Yu Shyr

Publications of Yu Shyr

• Intensity-Modulated Radiation Therapy with Concurrent Carboplatin and Paclitaxel for Locally Advanced Head and Neck Cancer: Toxicities and Efficacy.

  Authors: Gregory Vlacich, Roberto Diaz, Steven W Thorpe, Barbara A Murphy, Wyndee Kirby, Robert J Sinard, Bashar Shakhtour, Yu Shyr, Patrick Murphy, James L Netterville, Wendell G Yarbrough, Anthony J Cmelak

  The oncologist. 05/2012;

  AbstractBackground. Intensity-modulated radiation therapy (IMRT) and alternative chemotherapy regimens strive to maintain efficacy while minimizing toxicity in locally advanced head and neck cancerAbstractBackground. Intensity-modulated radiation therapy (IMRT) and alternative chemotherapy regimens strive to maintain efficacy while minimizing toxicity in locally advanced head and neck cancer (LAHNC) treatment. Our experience with concurrent IMRT and taxane-based chemotherapy is presented.Methods. A retrospective review of 150 consecutive patients with LAHNC treated with IMRT and concurrent taxane-based chemotherapy with curative intent was performed. The IMRT fractionation regimen consisted of 69.3 Gy to gross disease (2.1 Gy/fraction) and 56.1 Gy to prophylactic nodal sites (1.7 Gy/fraction). Weekly paclitaxel (30 mg/m(2)) and carboplatin (area under the concentration-time curve [AUC], 1) were given concurrently to all patients, and 69% received weekly induction with paclitaxel (60 mg/m(2)) and carboplatin (AUC, 2).Results. Over 90% of patients received the prescribed radiation dose. Ninety-six percent completed five or more cycles of concurrent chemotherapy, with similar tolerability for induction chemotherapy. A percutaneous endoscopic gastrostomy (PEG) tube was required in 80 patients, with 10 maintaining PEG use >18 months. Acute grade 4 mucositis and dermatitis developed in 2.0% and 4.0% of patients, respectively. No patient experienced nadir sepsis, grade ≥3 late xerostomia, or significant nephropathy or gastrointestinal toxicity. Median follow-up was 30 months. The 3-year locoregional control rate was 83.2% with disease-free survival and overall survival rates of 78.8% and 76.5%, respectively.Conclusion. Rates of acute and late toxicities were low, with excellent radiation dose delivery and impressive tumor control at 3 years, suggesting that concurrent carboplatin and paclitaxel with IMRT is a reasonable therapeutic option for the curative treatment of LAHNC.

• The Pan-ErbB Negative Regulator Lrig1 Is an Intestinal Stem Cell Marker that Functions as a Tumor Suppressor.

  Authors: Anne E Powell, Yang Wang, Yina Li, Emily J Poulin, Anna L Means, Mary K Washington, James N Higginbotham, Alwin Juchheim, Nripesh Prasad, Shawn E Levy, Yan Guo, Yu Shyr, Bruce J Aronow, Kevin M Haigis, Jeffrey L Franklin, Robert J Coffey

  Cell. 03/2012; 149(1):146-58.

  Lineage mapping has identified both proliferative and quiescent intestinal stem cells, but the molecular circuitry controlling stem cell quiescence is incompletely understood. By lineage mapping, weLineage mapping has identified both proliferative and quiescent intestinal stem cells, but the molecular circuitry controlling stem cell quiescence is incompletely understood. By lineage mapping, we show Lrig1, a pan-ErbB inhibitor, marks predominately noncycling, long-lived stem cells that are located at the crypt base and that, upon injury, proliferate and divide to replenish damaged crypts. Transcriptome profiling of Lrig1(+) colonic stem cells differs markedly from the profiling of highly proliferative, Lgr5(+) colonic stem cells; genes upregulated in the Lrig1(+) population include those involved in cell cycle repression and response to oxidative damage. Loss of Apc in Lrig1(+) cells leads to intestinal adenomas, and genetic ablation of Lrig1 results in heightened ErbB1-3 expression and duodenal adenomas. These results shed light on the relationship between proliferative and quiescent intestinal stem cells and support a model in which intestinal stem cell quiescence is maintained by calibrated ErbB signaling with loss of a negative regulator predisposing to neoplasia.

• Added Value of a Serum Proteomic Signature in the Diagnostic Evaluation of Lung Nodules.

  Authors: Chad V Pecot, Ming Li, Xueqiong J Zhang, Rama Rajanbabu, Ciara Calitri, Aaron Bungum, James R Jett, Joe B Putnam, Carol Callaway-Lane, Steve Deppen, Eric L Grogan, David P Carbone, John A Worrell, Karel G M Moons, Yu Shyr, Pierre P Massion

  Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 02/2012;

  BACKGROUND: Current management of lung nodules is complicated by nontherapeutic resections and missed chances for cure. We hypothesized that a serum proteomic signature may add diagnostic informationBACKGROUND: Current management of lung nodules is complicated by nontherapeutic resections and missed chances for cure. We hypothesized that a serum proteomic signature may add diagnostic information beyond that provided by combined clinical and radiographic data.METHODS: Cohort A included 265 and cohort B 114 patients. Using multivariable logistic regression analysis we calculated the area under the receiver operating characteristic curve (AUC) and quantified the added value of a previously described serum proteomic signature beyond clinical and radiographic risk factors for predicting lung cancer using the integration discrimination improvement (IDI) index.RESULTS: The average computed tomography (CT) measured nodule size in cohorts A and B was 37.83 versus 23.15 mm among patients with lung cancer and 15.82 versus 17.18 mm among those without, respectively. In cohort A, the AUC increased from 0.68 to 0.86 after adding chest CT imaging variables to the clinical results, but the proteomic signature did not provide meaningful added value. In contrast, in cohort B, the AUC improved from 0.46 with clinical data alone to 0.61 when combined with chest CT imaging data and to 0.69 after adding the proteomic signature (IDI of 20% P = 0.0003). In addition, in a subgroup of 100 nodules between 5 and 20 mm in diameter, the proteomic signature added value with an IDI of 15% (P ≤ 0.0001).CONCLUSIONS: The results show that this serum proteomic biomarker signature may add value to the clinical and chest CT evaluation of indeterminate lung nodules.Impact: This study suggests a possible role of a blood biomarker in the evaluation of indeterminate lung nodules. Cancer Epidemiol Biomarkers Prev; 1-7. ©2012 AACR.

• The use of next generation sequencing technology to study the effect of radiation therapy on mitochondrial DNA mutation.

  Authors: Yan Guo, Qiuyin Cai, David C Samuels, Fei Ye, Jirong Long, Chung-I Li, Jeanette F Winther, E Janet Tawn, Marilyn Stovall, Päivi Lähteenmäki, Nea Malila, Shawn Levy, Christian Shaffer, Yu Shyr, Xiao-Ou Shu, John D Boice

  Mutation research. 02/2012; 744(2):154-60.

  The human mitochondrial genome has an exclusively maternal mode of inheritance. Mitochondrial DNA (mtDNA) is particularly vulnerable to environmental insults due in part to an underdeveloped DNAThe human mitochondrial genome has an exclusively maternal mode of inheritance. Mitochondrial DNA (mtDNA) is particularly vulnerable to environmental insults due in part to an underdeveloped DNA repair system, limited to base excision and homologous recombination repair. Radiation exposure to the ovaries may cause mtDNA mutations in oocytes, which may in turn be transmitted to offspring. We hypothesized that the children of female cancer survivors who received radiation therapy may have an increased rate of mtDNA heteroplasmy mutations, which conceivably could increase their risk of developing cancer and other diseases. We evaluated 44 DNA blood samples from 17 Danish and 1 Finnish families (18 mothers and 26 children). All mothers had been treated for cancer as children and radiation doses to their ovaries were determined based on medical records and computational models. DNA samples were sequenced for the entire mitochondrial genome using the Illumina GAII system. Mother's age at sample collection was positively correlated with mtDNA heteroplasmy mutations. There was evidence of heteroplasmy inheritance in that 9 of the 18 families had at least one child who inherited at least one heteroplasmy site from his or her mother. No significant difference in single nucleotide polymorphisms between mother and offspring, however, was observed. Radiation therapy dose to ovaries also was not significantly associated with the heteroplasmy mutation rate among mothers and children. No evidence was found that radiotherapy for pediatric cancer is associated with the mitochondrial genome mutation rate in female cancer survivors and their children.

• RAF265 Inhibits the Growth of Advanced Human Melanoma Tumors.

  Authors: Yingjun Su, Anna E Vilgelm, Mark C Kelley, Oriana Hawkins, Yan Liu, Kelli L Boyd, Sara Kantrow, Ryan Splittgerber, Sarah P Short, Tammy Sobolik-Delmaire, Snjezana Zaja-Milatovic, Kimberly B Dahlman, Katayoun I Amiri, Aixiang Jiang, Pengcheng Lu, Yu Shyr, Darrin Stuart, Shawn E Levy, Jeffrey A Sosman, Ann Richmond

  Clinical cancer research : an official journal of the American Association for Cancer Research. 02/2012;

  PURPOSE: The purpose of this pre-clinical study was to determine the effectiveness of RAF265, a multi-kinase inhibitor, for treatment of human metastatic melanoma and to characterize traitsPURPOSE: The purpose of this pre-clinical study was to determine the effectiveness of RAF265, a multi-kinase inhibitor, for treatment of human metastatic melanoma and to characterize traits associated with drug response. EXPERIMENTAL DESIGN: Advanced metastatic melanoma tumors from 34 patients were orthotopically implanted to nude mice. Tumors that grew in mice (17/34) were evaluated for response to RAF265 (40 mg/kg, QD) over 30 days. The relation between patient characteristics, gene mutation profile, global gene expression profile, and RAF265 effects on tumor growth, MEK/ERK phosphorylation, proliferation, and apoptosis markers were evaluated. RESULTS: Nine of the 17 tumors that successfully implanted (53%) were mutant BRAF (BRAFV600E/K), while 8 of 17 (47%) were BRAF wild-type (BRAFWT). Tumor implants from 7/17 patients (41%) responded to RAF265 treatment with >50% reduction in tumor growth. Five of the 7 (71%) responders were BRAFWT, of which one carried c-KIT L576P and another N-RASQ61R, while only 2 (29%) of the responding tumors were BRAFV600E/K. Gene expression microarray data from non-implanted tumors revealed responders exhibited enriched expression of genes involved in cell growth, proliferation, development, cell signaling, gene expression, and cancer pathways. While response to RAF265 did not correlate with pERK1/2 reduction, RAF265 responders did exhibit reduced pMEK1, reduced proliferation based upon reduced Ki67, cyclin D1 and PLK1, and induction of the apoptosis mediator BIM. CONCLUSIONS: Orthotopic implants of patient tumors in mice may predict prognosis and treatment response for melanoma patients. A sub-population of human melanoma tumors respond to RAF265 and can be characterized by gene mutation and gene expression profiles.

• Loss of TGF-β Responsiveness in Prostate Stromal Cells Alters Chemokine Levels and Facilitates the Development of Mixed Osteoblastic/Osteolytic Bone Lesions.

  Authors: Xiaohong Li, Julie A Sterling, Kang-Hsien Fan, Robert L Vessella, Yu Shyr, Simon W Hayward, Lynn M Matrisian, Neil A Bhowmick

  Molecular cancer research : MCR. 01/2012;

  Loss of transforming growth factor-beta (TGF-β) type II receptor (TβRII, encoded by Tgfbr2) expression in the prostate stroma contributes to prostate cancer (PCa) initiation, progression, andLoss of transforming growth factor-beta (TGF-β) type II receptor (TβRII, encoded by Tgfbr2) expression in the prostate stroma contributes to prostate cancer (PCa) initiation, progression, and invasion. We evaluated whether TβRII loss also affected PCa bone metastatic growth. Immunohistological analysis revealed that TβRII expression was lost in cancer-associated fibroblasts in human PCa bone metastatic tissues. We recapitulated the human situation with a conditional stromal Tgfbr2 knockout (Tgfbr2-KO) mouse model. Conditioned media from primary cultured Tgfbr2-KO or control Tgfbr2-flox prostatic fibroblasts (koPFCM or wtPFCM, respectively) were applied to C4-2B PCa cells prior to grafting the cells tibially. We found that koPFCM promoted PCa cell growth in the bone and development of early mixed osteoblastic/osteolytic bone lesions. Further, the koPFCM promoted greater C4-2B adhesion to type-1 collagen, the major component of bone matrix, compared to wtPFCM treated C4-2B. Cytokine antibody array analysis revealed that koPFCM had more than 2-fold elevation in granulocyte colony-stimulating factor, CXCL1, CXCL16, and CXCL5 expression relative to wtPFCM. Interestingly, neutralizing antibodies of CXCL16 or CXCL1 was able to reduce koPFCM-associated C4-2B collagen I adhesion to that comparable to wtPFCM mediated adhesion. Collectively, our data indicate that loss of TGF-β responsiveness in prostatic fibroblasts results in upregulation of CXCL16 and CXCL1; and that these paracrine signals increase PCa cell adhesion in the bone matrix. These microenvironment changes at the primary tumor site can mediate early establishment of PCa cells in the bone and support subsequent tumor development at the metastatic site.

• Analysis of microsatellite mutations in buccal cells from a case-control study for lung cancer.

  Authors: Jessica L Baumann, Ming Li, Aslak Poulsen, Nicholson S Chadwick, Qiuyin Cai, Christine H Chung, Yu Shyr, Jørgen H Olsen, Wei Zheng, Robbert J C Slebos

  Cancer epidemiology. 11/2011; 36(1):e33-9.

  Exposure to tobacco carcinogens is the major cause of human lung cancer, but even heavy smokers have only about a 10% life-time risk of developing lung cancer. Currently used screening processes,Exposure to tobacco carcinogens is the major cause of human lung cancer, but even heavy smokers have only about a 10% life-time risk of developing lung cancer. Currently used screening processes, based largely on age and exposure status, have proven to be of limited clinical utility in predicting cancer risk. More precise methods of assessing an individual's risk of developing lung cancer are needed. Because of their sensitivity to DNA damage, microsatellites are potentially useful for the assessment of somatic mutational load in normal cells. We assessed mutational load using hypermutable microsatellites in buccal cells obtained from lung carcinoma cases and controls to test if such a measure could be used to estimate lung cancer risk. There was no significant association between smoking status and mutation frequency with any of the markers tested. No significant association between case status and mutation frequency was observed. Age was significantly related to mutation frequency in the microsatellite marker D7S1482. These observations indicate that somatic mutational load, as measured using mutation frequency of microsatellites in buccal cells, increases with increasing age but that subjects who develop lung cancer have a similar mutational load as those who remain cancer free. This finding suggests that mutation frequency of microsatellite mutations in buccal cells may not be a promising biomarker for lung cancer risk.

• TGF-β Receptor II Loss Promotes Mammary Carcinoma Progression by Th17 Dependent Mechanisms.

  Authors: Sergey V Novitskiy, Michael W Pickup, Agnieszka E Gorska, Philip Owens, Anna Chytil, Mary Aakre, Huiyun Wu, Yu Shyr, Harold L Moses

  Cancer discovery. 10/2011; 1(5):430-441.

  We report that IL-17 significantly increases the secretion of CXCL1 and CXCL5 from mammary carcinoma cells, which is downregulated by TGF-β through the type II TGF-β receptor (TβRII). Carcinoma cellsWe report that IL-17 significantly increases the secretion of CXCL1 and CXCL5 from mammary carcinoma cells, which is downregulated by TGF-β through the type II TGF-β receptor (TβRII). Carcinoma cells with conditional knockout of TβRII (Tgfbr2(KO)) have enhanced sensitivity to IL-17a in the stimulation of chemokine secretion. During polyoma middle T (PyMT) induced tumor progression, levels of Th17 inducing cytokines TGF-β, IL-6, IL-23 were increased in PyMT/Tgfbr2(KO) tumors, which was associated with an increased number of Th17 cells. IL-17 increased the suppressive function of MDSCs on T cells through the upregulation of Arg, IDO, and COX2. Treatment of PyMT/Tgfbr2(KO) mice with anti-IL-17 Ab decreased carcinoma growth and metastatic burden. Analysis of human breast cancer transcriptome databases showed a strong association between IL-17 gene expression and poor outcome in lymph node positive, estrogen receptor negative or luminal B subtypes suggesting potential therapeutic approaches.

• A kinome-wide screen identifies the insulin/IGF-I receptor pathway as a mechanism of escape from hormone dependence in breast cancer.

  Authors: Emily M Fox, Todd W Miller, Justin M Balko, Maria G Kuba, Violeta Sánchez, R Adam Smith, Shuying Liu, Ana María González-Angulo, Gordon B Mills, Fei Ye, Yu Shyr, H Charles Manning, Elizabeth Buck, Carlos L Arteaga

  Cancer research. 09/2011; 71(21):6773-84.

  Estrogen receptor α (ER)-positive breast cancers adapt to hormone deprivation and become resistant to antiestrogens. In this study, we sought to identify kinases essential for growth of ER(+) breastEstrogen receptor α (ER)-positive breast cancers adapt to hormone deprivation and become resistant to antiestrogens. In this study, we sought to identify kinases essential for growth of ER(+) breast cancer cells resistant to long-term estrogen deprivation (LTED). A kinome-wide siRNA screen showed that the insulin receptor (InsR) is required for growth of MCF-7/LTED cells. Knockdown of InsR and/or insulin-like growth factor-I receptor (IGF-IR) inhibited growth of 3 of 4 LTED cell lines. Inhibition of InsR and IGF-IR with the dual tyrosine kinase inhibitor OSI-906 prevented the emergence of hormone-independent cells and tumors in vivo, inhibited parental and LTED cell growth and PI3K/AKT signaling, and suppressed growth of established MCF-7 xenografts in ovariectomized mice, whereas treatment with the neutralizing IGF-IR monoclonal antibody MAB391 was ineffective. Combined treatment with OSI-906 and the ER downregulator fulvestrant more effectively suppressed hormone-independent tumor growth than either drug alone. Finally, an insulin/IGF-I gene expression signature predicted recurrence-free survival in patients with ER(+) breast cancer treated with the antiestrogen tamoxifen. We conclude that therapeutic targeting of both InsR and IGF-IR should be more effective than targeting IGF-IR alone in abrogating resistance to endocrine therapy in breast cancer.

• ERα-dependent E2F transcription can mediate resistance to estrogen deprivation in human breast cancer.

  Authors: Todd W Miller, Justin M Balko, Emily M Fox, Zara Ghazoui, Anita Dunbier, Helen Anderson, Mitch Dowsett, Aixiang Jiang, R Adam Smith, Sauveur-Michel Maira, H Charles Manning, Ana M González-Angulo, Gordon B Mills, Catherine Higham, Siprachanh Chanthaphaychith, Maria G Kuba, William R Miller, Yu Shyr, Carlos L Arteaga

  Cancer discovery. 09/2011; 1(4):338-351.

  Most estrogen receptor α (ER)-positive breast cancers initially respond to antiestrogens, but many eventually become estrogen-independent and recur. We identified an estrogen-independent role for ERMost estrogen receptor α (ER)-positive breast cancers initially respond to antiestrogens, but many eventually become estrogen-independent and recur. We identified an estrogen-independent role for ER and the CDK4/Rb/E2F transcriptional axis in the hormone-independent growth of breast cancer cells. ER downregulation with fulvestrant or siRNA inhibited estrogen-independent growth. Chromatin immunoprecipitation identified ER genomic binding activity in estrogen-deprived cells and primary breast tumors treated with aromatase inhibitors. Gene expression profiling revealed an estrogen-independent, ER/E2F-directed transcriptional program. An E2F activation gene signature correlated with a lesser response to aromatase inhibitors in patients' tumors. siRNA screening showed that CDK4, an activator of E2F, is required for estrogen-independent cell growth. Long-term estrogen-deprived cells hyperactivate phosphatidylinositol 3-kinase (PI3K) independently of ER/E2F. Fulvestrant combined with the pan-PI3K inhibitor BKM120 induced regression of ER+ xenografts. These data support further development of ER downregulators and CDK4 inhibitors, and their combination with PI3K inhibitors for treatment of antiestrogen-resistant breast cancers.

• The discovery of novel protein-coding features in mouse genome based on mass spectrometry data.

  Authors: Xiao-Bin Xing, Qing-Run Li, Han Sun, Xing Fu, Fei Zhan, Xiu Huang, Jing Li, Chun-Lei Chen, Yu Shyr, Rong Zeng, Yi-Xue Li, Lu Xie

  Genomics. 08/2011; 98(5):343-51.

  Identifying protein-coding genes in eukaryotic genomes remains a challenge in post-genome era due to the complex gene models. We applied a proteogenomics strategy to detect un-annotatedIdentifying protein-coding genes in eukaryotic genomes remains a challenge in post-genome era due to the complex gene models. We applied a proteogenomics strategy to detect un-annotated protein-coding regions in mouse genome. High-accuracy tandem mass spectrometry (MS/MS) data from diverse mouse samples were generated by LTQ-Orbitrap mass spectrometer in house. Two searchable diagnostic proteomic datasets were constructed, one with all possible encoding exon junctions, and the other with all putative encoding exons, for the discovery of novel exon splicing events and novel uninterrupted protein-coding regions. Altogether 29,586 unique peptides were identified. Aligning backwards to the mouse genome, the translation of 4471 annotated genes was validated by the known peptides; and 172 genic events were defined in mouse genome by the novel peptides. The approach in the current work can provide substantial evidences for eukaryote genome annotation in encoding genes.

• Nonsteroidal anti-inflammatory drug use and risk of adenomatous and hyperplastic polyps.

  Authors: Harvey J Murff, Martha J Shrubsole, Zhi Chen, Walter E Smalley, Heidi Chen, Yu Shyr, Reid M Ness, Wei Zheng

  Cancer prevention research (Philadelphia, Pa.). 07/2011; 4(11):1799-807.

  Adenomatous polyps are known precursor lesions for colorectal cancer and some hyperplastic polyps also have malignant potential. The use of aspirin and nonsteroidal anti-inflammatory drugs (NSAID) isAdenomatous polyps are known precursor lesions for colorectal cancer and some hyperplastic polyps also have malignant potential. The use of aspirin and nonsteroidal anti-inflammatory drugs (NSAID) is associated with a reduced risk of adenomatous polyps; however, less evidence exists with regard to NSAID use and hyperplastic polyp risk. We conducted a colonoscopy-based case-control study including 2,028 polyp cases (1,529 adenomatous and 499 hyperplastic) and 3,431 polyp-free controls. Multivariate logistic regression models were constructed to derived adjusted ORs and 95% CIs as the measure of the association between NSAID use and polyp risk. Use of baby aspirin, regular aspirin, and nonaspirin NSAIDs, were associated with a reduced risk of adenomatous polyps (OR = 0.79, 95% CI: 0.66-0.93, OR = 0.73, 95% CI: 0.58-0.90, and OR = 0.67, 95% CI: 0.53-0.86, respectively). Baby aspirin was also associated with a reduced risk of hyperplastic polyps (OR = 0.74, 0.56-0.97). Although a dose response was seen with adenoma risk and regular use of any NSAIDs (less than 7 doses per week, 7 doses per week, and greater than 7 doses per week), a dose response was not seen with hyperplastic polyps. We found no evidence of interaction between NSAID dose and duration and polyp risk. The use of any NSAID regardless of type was associated with a reduced risk of adenomatous polyps; however, regular aspirin and COX-2 inhibitors use was not associated with hyperplastic polyp risk.

• Fish, shellfish, and long-chain n-3 fatty acid consumption and risk of incident type 2 diabetes in middle-aged Chinese men and women.

  Authors: Raquel Villegas, Yong-Bing Xiang, Tom Elasy, Hong-Lan Li, Gong Yang, Hui Cai, Fei Ye, Yu-Tang Gao, Yu Shyr, Wei Zheng, Xiao-Ou Shu

  The American journal of clinical nutrition. 06/2011; 94(2):543-51.

  Long-chain polyunsaturated n-3 (omega-3) fatty acids, found mainly in fish, have been postulated to reduce type 2 diabetes (T2D) risk. However, the role of long-chain n-3 fatty acids and fish intakeLong-chain polyunsaturated n-3 (omega-3) fatty acids, found mainly in fish, have been postulated to reduce type 2 diabetes (T2D) risk. However, the role of long-chain n-3 fatty acids and fish intake in the development of T2D remains unresolved. We examined associations between fish, shellfish, and long-chain n-3 fatty acids and the risk of T2D in a middle-aged Chinese population. This was a prospective population-based cohort study in 51,963 men and 64,193 women free of T2D, cardiovascular disease, and cancer at baseline with valid dietary information. Dietary intake, physical activity, and anthropometric measurements were collected. A Cox regression model was used to evaluate the association of fish, shellfish, and long-chain n-3 fatty acid (in g/d) with risk of T2D. Fish, shellfish, and long-chain n-3 fatty acid intakes were inversely associated with T2D in women. The relative risks [RRs (95% CI)] for quintiles of fish intake were 1.00, 0.96 (0.86, 1.06), 0.84 (0.75, 0.94), 0.80 (0.71, 0.90), and 0.89 (0.78, 1.01) (P for trend = 0.003) and for shellfish were 1.00, 0.91 (0.82, 1.01), 0.79 (0.71, 0.89), 0.80 (0.71, 0.91), and 0.86 (0.76, 0.99) (P for trend = 0.006). In men, only the association between shellfish intake and T2D was significant. The RRs (95% CI) for quintiles of fish intake were 1.00, 0.92 (0.75, 1.13), 0.80 (0.65, 1.00), 0.89 (0.72, 1.11), and 0.94 (0.74, 1.17) (P for trend = 0.50) and for shellfish intake were 1.00, 0.93 (0.76, 1.12), 0.70 (0.56, 086), 0.66 (0.53, 0.82), and 0.82 (0.65, 1.02) (P for trend = 0.003). An inverse association between fish and shellfish intake and T2D in women was found. No evidence of a detrimental effect of fish intake in this population was observed.

• Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies.

  Authors: Brian D Lehmann, Joshua A Bauer, Xi Chen, Melinda E Sanders, A Bapsi Chakravarthy, Yu Shyr, Jennifer A Pietenpol

  The Journal of clinical investigation. 06/2011; 121(7):2750-67.

  Triple-negative breast cancer (TNBC) is a highly diverse group of cancers, and subtyping is necessary to better identify molecular-based therapies. In this study, we analyzed gene expression (GE)Triple-negative breast cancer (TNBC) is a highly diverse group of cancers, and subtyping is necessary to better identify molecular-based therapies. In this study, we analyzed gene expression (GE) profiles from 21 breast cancer data sets and identified 587 TNBC cases. Cluster analysis identified 6 TNBC subtypes displaying unique GE and ontologies, including 2 basal-like (BL1 and BL2), an immunomodulatory (IM), a mesenchymal (M), a mesenchymal stem-like (MSL), and a luminal androgen receptor (LAR) subtype. Further, GE analysis allowed us to identify TNBC cell line models representative of these subtypes. Predicted "driver" signaling pathways were pharmacologically targeted in these cell line models as proof of concept that analysis of distinct GE signatures can inform therapy selection. BL1 and BL2 subtypes had higher expression of cell cycle and DNA damage response genes, and representative cell lines preferentially responded to cisplatin. M and MSL subtypes were enriched in GE for epithelial-mesenchymal transition, and growth factor pathways and cell models responded to NVP-BEZ235 (a PI3K/mTOR inhibitor) and dasatinib (an abl/src inhibitor). The LAR subtype includes patients with decreased relapse-free survival and was characterized by androgen receptor (AR) signaling. LAR cell lines were uniquely sensitive to bicalutamide (an AR antagonist). These data may be useful in biomarker selection, drug discovery, and clinical trial design that will enable alignment of TNBC patients to appropriate targeted therapies.

• Lung cancer diagnosis from proteomic analysis of preinvasive lesions.

  Authors: S M Jamshedur Rahman, Adriana L Gonzalez, Ming Li, Erin H Seeley, Lisa J Zimmerman, Xueqiong J Zhang, M Lisa Manier, Sandra J Olson, Ronak N Shah, Alison N Miller, Joe B Putnam, York E Miller, Wilbur A Franklin, William J Blot, David P Carbone, Yu Shyr, Richard M Caprioli, Pierre P Massion

  Cancer research. 04/2011; 71(8):3009-17.

  Early detection may help improve survival from lung cancer. In this study, our goal was to derive and validate a signature from the proteomic analysis of bronchial lesions that could predict theEarly detection may help improve survival from lung cancer. In this study, our goal was to derive and validate a signature from the proteomic analysis of bronchial lesions that could predict the diagnosis of lung cancer. Using previously published studies of bronchial tissues, we selected a signature of nine matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) mass-to-charge ratio features to build a prediction model diagnostic of lung cancer. The model was based on MALDI MS signal intensity (MALDI score) from bronchial tissue specimens from our 2005 published cohort of 51 patients. The performance of the prediction model in identifying lung cancer was tested in an independent cohort of bronchial specimens from 60 patients. The probability of having lung cancer based on the proteomic analysis of the bronchial specimens was characterized by an area under the receiver operating characteristic curve of 0.77 (95% CI 0.66-0.88) in this validation cohort. Eight of the nine features were identified and validated by Western blotting and immunohistochemistry. These results show that proteomic analysis of endobronchial lesions may facilitate the diagnosis of lung cancer and the monitoring of high-risk individuals for lung cancer in surveillance and chemoprevention trials.

• Wave-spec: a preprocessing package for mass spectrometry data.

  Authors: Ming Li, Shuo Chen, Joan Zhang, Heidi Chen, Yu Shyr

  Bioinformatics (Oxford, England). 03/2011; 27(5):739-40.

  Wave-spec is a pre-processing package for mass spectrometry (MS) data. The package includes several novel algorithms that overcome conventional difficulties with the pre-processing of such data. InWave-spec is a pre-processing package for mass spectrometry (MS) data. The package includes several novel algorithms that overcome conventional difficulties with the pre-processing of such data. In this application note, we demonstrate step-by-step use of this package on a real-world MALDI dataset. AVAILABILITY: The package can be downloaded at http://www.vicc.org/biostatistics/supp.php. A shared mailbox (wave-spec@vanderbilt.edu) also is available for questions regarding application of the package.

• Angiocrine factors modulate tumor proliferation and motility through EphA2 repression of Slit2 tumor suppressor function in endothelium.

  Authors: Dana M Brantley-Sieders, Charlene M Dunaway, Meghana Rao, Sarah Short, Yoonha Hwang, Yandong Gao, Deyu Li, Aixiang Jiang, Yu Shyr, Jane Y Wu, Jin Chen

  Cancer research. 02/2011; 71(3):976-87.

  It is well known that tumor-derived proangiogenic factors induce neovascularization to facilitate tumor growth and malignant progression. However, the concept of "angiocrine" signaling, in whichIt is well known that tumor-derived proangiogenic factors induce neovascularization to facilitate tumor growth and malignant progression. However, the concept of "angiocrine" signaling, in which signals produced by endothelial cells elicit tumor cell responses distinct from vessel function, has been proposed, yet remains underinvestigated. Here, we report that angiocrine factors secreted from endothelium regulate tumor growth and motility. We found that Slit2, which is negatively regulated by endothelial EphA2 receptor, is one such tumor suppressive angiocrine factor. Slit2 activity is elevated in EphA2-deficient endothelium. Blocking Slit activity restored angiocrine-induced tumor growth/motility, whereas elevated Slit2 impaired growth/motility. To translate our findings to human cancer, we analyzed EphA2 and Slit2 expression in human cancer. EphA2 expression inversely correlated with Slit2 in the vasculature of invasive human ductal carcinoma samples. Moreover, analysis of large breast tumor data sets revealed that Slit2 correlated positively with overall and recurrence-free survival, providing clinical validation for the tumor suppressor function for Slit2 in human breast cancer. Together, these data support a novel, clinically relevant mechanism through which EphA2 represses Slit2 expression in endothelium to facilitate angiocrine-mediated tumor growth and motility by blocking a tumor suppressive signal.

• D2-40 lymphatic marker for detecting lymphatic invasion in thin to intermediate thickness melanomas: association with sentinel lymph node status and prognostic value-a retrospective case study.

  Authors: Laurel E Fohn, Adrian Rodriguez, Mark C Kelley, Fei Ye, Yu Shyr, George Stricklin, Jason B Robbins

  Journal of the American Academy of Dermatology. 02/2011; 64(2):336-45.

  Sentinel lymph node (SLN) status is the greatest prognostic factor of morbidity in melanoma. D2-40 antibody specifically marks lymphatic endothelium and has been used for identifying lymphaticSentinel lymph node (SLN) status is the greatest prognostic factor of morbidity in melanoma. D2-40 antibody specifically marks lymphatic endothelium and has been used for identifying lymphatic invasion (LI) in multiple cancers. We sought to determine the relationship between melanoma lymphatic invasion (as detected using D2-40 on primary melanoma biopsies/excisions) and the presence or absence of melanoma in subsequent SLN biopsy. We retrospectively evaluated LI using D2-40 on primary biopsies/excisions from patients with thin to intermediate thickness (Breslow thickness: ≤2.0 mm) melanomas, who underwent lymphatic mapping and SLN biopsy, and whose SLN status was known. Sixty-four cases met the criteria and were available for analysis. We analyzed patient age, patient sex, mitotic rate, ulceration, tumor depth, and D2-40 detected LI as predictors of SLN status. Lymphatic invasion detection increased from 3.1% using hematoxylin and eosin only to 21.9% using D2-40. Twelve of 14 patients with D2-40 LI were SLN positive (positive predictive value, 85.7%). D2-40 LI was detected in the primary biopsy specimen of 12 of 18 patients with a positive SLN (sensitivity 66.7%). Of 50 patients without D2-40 LI, 44 were SLN negative (negative predictive value, 88.0%). Of 46 SLN-negative patients, 44 did not have D2-40 LI (specificity, 95.7%). Results are retrospective and limited to SLN biopsy performed at one institution. On univariate and multivariate analysis, D2-40-detected LI was the most significant predictor of SLN status. D2-40 antibody staining to detect lymphatic invasion should be incorporated in routine melanoma biopsy evaluation.

• Differential regulation of the p73 cistrome by mammalian target of rapamycin reveals transcriptional programs of mesenchymal differentiation and tumorigenesis.

  Authors: Jennifer M Rosenbluth, Deborah J Mays, Aixiang Jiang, Yu Shyr, Jennifer A Pietenpol

  Proceedings of the National Academy of Sciences of the United States of America. 02/2011; 108(5):2076-81.

  The transcription factor p73 plays critical roles during development and tumorigenesis. It exhibits sequence identity and structural homology with p53, and can engage p53-like tumor-suppressiveThe transcription factor p73 plays critical roles during development and tumorigenesis. It exhibits sequence identity and structural homology with p53, and can engage p53-like tumor-suppressive programs. However, different pathways regulate p53 and p73, and p73 is not mutated in human tumors. Therefore, p73 represents a therapeutic target, and there is a critical need to understand genes and noncoding RNAs regulated by p73 and how they change during treatment regimens. Here, we define the p73 genomic binding profile and demonstrate its modulation by rapamycin, an inhibitor of mammalian target of rapamycin (mTOR) and inducer of p73. Rapamycin selectively increased p73 occupancy at a subset of its binding sites. In addition, multiple determinants of p73 binding, activity, and function were evident, and were modulated by mTOR. We generated an mTOR-p73 signature that is enriched for p73 target genes and miRNAs that are involved in mesenchymal differentiation and tumorigenesis, can classify rhabdomyosarcomas by clinical subtype, and can predict patient outcome.

• A gene expression signature from human breast cancer cells with acquired hormone independence identifies MYC as a mediator of antiestrogen resistance.

  Authors: Todd W Miller, Justin M Balko, Zara Ghazoui, Anita Dunbier, Helen Anderson, Mitch Dowsett, Ana M González-Angulo, Gordon B Mills, William R Miller, Huiyun Wu, Yu Shyr, Carlos L Arteaga

  Clinical cancer research : an official journal of the American Association for Cancer Research. 02/2011; 17(7):2024-34.

  Although most patients with estrogen receptor α (ER)-positive breast cancer initially respond to endocrine therapy, many ultimately develop resistance to antiestrogens. However, mechanisms ofAlthough most patients with estrogen receptor α (ER)-positive breast cancer initially respond to endocrine therapy, many ultimately develop resistance to antiestrogens. However, mechanisms of antiestrogen resistance and biomarkers predictive of such resistance are underdeveloped. We adapted four ER(+) human breast cancer cell lines to grow in an estrogen-depleted medium. A gene signature of estrogen independence was developed by comparing expression profiles of long-term estrogen-deprived (LTED) cells to their parental counterparts. We evaluated the ability of the LTED signature to predict tumor response to neoadjuvant therapy with an aromatase inhibitor and disease outcome following adjuvant tamoxifen. We utilized Gene Set Analysis (GSA) of LTED cell gene expression profiles and a loss-of-function approach to identify pathways causally associated with resistance to endocrine therapy. The LTED gene expression signature was predictive of high tumor cell proliferation following neoadjuvant therapy with anastrozole and letrozole, each in different patient cohorts. This signature was also predictive of poor recurrence-free survival in two studies of patients treated with adjuvant tamoxifen. Bioinformatic interrogation of expression profiles in LTED cells revealed a signature of MYC activation. The MYC activation signature and high MYC protein levels were both predictive of poor outcome following tamoxifen therapy. Finally, knockdown of MYC inhibited LTED cell growth. A gene expression signature derived from ER(+) breast cancer cells with acquired hormone independence predicted tumor response to aromatase inhibitors and associated with clinical markers of resistance to tamoxifen. Activation of the MYC pathway was associated with this resistance.