclusion: Overexpression of FUT2, FUT6, and FUT7 were associated with statistically significant increases in survivorship. FUT6 and FUT7 are prominently expressed in immune cells, while FUT2 is expressed in endoderm-derived epithelium. Therefore, FUT6 and FUT7 expression may indicate immune cell infiltration into tumor tissue. Future studies will seek to sort tumor tissue based on cell type, to gain an understanding of the cell-type specific glycosyltransferase expression in HNSCC tumors. Our current results will serve as the foundation to interrogate the role of fucosylated glycoproteins in HNSCC metastasis. Citation Format: Kevin Brown Chandler, Brittany Montesino, Nan Hu, Juan M. Lozano, Robert Sackstein. Fucosyltransferase expression is associated with head and neck cancer survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2400.

F-box and WD repeat domain containing 7 (FBXW7) is a substrate receptor of the ubiquitin ligase SKP1-Cullin1-F-box complex and a potent tumor suppressor that prevents unregulated cell growth and tumorigenesis. However, little is known about FBXW7-mediated control of cell metabolism and related functions in cancer therapy. Here, we report that FBXW7 expression inversely correlates with the expression levels of the key metabolic enzyme isocitrate dehydrogenase 1 (IDH1) in patients with glioma and public glioma datasets. Deletion of FBXW7 significantly increased both wild-type (WT) and mutant IDH1 expression, which was mediated by blocking degradation of sterol regulatory element binding protein 1 (SREBP1). The upregulation of neomorphic mutant IDH1 by FBXW7 deletion stimulated production of the oncometabolite 2-hydroxyglutarate at the expense of increasing pentose phosphate pathway activity and NADPH consumption, limiting the buffering ability against radiation-induced oxidative stress. In addition, FBXW7 knockout and IDH1 mutations induced nonhomologous end joining and homologous recombination defects, respectively. In vitro and in vivo, loss of FBXW7 dramatically enhanced the efficacy of radiation treatment in IDH1-mutant cancer cells. Taken together, this work identifies FBXW7 deficiency as a potential biomarker representing both DNA repair and metabolic vulnerabilities that sensitizes IDH1-mutant cancers to radiotherapy. Significance: Deficiency of FBXW7 causes defects in DNA repair and disrupts NADPH homeostasis in IDH1-mutant glioma cells, conferring high sensitivity to radiotherapy.

Higher mammographic density (MD) is a known risk factor for breast cancer (BC), however, studies examining determinants of density in Chinese populations are limited. Asian women tend to have higher MD compared to European women, and yet they have a lower overall BC incidence rate. The goal of this study was to investigate the influence of established BC risk factors on quantitatively measured MD among Chinese women. The study population included 7,351 Chinese women, who had mammograms at the National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China, between 2016 and 2017 for different indications, including but not limited to screening exam, breast pain, and suspected breast tumors. Only subjects with BI-RADS (Breast Imaging-Reporting and Data System) diagnostic classification of 1 (negative, n= 2,293), 2 (benign, n= 3,519), and 3 (probably benign, n= 1,539) were included in this analysis. VolparaDensity software was used to obtain quantitative MD measures including absolute dense breast volume and percent breast density. We conducted multivariable linear regression modeling on each density measurement to test for its associations with well-established breast cancer risk factors. The mean age of this study population was 50.1 years old (range= (25, 82)), the average body mass index (BMI) was 24.0 kg/m2 (range= (14.2, 48.9)), and about 46% of women were postmenopausal. The mean absolute dense and percent dense volumes were 58.4 (SD= 32.1) and 14.8 (SD= 7.1, equivalent to Volpara Density Grade= 3), respectively. Associations between quantitative MD measures and BC risk factors did not vary significantly across the three BI-RADS diagnostic classes and we therefore combined these patients in subsequent analyses. Most risk factors we examined showed similar associations with dense volume and percent density. For example, both dense volume and percent density were inversely associated with age, parity, longer duration (> 1 year) of breastfeeding, and postmenopausal status, while they were positively associated with age at menopause. In contrast, the associations with age at menarche and BMI showed opposite directions for dense volume and percent density. While increasing BMI was positively associated with dense volume, it was inversely associated with percent density. Age at menarche, however, was inversely correlated with dense volume, but positively associated with percent density. When stratifying by menopausal status, the associations for age, BMI, and parity were similar among pre- and post-menopausal women, while the associations for age at first birth and breastfeeding were stronger among postmenopausal women. In general, observed breast cancer risk factor associations with quantitative breast density metrics in this Chinese population are similar to those previously reported in Western women. We did not observe striking differences in associations of breast density with reproductive factors and BMI among Asian women in this large analysis based on quantitative density measurements. Other risk factors such as genetic susceptibility loci associated with MD should be examined in large Asian studies to further our understanding on how MD influences breast cancer risk in Asian populations. Citation Format: Hela Koka, Yuan Tian, Deng Lu, Kai Yu, Er-Ni Li, Changyuan Guo, Bin Zhu, Jennifer L Guida, Ariane Chan, Nan Hu, Ning Lu, Gretchen Gierach, Jing Li, Xiaohong R Yang. Mammographic density in relation to breast cancer risk factors among Chinese women [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-01-26.

Epidemiological studies have shown that associations between breast cancer risk and risk factors vary by tumor pathology such as estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) status. Mammographic density (MD) is a strong risk factor for breast cancer, but data on the association between MD and breast cancer subtypes have been inconsistent and most studies have been conducted among Western women. The goal of this study was to evaluate the association between MD and breast cancer subtypes in an Asian population where the proportion of dense breast tissue is higher but the overall breast cancer incidence rate is much lower compared with Western countries. Breast cancer cases from a cancer hospital in Beijing, China with MD and ER, PR, and HER2 immunohistochemical (IHC) data were included in this analysis. To reduce subtype misclassification, we excluded cases that were HER2 2+ for IHC but had no FISH data. Tumor subtypes were defined as Luminal A (ER+ or PR+ and HER2-, N=376), Luminal B (ER+ or PR+ and HER2+, N=97), HER2-overexpressing (ER- and PR- and HER2+, N=71), and triple negative (TN, ER- and PR- and HER2-, N=66). MD was assessed on digital mammograms and categorized into four levels using the Breast Imaging Reporting and Data System (BI-RADS) scoring system (a=almost entirely fat, b=scattered fibroglandular densities, c=heterogeneously dense, and d=extremely dense). Because there were few cases with almost entirely fat breasts, we combined MD levels "a" and "b" as our reference group. Polychotomous logistic regression was used to assess the association between MD and breast cancer subtypes with the adjustment of age, menopausal status, parity, age at menarche, and body mass index (BMI) since all these variables showed significant inverse associations with MD (P=0.002 for age at menarche and P Citation Format: Yang XR, Li J, Li E-N, Guida JL, Li M, Sung H, Lu N, Hu N, Gierach GL. Association between mammographic density and breast cancer subtypes among Chinese women. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-10-10.

The ability to evade apoptosis is a hallmark of cancer. B-cell lymphoma-2 (Bcl-2), an anti-apoptosis protein, is overexpressed and leads to oncogenesis or drug resistance in various tumor types, including lymphoma and leukemia. Bcl-2 is a well-validated target for B cell malignancies as demonstrated by a Bcl-2 inhibitor venetoclax which was recently approved for the treatment of chronic lymphocytic leukemia (CLL) and is currently in phase III clinical development for other hematologic malignancies. With longer term treatment, recurrent mutation G101V in Bcl-2 has been reported to mediate resistance to venetoclax in patients with CLL. Herein, we report the pharmacological properties of BGB-11417, a highly potent and selective BCL-2 inhibitor, in preclinical models. BGB-11417 potently inhibited both wildtype and G101V-mutated Bcl-2 in SPR binding assay with IC50 of 0.035 and 0.28 nM, respectively. BGB-11417 was a more potent Bcl-2 inhibitor than venatoclax in both enzymatic and cellular assays. In a binding assay for BH3 peptide and Bcl-2, BGB-11417 and venatoclax showed an IC50 of 0.014 nM and 0.2 nM, respectively. In addition, BGB-11417 potently inhibited the proliferation of a Bcl-2 dependent acute lymphoblastic leukemias (ALL) cell line RS4;11 with an IC50 of 0.81 nM, but not a Bcl-xL dependent T-ALL cell line Molt-4. Moreover, BGB-11417 exhibited potent cell killing activity against a variety of lymphoma and leukemia cell lines, including follicular lymphomas (FL), mantle cell lymphomas (MCL), diffuse large B-cell lymphomas (DLBCL) and acute myeloid leukemias (AML). BGB-11417 was also highly selective, showing ≥2000 folds selectivity to Bcl-xL, BCL-W, MCL-1 and BCL2A1. In pharmacokinetics (PK) and pharmacodynamics (PD) studies, oral administration of BGB-11417 displayed a clear PK and PD correlation in RS4;11 ALL xenografts as shown by the increase of cleaved caspase 3 level with the increase of BGB-11417 concentration in tumor tissue. Furthermore, BGB-11417 demonstrated significantly greater efficacy than venetoclax in human ALL, MCL and DLBCL xenograft models without body weight loss. Collectively, BGB-11417 is a potent and highly selective Bcl-2 inhibitor with superior anti-tumor activities compared with venetoclax in preclinical studies. The phase I study of BGB-11417 for treatment of hematological cancers is ongoing. Citation Format: Nan Hu, Yunhang Guo, Hai Xue, Ye Liu, Yin Guo, Fan Wang, Xiaomin Song, Ying Guo, Shuaishuai Chen, Haipeng Xu, Taichang Zhang, Yanwen Ma, Xuebing Sun, Yuan Hong, Yutong Zhu, Aiying Xu, Zhenzhen Cheng, Haimei Xing, Zhiwei Wang, Xuesong Liu, Lai Wang. Preclinical characterization of BGB-11417, a potent and selective Bcl-2 inhibitor with superior antitumor activities in haematological tumor models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3077.

Background Results from epidemiological studies are in support of heterogeneous relationships between body mass index (BMI) and breast cancer (BC) subtypes. Compared with luminal BC (LBC), pre-menopausal obesity is more frequently associated with triple-negative (TN) BC, while the converse has been reported for post-menopausal obesity. Given the dynamic range of hormone receptor expression in LBC, categorical combinations of immunohistochemical (IHC) markers for subtype definition may mask etiological heterogeneity within this subtype. Herein, we leveraged quantitative measures of tumor clinicopathological and IHC characteristics to define phenotypes of luminal BC and to assess relationships with BMI. Methods Participants were 6,412 women with invasive breast cancer who were diagnosed and treated in a tertiary hospital in Beijing, China between 2008-2016. We computed the Nottingham prognostic index (NPI)-score (based on tumor size, grade and lymph nodes) and IHC4-score (based on ER, PR, HER2 and KI67) and stratified LBC patients into four subgroups using quartiles of these scores: Lum-Q1 (least aggressive), Lum-Q2, Lum-Q3, and Lum-Q4 (most aggressive). Multinomial logistic regression models, adjusted for age, parity, menarcheal age, and family history, were used to test the associations between BMI [Kg/m2: underweight (30)] and luminal subgroups, overall and by age categories (as proxy for menopausal status). We also included TNBC as a comparison group. Results The most aggressive LBC patients (Lum-Q4), defined by the NPI-score, were significantly more likely to be overweight [OR (95% CI) vs normal = 1.44 (1.12-1.86)] and obese [OR (95% CI) vs normal = 1.55 (0.98-2.46)] than the least aggressive LBC (Lum-Q1) patients, regardless of menopausal status. On the other hand, Lum-Q4 patients, defined by the IHC4-score, were significantly more likely to be underweight [OR (95% CI) vs normal = 2.21 (1.07-4.56)] in all women but less likely to be overweight [OR (95% CI) vs normal = 0.65 (0.50-0.85)] and obese [OR (95% CI) vs normal = 0.53 (0.35-0.82)] among post-menopausal women compared to Lum-Q1 patients (P-interaction (BMI & age) = 0.004). These associations were very similar to those when comparing TNBC to Lum-Q1 patients (defined by either NPI or IHC4 scores). Conclusion Aggressive phenotypes of LBC demonstrate associations with BMI that are analogous to TNBC. Discordant BMI associations with NPI and IHC4, and by menopausal status for the IHC4-score only, may be indicative of a positive association between excess adiposity and tumor clinicopathological parameters in the NPI-score, regardless of menopausal status. Conversely, its association with the IHC4-score may be driven by complex hormonal mechanisms that vary by menopausal status. Future analysis will focus on disentangling these relationships. Citation Format: Mustapha Abubakar, Changyuan Guo, Hela Koka, Bin Zhou, Eric Tang, Joseph Deng, Nan Hu, Ning Lu, Xiaohong R. Yang. Aggressive phenotypes of luminal breast cancer demonstrate associations with body mass index analogous to triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 617.

Genomic instability plays an important role in most human cancers. To characterize genomic instability in esophageal squamous cell carcinoma (ESCC), we examined loss of heterozygosity (LOH), copy number (CN) loss, CN gain, and gene expression using the Affymetrix GeneChip Human Mapping 500K (n = 30 cases) and Human U133A (n = 17 cases) arrays in ESCC cases from a high-risk region of China. We found that genomic instability measures varied widely among cases and separated them into two groups: a high-frequency instability group (two-thirds of all cases with one or more instability category of ≥10%) and a low-frequency instability group (one-third of cases with instability of

Previous studies showed that chromosomal instability was common in esophageal squamous cell carcinoma (ESCC); however, the mechanisms underlying this instability are unknown. Individuals with deficiencies in telomere maintenance are susceptible to enhanced telomere loss during cell proliferation; such deficiencies could result in telomere dysfunction and genomic instability. We investigated the association between genome-wide chromosomal changes in cancer cells and telomere length/attrition in cancer/stroma cells in 47 ESCC patients. Genome-wide detection of loss of heterozygosity was performed using the Affymetrix GeneChip single nucleotide polymorphism arrays. Telomere length was assessed separately for cancer cells, carcinoma-associated fibroblasts (CAF), infiltrative lymphocytes, and adjacent normal epithelial cells by quantitative fluorescent in situ hybridization using paraffin-embedded sections. Telomere length differed significantly among cell types, such that length in infiltrative lymphocytes > CAFs > cancer cells. Shortened telomeres were observed in cancer cells in 44 of 47 (94%) of the tumors examined. Telomere length in CAFs was significantly associated with chromosomal instability on 4q and 13q and lymphocyte telomere length was significantly associated with instability on chromosomal arms 15q. Although telomere length in cancer cells was not associated with chromosome arm instability, telomere attrition in cancer cells, defined as the telomere length in CAFs minus the telomere length in cancer cells, was significantly associated with chromosomal instability on 13q and 15q. This study provides evidence that telomere shortening is a common genetic alteration in ESCC and that chromosome arm instability is related to both telomere attrition in cancer cells and telomere length in tumor stroma cells. [Cancer Res 2009;69(4):1604–14]

Germline mutations in the BRCA1 and BRCA2 genes result in predisposition to breast and ovarian cancer. Detection of BRCA mutation carriers can lead to improved prevention and therapeutic interventions such as the targeted therapy using poly ADP ribose polymerase (PARP) inhibitors, which are particularly effective in BRCA mutation carriers. The spectrum of BRCA mutations varies depending on geographic origin, population, and ethnic group; however, the prevalence of BRCA mutations in non-Caucasian populations has been poorly characterized, particularly in a population-based setting. The goal of this study was to characterize the spectrum of germline mutations in BRCA1/2 and PALB2 in unselected breast cancer cases who were seen in Sarawak General Hospital, Malaysia, where 93% of the breast cancer patients in Sarawak are treated. We performed targeted sequencing using a validated AmpliSeq panel on 467 cases with available risk factor questionnaire and clinical follow-up data. Breast cancer subtypes were defined by the joint expression of ER, PR, and HER2. Common variants with frequency >1% in any public database (1000 Genome, Exome Sequencing Project, The Exome Aggregation Consortium) were excluded. Pathogenic variants included known pathogenic variants in ClinVar, loss of function variants (frameshift and stop-gain), and variants that alter the first or second base of the splice site. Variants of unknown significance (VUS) were also defined using the ClinVar classification. We found 10 BRCA1 pathogenic variants in 12 patients, 10 BRCA2 pathogenic variants in 15 patients, and 4 PALB2 pathogenic variants in 4 patients, which gave a BRCA mutation prevalence of 5.78% among the unselected breast cancer cases in this population. All these variants were extremely rare in the general population ( Citation Format: Xiaohong (Rose) Yang, Beena Devi, Hyuna Sung, Jennifer Guida, Yanzi Xiao, Lisa Garland, Nan Hu, Maria Rodriguez-Herrera, Chaoyu Wang, Kristine Jones, Wen Luo, Belynda Hicks, Tieng Swee Tang, Karobi Moitra, Mike Dean. Prevalence and spectrum of germline rare variants in BRCA1/2 and PALB2 among breast cancer cases in Sarawak, Malaysia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1294. doi:10.1158/1538-7445.AM2017-1294

Background BGB-3111 is a novel, irreversible, second generation BTK inhibitor with better selectivity profile and DMPK property compared to ibrutinib. It has demonstrated promising anti-tumor activities in patients with advanced B cell malignancies. Given BTK is expressed in all hematopoietic lineages except for T lymphocytes, it is reasonable to explore the immune modulatory effect of BGB-3111. In this study, we sought to investigate the anti-tumor activity of BGB-3111 in solid tumor models. Methods Cell viability was assessed with Cell Titer Glo® assay and half maximal inhibitory concentrations (IC50) were estimated. In vivo activity was assessed in subcutaneous mouse xenograft models. Treatments were administered by oral gavage and individual body weight and tumor volume was recorded twice weekly. Results In vitro studies showed that MDA-MB-436 cells are insensitive to BGB-3111, which do not expresse BTK. In both human breast cancer MDA-MB-436 and human A431 epidermoid carcinoma subcutaneous xenograft models, the tumor cells were co-injected with peripheral blood mononuclear cells (PBMCs) of healthy donors. In MDA-MB-436 model, BGB-3111 (15 mg/kg, BID) single agent significantly induced tumor growth inhibition (TGI) of 55%, whereas showed no anti-tumor effect if no PBMCs co-injected. Furthermore, co-treatment of BGB-3111 (15 mg/kg, BID) and anti-PD-1 antibody BGB-A317 (10 mg/kg, QW) demonstrated enhanced therapeutic effect in A431 allogeneic model. Interestingly, in BCLU200 and BCLU054 NSCLC primary tumor xenograft models (without PBMC co-injection), BGB-3111 (15 mg/kg, BID) also demonstrated significant anti-tumor activity. Conclusions In summary, BGB-3111 showed interesting activity in solid tumor models, suggesting BTK inhibitor might have potential to be used beyond hematology malignancies. . Citation Format: Nan Hu, Jiye Zhang, Min He, Shuo Zhang, Yong Liu, Lai Wang. BTK inhibitor BGB-3111 demonstrates anti-tumor activity in solid tumor models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2010. doi:10.1158/1538-7445.AM2017-2010

Background Helicobacter pylori (Hp) is the primary cause of gastric cancer but we know little of its relative abundance and other microbes in the stomach, especially at the time of gastric cancer diagnosis. Here we characterized the taxonomic and derived functional profiles of gastric microbiota in 157 non-malignant gastric tissue samples from two different sets of gastric cancer patients, and compared them with microbial profiles of oral, stool, nasal, vagina and skin samples from Human Microbiome Project. Results We show that Hp is the most abundant member of gastric microbiota in both Chinese and Mexican samples (51% and 24% respectively), followed by the genera commonly seen in the oral microbiota. Taxonomic (phylum) profiles of stomach microbiota largely resembled oral microbiota when the Helicobacter reads were removed. The functional profiles of stomach microbiota, however, were distinct from those found in other body sites and had higher inter-subject dissimilarity. Gastric microbiota composition did not differ by Hp colonization status or stomach anatomic site, but did differ between paired non-malignant and tumor tissues in either Chinese or Mexican samples. Conclusions Our study is the first to show that Hp is the dominant member of the gastric microbiota in many gastric cancer patients rather than diminished or depleted as traditionally believed. Our results provide insights on the gastric microbiota composition and function in gastric cancer patients, which may have important clinical implications. Citation Format: Guoqin Yu, Javier Torres, Nan Hu, Rafael Medrano-Guzman, Roberto Herrera-Goepfert, Michael S. Humphrys, Lemin Wang, Chaoyu Wang, Ti Ding, Jacques Ravel, Philip R. Taylor, Christian Abnet, Alisa Goldstein. Molecular characterization of the human stomach microbiota in gastric cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3257. doi:10.1158/1538-7445.AM2017-3257

Gastric cancer (GC) is the third common cause of cancer related deaths worldwide and its risk is partially mediated by inherited factors. However, the majority of GC heritability remains to be discovered. The goal of this study was to identify novel GC genes. To identify novel GC genes, we undertook a multi-staged approach of whole exome sequencing (WES), followed by targeted sequencing and genotyping in germline DNA samples from hereditary diffuse GC (HDGC) and isolated GC cases recruited in Europe and Latin America. We also performed WES in 4 available tumor samples to analyze loss of heterozygosity and somatic mutation signature. Our study identified eleven cases with mutations in homologous recombination repair (HR) genes, including seven with PALB2 mutations, three with BRCA1 mutations and one with a RAD51C mutation. Out of 361 total unrelated GC cases analyzed, 6.45% of the HDGC cases (2 out of 31) and 2.7% (9 out of 330) of isolated/non-HDGC cases had mutations in PALB2, BRCA1 or RAD51C. Most of these mutations are known as pathogenic in other cancer types and three were shared by multiple Hispanic and European cases. None of these mutations were present in 1,170 population-matched controls (P=5.75x10-7). Tumor samples from four mutation carriers exhibited mutational signature indicative of defects in HR pathway. Our results suggest that mutations in HR genes are likely involved in GC susceptibility. Our findings have potential clinical implications as these cases and their families could benefit from risk reducing surveillance and possibly benefit from platinum or PARP inhibitor based therapies. Citation Format: Ruta Sahasrabudhe, Paul Lott, Mabel Bohorquez, Ted Toal, Ana Estrada, John Suarez, Alejandro Brea-Fernández, Jose Cameselle-Teijeiro, Carla Pinto, Irma Ramos, Alejandra Mantilla, Rodrigo Prieto, Alejandro Corvalan, Enrique Norero, Carolina Alvarez, Teresa Tapia, Pilar Carvallo, Luz Gonzalez, Alicia Cock-Rada, Angela Solano, Florencia Neffa, Adriana Della Valle, Chris Yau, Gabriela Soares, Alexander Borowsky, Xiao-You Han, Li-JI He, Phillip Taylor, Alisa Goldstein, Nan Hu, Javier Torres, Magdalena Echeverry, Clara Ruiz-Ponte, Manuel Teixeira, Luis G. Carvajal-Carmona. Germline mutations in PALB2, BRCA1 and RAD51C observed in gastric cancer cases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-158. doi:10.1158/1538-7445.AM2017-LB-158

Esophageal cancer is the eighth most common and sixth most frequent fatal human cancer in the world, and the fourth most common incident cancer in China. Shanxi Province, a region in north central China, has among the highest esophageal cancer rates in China, and nearly all of these cases are esophageal squamous cell carcinoma (ESCC). Understanding the molecular mechanisms underlying esophageal carcinogenesis and its molecular pathology will facilitate the development of biomarkers for early detection to reduce ESCC mortality. Genome-wide association studies (GWAS) have found many loci associated with the development of ESCC, however, most of the significant SNPs identified by GWAS are noncoding variants with unknown functions located in intergenic regions far from genes and are difficult to study functionally. As an initial effort to identify causal variants for ESCC, we focused here on loci near genes with known biological functions. Our analysis consists of three steps. We identified some functional variants for ESCC in the second and third steps of the analysis. First, from the GWAS analysis we selected those loci in or around the genes in three important pathways - inflammation, immunity, and DNA repair - using information from KEGG, Biocarta, and GO databases. We selected loci which had their 95% confidence intervals of the odds ratios not including OR = 1 based on GWAS analysis. Second, we integrated the expression and genotype data from ESCC somatic and germline samples and computed eQTLs using the normal tissues for n = 100 cases which had both gene expression data and GWAS genotype data. We found some interesting results from the second step analysis. The top 20 most significant genes included XPC, TP73, CASP8, DAPK1, IGF1R and LEPR, which were implicated in different cancers (Cancer Genetics Web: http://www.cancer-genetics.org). CASP8 was known to be involved in apoptosis processes. It was significantly associated with early onset of esophageal adenocarcinoma (Wu et al, Neoplasia. 2011 Apr;13(4):386-92). It had been shown that IGF1R had a key role in malignant progression of esophageal cancer (Kalinina et al, Int J Cancer. 2010 Oct 15;127(8):1931-40; Doyle et al, Am J Gastroenterol. 2012 Feb;107(2):196-204). Finally, we further intersected these significant loci in the eQTL analysis with the loci that had significant association between genotype and the somatic DNA copy number alterations. One of the significant genes was ST6GAL1. It had been reported this gene may promote malignant progression by promoting the TGF-beta induced EMT through down-regulation of E-cadherin-mediated cell adhesion and up-regulation of integrin-mediated cell migration (J. Lu et al, J Biol Chem. 2014 Dec 12;289(50):34627-41). We also found some novel genes in the analyses and their relation to ESCC will be investigated in future. Citation Format: Howard H. Yang, Hua Su, Huaitian Liu, Nan Hu, Chaoyu Wang, Lemin Wang, Ti Ding, Carol Giffen, Alisa M. Goldstein, Philip R. Taylor, Maxwell P. Lee. Integrated analysis of ESCC tumor/normal tissues and patient blood samples using expression, genotypes and DNA somatic change data. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2561.

Background BGB-3111 is a novel, irreversible, second generation BTK inhibitor with better selectivity profile and DMPK property compared to ibrutinib. It has demonstrated promising anti-tumor activities in patients with advanced B cell malignancies, including mantle cell lymphoma (MCL). Lenalidomide is an immunomodulatory agent with single-agent activity in several histologic subtypes of B-cell non-Hodgkin lymphoma (NHL). It was approved for the treatment of patients with MCL whose disease has relapsed or progressed after two prior therapies, one of which included bortezomib. In this study, we sought to investigate the combination activities of BGB-3111 and lenalidomide in MCL models. Methods In vitro drug efficacy was determined using MCL cell lines including REC-1, MINO and JEKO-1. Cell viability was assessed with Cell Titer Glo® assay and half maximal inhibitory concentrations (IC50) were estimated upon exposure to single agents or drug combinations. In vivo activity was assessed in REC-1 and MINO subcutaneous mouse xenograft models. Treatments were administered by oral gavage when tumors were palpable and individual body weight and tumor volume was recorded twice weekly. Results The in vitro combination activity of BGB-3111 and lenalidomide was tested in MCL cell lines. Strong synergy was observed in REC-1 and MINO cells, but not in JEKO-1 cells. When tested in vivo, both BGB-3111 (7.5 mg/kg, BID) and lenalidomide (30 mg/kg, QD) significantly inhibited the REC-1 xenograft tumor growth with TGI of 86% and 56%, respectively. The combination treatment resulted in 100% TGI. In MINO xenograft model, combination treatment of BGB-3111 (30 mg/kg, BID) and lenalidomide (30 mg/kg, QD) was also more efficacious than either single agent. Conclusions In summary, BGB-3111 and lenlidomide showed interesting in vitro and in vivo combination activity in MCL models, providing rationale for testing this combination in clinic. Citation Format: Nan Hu, Shuo Zhang, Min He, Jiye Zhang, Bin Jiang, Zhijian Sun, Lusong Luo, Lai Wang. BTK inhibitor BGB-3111 synergizes with lenalidomide in MCL models. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4796.

Patients with non-small cell lung cancer with activating EGFR mutations initially respond to first-generation and second-generation EGFR inhibitors. However, clinical efficacy is limited by acquired resistance, frequently driven by the EGFR T790M mutation. In addition, patients oftentimes experience severe side effects including rash and diarrhea due to the inhibition profile against wild-type EGFR. AZD9291 and CO-1686 are the leading third-generation irreversible EGFR inhibitors in clinical development. They selectively inhibit T790M EGFR, while sparing wild-type EGFR. In this study, we investigated the covalent binding efficiency of these two irreversible EGFR inhibitors using biochemical and cellular assays. We discovered that these two inhibitors had dramatic difference in covalent binding efficiencies in WT and mutant EGFR binding at biochemical and cellular levels. In pEGFR cellular assay, AZD9291 displayed much prolonged inhibition of pEGFR than CO-1686. In CO-1686 treated cells, recovery of pEGFR had reached 50% of control levels only after 4 hours. In the meantime, pEGFR in AZD9291 treated cells had no recovery even after 24 hours. These data may suggest different covalent bond formation efficiency and reversibility between different types of irreversible EGFR inhibitors. This may be one of the important factors for consideration when develop third-generation EGFR inhibitors. Citation Format: Zhen Qin, Xuebing Sun, Ye Liu, Yunguang Du, Miao Wang, Nan Hu, Jiye Zhang, Hao Peng, Lai Wang, Min Wei, Lusong Luo. Investigations of covalent binding efficiency for third-generation EGFR irreversible inhibitors AZD9291 and CO-1686. [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 2589. doi:10.1158/1538-7445.AM2015-2589

Background: Populations in north central China are at high risk for esophageal squamous cell carcinoma (ESCC) and gastric cancer (GC), and genetic variation in epigenetic machinery genes and pathways may contribute to this risk. Methods: We used the adaptive multilocus joint test (AdaJoint) to analyze 191 epigenetic genes involved in DNA methylation, chromatin remodeling, and microRNA biosynthesis in 1942 ESCC and 1758 GC cases [1126 cardia (GCA) and 632 non-cardia adenocarcinoma (GNCA)] and 2111 controls with Chinese ancestry. We examined the regulatory function of risk SNPs using in silico analyses and expression quantitative trait loci (eQTL) analysis in normal esophageal and gastric tissues. Results: Significant pathway-based associations were observed for the overall epigenetics (P = 3.4E-02) and chromatin remodeling (P = 3.9E-02) pathways with GCA risk, but not GC, GNCA or ESCC. SETD1B, CBX4, KAT5, ZGPAT, BTD, EED, SMARCD1, POLE3, AGO2, RING1 and MBD3L1 were associated with ESCC risk, and SUV42OH1, ASH1L, KAT5, JARID2, PRMT1, MBD3L1, SRRT, KDM5A, DROSHA and KAT6A were associated with GC risk overall (nominal P < 0.05). We identified EED rs10898459 (rho = -0.22, P = 2.9E-02) as a potential esophageal eQTL; DICER1 rs7157322 (rho = -0.42, P = 1.4E-02) and PPP1CA rs1790733 (rho = -0.41, P = 2.1E-03) as potential gastric eQTLs; and ASH1L rs12724079 and rs8179271 as potential gastric subtype eQTLs. Significance: As one of the first attempts to investigate epigenetic gene and pathway-level associations, our results suggest that chromatin remodeling and epigenetic pathways warrant further evaluation in relation to GC risk in other populations. Citation Format: Hyuna Sung, Howard H. Yang, Han Zhang, Qi Yang, Nan Hu, Ze-Zhong Tang, Hua Su, Lemin Wang, Chaoyu Wang, Ti Ding, Jin-Hu Fan, You-Lin Qiao, William Wheeler, Carol Giffen, Laurie Burdett, Zhaoming Wang, Maxwell P. Lee, Stephen J. Chanock, Sanford M. Dawsey, Neal D. Freedman, Christian C. Abnet, Alisa M. Goldstein, Kai Yu, Philip R. Taylor, Paula L. Hyland. Common genetic variants in epigenetic machinery genes and risk of upper gastrointestinal 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 4622. doi:10.1158/1538-7445.AM2015-4622

We conducted a joint (pooled) analysis of three genome-wide association studies (GWAS) of esophageal squamous cell carcinoma (ESCC) in ethnic Chinese (5,337 ESCC cases and 5,787 controls) with 9,654 ESCC cases and 10,058 controls for follow-up. In a logistic regression model adjusted for age, sex, study, and two eigenvectors, two new loci achieved genome-wide significance, marked by rs7447927 at 5q31.2 (per-allele odds ratio (OR) = 0.85, 95% Confidence Interval (CI) = 0.82-0.88; P = 7.72x10-20) and rs1642764 at 17p13.1 (per-allele OR = 0.88, 95% CI = 0.85-0.91; P = 3.10x10-13). rs7447927 is a synonymous single nucleotide polymorphism (SNP) in TMEM173 and rs1642764 is an intronic SNP in ATP1B2, near TP53. Furthermore, a locus in the HLA class II region at 6p21.32 (rs35597309) achieved genome-wide significance in the two populations at highest risk for ESSC (per-allele OR = 1.33, 95% CI = 1.22-1.46; P = 1.99x10-10). Our joint analysis revealed new ESCC susceptibility loci overall as well as a new locus unique to the ESCC high risk Taihang Mountain region. Citation Format: Chen Wu, Zhaoming Wang, Xin Song, Xiao-Shan Feng, Christian C. Abnet, Jie He, Nan Hu, Xian-Bo Zuo, Wen Tan, Xue-Jun Zhang, Neal D. Freedman, Alisa M. Goldstein, Dongxin Lin, Philip R. Taylor, Li-Dong Wang, Stephen J. Chanock. Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations reveals new susceptibility loci. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2204. doi:10.1158/1538-7445.AM2014-2204

Background: In China, esophageal cancer is the fourth leading cause of cancer death and essentially all cases are histologically esophageal squamous cell carcinoma (ESCC). Agnostic pathway-based analyses applied to GWAS data can identify biological pathways and/or groups of genes enriched with disease-associated variants whose individual effect sizes may be too small to be detected by standard single locus methods. Methods: We used the adaptive rank-truncated product (ARTP) method to analyze 1,827 pathways containing 69,420 genes in GWAS data from 1942 ESCC cases and 2111 controls with Chinese ancestry. Pathways were retrieved from five databases: KEGG, BioCarta, Reactome, HumanCys and NCI-Nature curated. Statistical significance was determined by permutation. Results: Associations with ESCC risk (P Citation Format: Paula L. Hyland, Han Zhang, Qi Yang, Shih-Wen Lin, Dennis Maeder, Nan Hu, Ze-Zhong Tang, Hua Su, Lemin Wang, Chaoyu Wang, Ti Ding, Jin-Hu Fan, You-Lin Qiao, William Wheeler, Carol Giffen, Laurie Burdett, Zhaoming Wang, Stephen J. Chanock, Sanford M. Dawsey, Neal D. Freedman, Christian C. Abnet, Alisa M. Goldstein, Kai Yu, Philip R. Taylor. Pathway analysis of genome-wide association study data highlights taste transduction and metabolic pathways and esophageal squamous cell carcinoma susceptibility. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2203. doi:10.1158/1538-7445.AM2014-2203

Introduction: Barrett's esophagus (BE) is the precursor lesion of esophageal adenocarcinoma (EA). The male-to-female incidence rate ratio of BE is ∼2 while EA is ∼6 for reasons that remain unknown. We assessed whether sex steroid hormones were associated with BE in a male population. Methods: The Barrett's Esophagus Early Detection Case Control Study (BEEDS) was based at the National Naval Medical Center (NMMC). We quantitated 13 sex steroid hormones, using mass spectrometry, and sex hormone binding globulin (SHBG), using ELISA, in 173 male BE patients and 213 endoscopy-negative controls. We also calculated free estradiol and free testosterone using formulas known to accurately estimate such. We used multivariable logistic regression to estimate odds ratios (ORs) and 95% confidence intervals (CIs) adjusted for smoking status, alcohol consumption, body mass index (BMI; kg/m2), heartburn, regurgitation, and gastroesophageal symptom score (excluding heartburn and regurgitation). Results: Free testosterone was positively associated with BE risk, peaking in the highest quartile with an OR of 4.42 (95%CI: 1.91, 10.24, p=0.0005). Estrone-sulphate was inversely associated with BE risk (OR 4th quartile=0.23, 95%CI:0.10, 0.53, p=0.0006). No other hormone was associated with BE risk. Relationships were not modified by age or BMI. Conclusion: High testosterone may delay re-epithelization of esophageal lesions leading to increased risk of metaplastic growth. Citation Format: Michael B. Cook, Shannon Wood, Brooks D. Cash, Patrick Young, Ruben D. Acosta, Roni T. Falk, Ruth Pfeiffer, Nan Hu, Carol Giffen, Veronique Turcotte, Patrick Caron, Chantal Guillemette, Sanford M. Dawsey, Christian C. Abnet, Paula L. Hyland, Philip R. Taylor. An analysis of circulating sex steroid hormones in relation to Barrett's esophagus. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2207. doi:10.1158/1538-7445.AM2014-2207

PURPOSE: Several observational studies and multinutrient interventional trials suggest that selenium compounds have potential chemopreventive effects on esophageal and gastric carcinogenesis, presumably via their influence on selenoproteins. We aimed to investigate associations between genetic variants in selenoprotein genes and risk of esophageal squamous cell carcinoma (ESCC), gastric carcinoma (GC) and GC subsets: cardia (GCA) and non-cardia (GNCA) using data from a genome-wide association study in a Han Chinese population in which ESCC and GC are predominant cancers. METHODS: 1944 ESCC cases, 1758 GC cases (1126 GCA and 632 GNCA) and 2111 controls from the Shanxi Upper GI Cancer Genetics project and the Linxian Nutritional Intervential Trials were genotyped for 243 SNPs in 24 selenoprotein genes. Logistic regression models were applied to evaluate SNP-level associations. Pathway- and gene-level associations were determined using the resampling-based adaptive rank-truncated product approach. RESULTS: Selenoproteins as a whole pathway were not significantly associated with ESCC (p=0.398) or GC (p=0.608), but five significant (p Citation Format: Sharon Li, Paula L. Hyland, Neal D. Freedman, Nan Hu, Hua Su, Lemin Wang, Chaoyu Wang, Ti Ding, Yuan Wang, Jin-Hu Fan, You-Lin Qiao, Xiaoqin Xiong, Kai Yu, Alisa M. Goldstein, Sanford M. Dawsey, Philip R. Taylor, Christian C. Abnet, Shih-Wen Lin. Genetic variants in selenoprotein genes and risk of esophageal squamous cell carcinoma and gastric cancer in a Chinese population. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2206. doi:10.1158/1538-7445.AM2014-2206

Whole genome association studies of complex human diseases represent a new paradigm in the postgenomic era. In this study, we report application of the Affymetrix, Inc. (Santa Clara, CA) high-density single nucleotide polymorphism (SNP) array containing 11,555 SNPs in a pilot case-control study of esophageal squamous cell carcinoma (ESCC) that included the analysis of germ line samples from 50 ESCC patients and 50 matched controls. The average genotyping call rate for the 100 samples analyzed was 96%. Using the generalized linear model (GLM) with adjustment for potential confounders and multiple comparisons, we identified 37 SNPs associated with disease, assuming a recessive mode of transmission; similarly, 48 SNPs were identified assuming a dominant mode and 53 SNPs in a continuous mode. When the 37 SNPs identified from the GLM recessive mode were used in a principal components analysis, the first principal component correctly predicted 46 of 50 cases and 47 of 50 controls. Among all the SNPs selected from GLMs for the three modes of transmission, 39 could be mapped to 1 of 33 genes. Many of these genes are involved in various cancers, including GASC1, shown previously to be amplified in ESCCs, and EPHB1 and PIK3C3. In conclusion, we have shown the feasibility of the Affymetrix 10K SNP array in genome-wide association studies of common cancers and identified new candidate loci to study in ESCC.

Tumor and matched normal tissue from 19 esophageal squamous cell carcinoma patients from a high-risk area of China were analyzed with 7680 gene cDNA microarrays. Forty-one genes were differentially expressed (P0.001;/==" BORDER="0"2-fold change) between tumor and matched normal samples (13 overexpressed and 28 underexpressed). Hierarchical clustering showed consistent molecular profiles across patients. Multidimensional scaling plots visually distinguished cases by family history status, which was confirmed statistically using a global permutation test (P = 0.007); we then identified 152 genes of which the expression differed in tumors from family history positive versus negative cases (55 overexpressed and 97 underexpressed at P0.001). These data indicate that molecular profiles in esophageal squamous cell carcinoma are highly consistent and that expression patterns in familial cases differ from those in sporadic cases.

We mapped a tumor suppressor gene locus to an 800-kb interval on human chromosome 13q12.11 for esophageal squamous cell carcinoma (ESCC). Two genes, ML-1 and RNF6, are located within this 800-kb interval. We analyzed both genes for the presence of mutations in 24 ESCC primary tumors and 16 tumor cell lines by directly sequencing the PCR products that were amplified from each exon. No mutation was detected in ML-1. In contrast, three somatic mutations in the RNF6 gene were detected in the ESCC primary tumors, and one mutation was also found in a tumor cell line. Identification of multiple somatic mutations in RNF6 suggests that RNF6 is a potential tumor suppressor gene involved in the pathogenesis of ESCC.

Chromosome 9p21 has been implicated in the pathogenesis of cutaneous malignant melanoma (CMM), glioma, non-small cell lung cancer, and leukemia. This region includes cyclin-dependent kinase inhibitor 2A (CDKN2A), the major known high-risk susceptibility gene for CMM; CDKN2B; antisense noncoding RNA in the INK4 locus (ANRIL), a GWAS hotspot for multiple phenotypes including cancers; methylthioadenosine phosphorylase (MTAP), a gene with tumor suppressor function and a cluster of type I interferon (IFN) genes. The goal of this study was to examine the association between genetic variation in the 9p21 region and multiple cancer outcomes using genotyping data from studies participating in the National Cancer Institute's (NCI) iSelect project. We evaluated up to 202 tagSNPs in 22 genes in the 9p21 region (19.9-32.8 Mb), in case-control studies of thyroid cancer (THC), endometrial cancer (EC), testicular cancer (TC), renal cell carcinoma (RCC), colorectal cancer (CRC), colorectal adenoma (CA), esophageal squamous cell carcinoma (ESCC), gastric cardia cancer (GCC) and osteosarcoma (OS). The number of cases in each of the nine studies ranged from 96 to 1234. We first performed single SNP-based analyses for each study separately, using logistic regression adjusted for age and study-specific covariates. To combine SNP based analyses, we used a newly developed subset-based statistical approach (ASSET), which allow for heterogeneity of SNP effect on different outcomes. This approach exhaustively explores subsets of studies for the presence of association signals, and then evaluates the significance from subsets with the strongest association signal, meanwhile accounting for multiple tests required by the subset search. Gene based P-values were computed using an adaptive rank truncated product (ARTP) statistic and a permutation-based sampling procedure (10,000 permutations) that took into account the numbers of SNPs in each gene and their linkage disequilibrium structure. When analyzing each study separately, we found that a SNP (rs3731257) in CDKN2A was significantly associated with the risk of ESCC after Bonferroni correction for number of SNPs and studies (P=7 x 10-6). Meta-analyses by ASSET found that this SNP was significantly associated with both ESCC and EC (PASSET Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-330. doi:1538-7445.AM2012-LB-330

Objectives: Both iron overload and iron deficiency cause oxidative stress and DNA damage, which increase carcinogenesis risk, especially in the gastrointestinal (GI) tract. In animal models, iron overload causes forestomach tumors, and in epidemiologic studies, high heme iron intake is associated with some upper GI cancers. Hemochromatosis, which results in excessive iron absorption in the GI tract, is also associated with GI cancer. The mechanism of increased cancer risk may involve the impairment of iron-dependent metabolic functions related to genome protection and maintenance. Genetic variants of genes with iron-dependent metabolic functions may confer differential GI cancer risk. Therefore, we comprehensively examined the genetic variants of these genes and risk of esophageal squamous cell carcinoma (ESCC) and gastric cardia adenocarcinoma (GCA) in a high-risk population in China. Methods: We genotyped 249 tag single nucleotide polymorphisms (SNPs) in 23 genes with known iron-dependent metabolic function in 1027 ESCC cases and 752 GCA cases plus 1452 controls from two epidemiologic studies in a high-risk region in China. For all genes as a single pathway and each gene individually, we calculated summary p-values using the adaptive rank truncated product (ARTP) method. For SNPs, logistic regression models were used to estimate odds ratios (OR) and 95% confidence intervals (CI). Results: In pathway-based tests, the iron pathway was not associated with either ESCC (p=0.320) or GCA (p=0.550). However, in gene-based tests, HMOX2 (heme oxygenase 2, p=0.018) and BMP2 (bone morphogenetic protein 2, p=0.032) were associated with ESCC risk, and IREB2 (iron-responsive element binding protein 2, p=0.033) was associated with GCA risk. In SNP-based tests, RS235756 (OR=0.78, CI=0.66-0.91) and RS910141 (OR=0.76, CI=0.63-0.93) tagged to BMP2 (linkage disequilibrium of pairwise r2=0.55) were associated with ESCC risk. RS6500609 (OR=1.30, CI=1.08-1.57) tagged to HMOX2 was also associated with ESCC risk. RS12910090 (OR=0.83, CI=0.72-0.94) and RS2568500 (OR=0.83, CI=0.73-0.95) tagged to IREB2 (r2=0.90) were associated with GCA risk. RS11630228 (OR=1.21, CI=1.06-1.38) also tagged to IREB2 (r2 Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2632. doi:1538-7445.AM2012-2632

Esophageal squamous cell carcinoma (ESCC) is the predominant histological subtype of esophageal cancer and is characterized by high mortality. Our previous work analyzing candidate tumor associated genes in ESCC highlighted the important differences in mRNA expression between the normal esophageal and tumor epithelial compartments. However, to date there are limited studies examining expression changes that occur during esophageal squamous cell differentiation versus those associated with ESCC tumorigenesis. To address this issue, we microdissected the basal cell layer and differentiated cell layer from normal epithelium and compared these expression profiles with matched tumor samples in twelve patients using gene expression microarrays (Hu133A 2.0, Affymetrix, Inc.) and qRT-PCR for selected miRNAs. Genes and pathways of interest were determined using class comparison and pathway analyses. Pathway expression of BRCA1 in the DNA damage response pathway presented the most significant difference (P Overall, the preliminary results indicate that tumor profiles were closer to basal cells than differentiated cells, consistent with their rapid growth rate and less well differentiated morphology. Investigation of gene expression patterns in normal cell types and ESCC provides novel insight into the transcript profiles associated with normal development versus carcinogenesis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2168.

Background: Esophageal cancer causes > 400,000 deaths/year in the world. Clinically useful early detection methods must identify these cancers and their precursor lesions at more curable stages. We conducted comparative genomic hybridization analyses of preneoplastic and invasive esophageal squamous cell carcinoma to look for gene copy number patterns that might be useful as early detection markers. The current effort focuses on aberrations associated with mild squamous dysplasia, the earliest histologic form of squamous preneoplasia. Methods: DNA was extracted from either biopsies or surgical resections from 122 esophageal tissues spanning a spectrum including normal mucosa, squamous preneoplasia, and invasive squamous cell carcinoma. High-resolution micro-array based comparative genomic hybridization (Agilent) was used to measure regions of chromosomal gain or loss with an emphasis on identifying changes associated with the transition from normal to mild dysplasia. Results: Chromosomal number aberrations were identified that involve several chromosomes, occur early in the neoplastic process, and progress with disease severity. Specific chromosomal number aberrations associated with mild squamous dysplasia, the earliest form of squamous preneoplasia, were uniquely identified. Conclusions: Comparative genomic hybridization identifies patterns of chromosomal number aberrations that may distinguish patients with and without high-grade squamous dysplasia or cancer. The current effort also identifies specific changes associated with mild squamous dysplasia, the earliest form of preneoplasia, and this may help elucidate mechanisms related to the initiation of carcinogenesis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1493.