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Sleep duration is implicated in the etiologies of chronic diseases and premature mortality. However, the genetic basis for sleep duration is poorly defined. We sought to identify novel genetic components influencing sleep duration in a multi-ethnic sample. Meta-analyses were conducted of genetic associations with self-reported, habitual sleep duration from seven Candidate Gene Association Resource (CARe) cohorts of over 25 000 individuals of African, Asian, European and Hispanic American ancestry. All individuals were genotyped for ∼50 000 SNPs from 2000 candidate heart, lung, blood and sleep genes. African-Americans had additional genome-wide genotypes. Four cohorts provided replication. A SNP (rs17601612) in the dopamine D2 receptor gene (DRD2) was significantly associated with sleep duration (P = 9.8 × 10(-7)). Conditional analysis identified a second DRD2 signal with opposite effects on sleep duration. In exploratory analysis, suggestive association was observed for rs17601612 with polysomnographically determined sleep latency (P = 0.002). The lead DRD2 signal was recently identified in a schizophrenia GWAS, and a genetic risk score of 11 additional schizophrenia GWAS loci genotyped on the IBC array was also associated with longer sleep duration (P = 0.03). These findings support a role for DRD2 in influencing sleep duration. Our work motivates future pharmocogenetics research on alerting agents such as caffeine and modafinil that interact with the dopaminergic pathway and further investigation of genetic overlap between sleep and neuro-psychiatric traits.

BACKGROUND AND OBJECTIVES: Polysomnography defines the pathophysiology of obstructive sleep apnea syndrome (OSAS) but does not predict some important comorbidities or their response to adenotonsillectomy. We assessed whether OSAS symptoms, as reflected on the Sleep-Related Breathing Disorders Scale of the Pediatric Sleep Questionnaire (PSQ), may offer clinical predictive value. METHODS: Baseline and 7-month follow-up data were analyzed from 185 participants (aged 5–9 years with polysomnographically confirmed OSAS) in the surgical treatment arm of the multicenter Childhood Adenotonsillectomy Trial. Associations were assessed between baseline PSQ or polysomnographic data and baseline morbidity (executive dysfunction, behavior, quality of life, sleepiness) or postsurgical improvement. RESULTS: At baseline, each 1-SD increase in baseline PSQ score was associated with an adjusted odds ratio that was ∼3 to 4 times higher for behavioral morbidity, 2 times higher for reduced global quality of life, 6 times higher for reduced disease-specific quality of life, and 2 times higher for sleepiness. Higher baseline PSQ scores (greater symptom burden) also predicted postsurgical improvement in parent ratings of executive functioning, behavior, quality of life, and sleepiness. In contrast, baseline polysomnographic data did not independently predict these morbidities or their postsurgical improvement. Neither PSQ nor polysomnographic data were associated with objectively assessed executive dysfunction or improvement at follow-up. CONCLUSIONS: PSQ symptom items, in contrast to polysomnographic results, reflect subjective measures of OSAS-related impairment of behavior, quality of life, and sleepiness and predict their improvement after adenotonsillectomy. Although objective polysomnography is needed to diagnose OSAS, the symptoms obtained during an office visit can offer adjunctive insight into important comorbidities and likely surgical responses.

Study objectives While actigraphy is considered objective, the process of setting rest intervals to calculate sleep variables is subjective. We sought to evaluate the reproducibility of actigraphy-derived measures of sleep using a standardized algorithm for setting rest intervals. Design Observational study. Setting Community-based. Participants A random sample of 50 adults aged 18-64 years free of severe sleep apnea participating in the Sueno sleep ancillary study to the Hispanic Community Health Study/Study of Latinos. Interventions N/A. Measurements and results Participants underwent 7 days of continuous wrist actigraphy and completed daily sleep diaries. Studies were scored twice by each of two scorers. Rest intervals were set using a standardized hierarchical approach based on event marker, diary, light, and activity data. Sleep/wake status was then determined for each 30-sec epoch using a validated algorithm, and this was used to generate 11 variables: mean nightly sleep duration, nap duration, 24-h sleep duration, sleep latency, sleep maintenance efficiency, sleep fragmentation index, sleep onset time, sleep offset time, sleep midpoint time, standard deviation of sleep duration, and standard deviation of sleep midpoint. Intra-scorer intraclass correlation coefficients (ICCs) were high, ranging from 0.911 to 0.995 across all 11 variables. Similarly, inter-scorer ICCs were high, also ranging from 0.911 to 0.995, and mean inter-scorer differences were small. Bland-Altman plots did not reveal any systematic disagreement in scoring. Conclusions With use of a standardized algorithm to set rest intervals, scoring of actigraphy for the purpose of generating a wide array of sleep variables is highly reproducible.

Introduction: Transforming growth factor-βs (TGF-βs) play a dual role in breast cancer, with context-dependent tumor-suppressive or pro-oncogenic effects. TGF-β antagonists are showing promise in early-phase clinical oncology trials to neutralize the pro-oncogenic effects. However, there is currently no way to determine whether the tumor-suppressive effects of TGF-β are still active in human breast tumors at the time of surgery and treatment, a situation that could lead to adverse therapeutic responses. Methods: Using a breast cancer progression model that exemplifies the dual role of TGF-β, promoter-wide chromatin immunoprecipitation and transcriptomic approaches were applied to identify a core set of TGF-β-regulated genes that specifically reflect only the tumor-suppressor arm of the pathway. The clinical significance of this signature and the underlying biology were investigated using bioinformatic analyses in clinical breast cancer datasets, and knockdown validation approaches in tumor xenografts. Results: TGF-β-driven tumor suppression was highly dependent on Smad3, and Smad3 target genes that were specifically enriched for involvement in tumor suppression were identified. Patterns of Smad3 binding reflected the preexisting active chromatin landscape, and target genes were frequently regulated in opposite directions in vitro and in vivo, highlighting the strong contextuality of TGF-β action. An in vivo-weighted TGF-β/Smad3 tumor-suppressor signature was associated with good outcome in estrogen receptor-positive breast cancer cohorts. TGF-β/Smad3 effects on cell proliferation, differentiation and ephrin signaling contributed to the observed tumor suppression. Conclusions: Tumor-suppressive effects of TGF-β persist in some breast cancer patients at the time of surgery and affect clinical outcome. Carefully tailored in vitro/in vivo genomic approaches can identify such patients for exclusion from treatment with TGF-β antagonists.

Although obstructive sleep apnea (OSA) is known to have a strong familial basis, no genetic polymorphisms influencing apnea risk have been identified in cross-cohort analyses. We utilized the National Heart, Lung, and Blood Institute (NHLBI) Candidate Gene Association Resource (CARe) to identify sleep apnea susceptibility loci. Using a panel of 46,449 polymorphisms from roughly 2,100 candidate genes on a customized Illumina iSelect chip, we tested for association with the apnea hypopnea index (AHI) as well as moderate to severe OSA (AHI≥15) in 3,551 participants of the Cleveland Family Study and two cohorts participating in the Sleep Heart Health Study. Among 647 African-Americans, rs11126184 in the pleckstrin (PLEK) gene was associated with OSA while rs7030789 in the lysophosphatidic acid receptor 1 (LPAR1) gene was associated with AHI using a chip-wide significance threshold of p-value

We present two novel entropy-based measures that quantify sleep-stage transition dynamics (sleep structure) from polysomnogram derived hypnograms: Walsh spectral entropy (WSE) and Haar spectral entropy (HSE). These measures quantify patterns of temporal regularity of a categorical time series without requiring numerical encoding (scaling) of the (categorical) sleep stages. Additionally, we show that conditional entropy (CE) is well suited for quantifying predictability of the hypnogram. The relationship of those measures with traditional sleep fragmentation indices (arousal index, total sleep time, and sleep efficiency) is explored for a 394 participant sample of the Cleveland Family Study, an epidemiologic study in which standardized single-night polysomnogram data were collected. The new entropy-based sleep structure measures (WSE, HSE, and CE) are positively correlated (moderate to weak) with the traditional sleep fragmentation indices. Because the sleep structure measures developed in this paper provide direct information related to temporal patterns of sleep that is not contained in traditional sleep fragmentation measures, the correlation between these new alternative sleep structure measures and the traditional sleep fragmentation measures is less important. Our goal is not to develop alternative measures that correlate highly with traditional measures of sleep fragmentation, but rather to provide methods to quantify sleep structure by examining other (e.g., dynamic sleep-stage transition) properties of the hypnogram. Additionally, the relationship of the new entropy-based and traditional measures with daytime sleepiness as quantified by the Epworth sleepiness scale (ESS) is investigated. Multiple linear regression analysis shows that WSE has a stronger relationship with ESS than the traditional measures, even after both are adjusted for common confounders (age, race, gender, and body mass index). This further suggests that the entropy-based measures, especially WSE, are capturing additional temporal patterns of sleep not captured in the traditional sleep fragmentation measures, and have a relationship with daytime sleepiness.

Tumor necrosis factor (TNF) antagonists [e.g., TNF soluble receptor (TNFsr)] improved survival in preclinical but not clinical sepsis trials. However fluid support-itself beneficial-is standard clinically but rarely employed in preclinical sepsis models. We hypothesized that these therapies may not have additive benefit.Antibiotic-treated rats (n = 156) were randomized to intratracheal or intravenous Escherichia coli challenges (LD50) and either placebo or TNFsr and 24 h fluid treatments alone or together. The survival effects of these therapies did not differ significantly comparing challenge routes. When averaged across route, while TNFsr or fluid alone decreased the hazard ratio of death significantly [ln ± standard error (SE): -0.65 ± 0.30 and -0.62 ± 0.30, respectively, p ≤ 0.05], together they did not (p = 0.16). Furthermore, the observed effect of TNFsr and fluid together on reducing the hazard ratio was significantly less than estimated (-0.37 ± 0.29 versus -1.27 ± 0.43, respectively, p = 0.027) based on TNFsr and fluid alone. While each treatment increased central venous pressure at 6 and 24 h, the observed effects of the combination were also less than estimated ones (p ≤ 0.0005).The individual survival benefits of TNFsr and fluids were not additive in this rat sepsis model. Investigating new sepsis therapies together with conventional ones during preclinical testing may be informative.

In this paper, decoding of LDPC convolutional codes with rational parity-check matrices (LDPC-CC-RPCM) is investigated. We show that Tanner graph of every LDPC-CC-RPCM can always be transformed into an equivalent one with enlarged girth and finite memory order suitable for practical pipeline decoder. Based on the transformed graph, a dynamic scheduling-aided decoding scheme with the enhancement of signal perturbation and error cancellation is presented to improve the convergence speed and bit-error-rate performance in both of the waterfall and error-floor regions. Simulation results also reveal that LDPC-CC-RPCM may outperform ordinary LDPC-CC with polynomial parity-check matrices in some cases under the same code rate and decoding complexity.

Previous studies on low-density parity-check convolutional codes (LDPC-CC) reveal that LDPC-CC with rational parity-check matrices (RPCM) suffer from the unaffordable decoding latency/complexity due to the infinite memory order and the poor bit-error-rate performance due to the existence of length-4 cycles in the Tanner graph. However, in this paper, we show that every LDPC-CC with RPCM can be associated with an equivalent Tanner graph which can avoid the infinite memory order and undesired short length cycles but still implements the same constraints specified by the RPCM. Together with the iterative decoding based on belief propagation with proper scheduling, simulation results indicate that LDPC-CC with RPCM can also provide satisfactory decoding performance.

In this paper, convolutional encoders are studied for unequal error protection (UEP) from an algebraic theoretical viewpoint. Given any convolutional code, UEP-optimal encoders with the smallest McMillan degree are constructed to minimize the coding complexity. The noncatastrophic property of encoder is also maintained to avoid the undesired catastrophic propagation of decoding errors.

The present paper reports theoretical and experimental research on the tunable output characteristics of periodically polarized lithium niobate. We made six equal distance crystal grating sections, with each distance being 0.5 mm and the polarization period range of 29.0-31.5 mm. Especially, at room temperature, the signal-wavelength tunable output in the range of 1 449.7-1 665.0 nm and idle-wavelength tunable output in the range of 3 989.2-2 946.0 nm were achieved by LD end-pumped Nd : YVO4 laser with Q-switch in sound-wave. The lowest excitation threshold was 108.0 mW, while the highest excitation threshold was 149.2 mW. When the pump power was 649 mW, the highest gained signal-wave output was 118.5 mW and its conversion efficiency was 18.26%. Meanwhile, the idle-wave output was 46.6 mW and its conversion efficiency was 7.18%. These parameters approached the practicality level.

In this paper, space-time coding schemes with full transmit diversity are investigated for unequal error protection (UEP). Effective performance indicies are proposed to measure the intrinsic UEP capability of space-time codes, based on which we demonstrate that space-time trellis codes and superorthogonal space-time trellis codes can be used for UEP as long as the corresponding encoders are properly designed. In addition, UEP convolutional codes are concatenated with space-time block codes to construct another full-diversity UEP scheme which can provide more choices of UEP levels. Finally, good UEP codes are given by a computer search.

Background The presence of the tetraspanins CD9, CD63, CD81 and CD82 at HIV-1 budding sites, at the virological synapse (VS), and their enrichment in HIV-1 virions has been well-documented, but it remained unclear if these proteins play a role in the late phase of the viral replication cycle. Here we used overexpression and knockdown approaches to address this question. Results Neither ablation of CD9, CD63 and/or CD81, nor overexpression of these tetraspanins was found to affect the efficiency of virus release. However, confirming recently reported data, tetraspanin overexpression in virus-producing cells resulted in the release of virions with substantially reduced infectivity. We also investigated the roles of these tetraspanins in cell-to-cell transmission of HIV-1. Overexpression of CD9 and CD63 led to reduced cell-to-cell transmission of this virus. Interestingly, in knockdown experiments we found that ablation of CD63, CD9 and/or CD81 had no effect on cell-free infectivity. However, knockdown of CD81, but not CD9 and CD63, enhanced productive particle transmission to target cells, suggesting additional roles for tetraspanins in the transmission process. Finally, tetraspanins were found to be downregulated in HIV-1-infected T lymphocytes, suggesting that HIV-1 modulates the levels of these proteins in order to maximize the efficiency of its transmission within the host. Conclusion Altogether, these results establish an active role of tetraspanins in HIV-1 producer cells.

In vitro propagation studies have established that human immunodeficiency virus type 1 (HIV-1) is most efficiently transmitted at the virological synapse that forms between producer and target cells. Despite the presence of the viral envelope glycoprotein (Env) and CD4 and chemokine receptors at the respective surfaces, producer and target cells usually do not fuse with each other but disengage after the viral particles have been delivered, consistent with the idea that syncytia, at least in vitro, are not required for HIV-1 spread. Here, we tested whether tetraspanins, which are well known regulators of cellular membrane fusion processes that are enriched at HIV-1 exit sites, regulate syncytium formation. We found that overexpression of tetraspanins in producer cells leads to reduced syncytium formation, while downregulation has the opposite effect. Further, we document that repression of Env-induced cell-cell fusion by tetraspanins depends on the presence of viral Gag, and we demonstrate that fusion repression requires the recruitment of Env by Gag to tetraspanin-enriched microdomains (TEMs). However, sensitivity to fusion repression by tetraspanins varied for different viral strains, despite comparable recruitment of their Envs to TEMs. Overall, these data establish tetraspanins as negative regulators of HIV-1-induced cell-cell fusion, and they start delineating the requirements for this regulation.

The effects of fractions partitioned from the ethanol extract of Acorus calamus L. (AC) on adipocyte differentiation were investigated using cultured mouse 3T3-L1 preadipocytes. The degree of differentiation was evaluated by measuring the cellular triglycerides and protein expression of the glucose transporter GLUT4 in 3T3-L1 cells. The ethyl acetate fraction of the AC extract (ACE) was found to enhance adipocyte differentiation as did rosiglitazone. The results of further fractionation of ACE indicated that the active fraction does not consist of beta-asarone, which is a toxic component of this plant. This finding suggests that ACE has potential insulin-sensitizing activity like rosiglitazone, and may improve type 2 diabetes.

To isolate and determine the chemical constituents from Ranunculus japonicus.Compounds were isolated by column chromatography, and identified by MS, NMR data.Nine compounds were obtained andelucidated as scoparone (1), tricin (2), protocatechuic acid (3), luteolin (4), anemonin (5), scopoletin (6), 5-hydroxy-6, 7-dimethoxyflavone (7), 5-hydroxy-7, 8-dimethoxyflavone (8), ternatolide (9), respectively.Compounds 1-9 were isolated from R. japonicus for the first time while compounds 7, 8 were separated from Ranunculus genus first time.

Obstructive sleep apnea (OSA) is associated with impaired quality of life (HRQL) or health status. Treatment with continuous positive airway pressure (CPAP) has variable impacts on HRQL, which may be influenced by the patient's tolerance of therapy. We aimed to determine the impact of nocturnal

The purpose of our study was to identify a gene expression signature that specifically reflects the tumor suppressive effects of transforming growth factor-β (TGF-β), for use as a negative selective biomarker in clinical trials using TGF-β antagonists. TGF-β effects are highly contextual, and the dogma is that tumor suppressive effects are active in the early stages of carcinogenesis, but that pro-progression effects come to dominate later on. Since TGF-β antagonists are in early phase clinical trials in cancer, it is important to know whether the tumor suppressive effects of TGF-β are still intact in any tumors at the time of diagnosis and treatment, as this would be a contraindication for anti-TGF-β therapy. Existing TGF-β-related gene expression signatures were not designed a priori to discriminate the tumor suppressive from the tumor promoting activities. To address this question, we applied integrated ChIP-chip and transcriptomic approaches in the MCF10A-based model of breast cancer progression. We have previously shown that TGF-β has tumor suppressor activity in the less malignant cell lines of the series (MCF10AT1k, MCF10Ca1h), but that this effect is lost in the most malignant cell line (MCF10Ca1a). Here we showed that the tumor suppressor activity in this model system is specifically dependent on the downstream signaling component Smad3 and not Smad2. Using promoter-wide ChIP-chip, we found that the genomic landscape of TGF-β induced Smad3 binding differed dramatically between the four cell lines, despite their close genetic relatedness and similar Smad3 levels and activation profiles. Interestingly, TGF-β induced Smad3 binding only at loci that were already transcriptionally active, suggesting that TGF-βs may primarily play a modulator rather than an instigator role in regulating transcription. This feature probably contributes importantly to the known contextuality of TGF-β activity. By focusing on the two malignant cell lines (MCF10CA1h and MCF10CA1a), we identified a core signature of 26 TGF-β/Smad3 regulated genes that was specifically associated with the tumor suppressor activity of TGF-β. Unexpectedly, the direction of regulation of 25% of these genes by TGF-β differed in vitro and in vivo, highlighting a further novel contribution to TGF-β contextuality. The in vivo weighted form of the TGF-β/Smad3 tumor suppressor signature (TSTSS) was associated with good outcome specifically in estrogen-receptor positive (ER+) breast cancer patients, suggesting that TGF-β tumor suppressive pathways are still active and influencing disease outcome in a subset of patients at the time of surgery. TGF-β is a potent growth inhibitor for most epithelial cells and the TSTSS was weakly inversely correlated with proliferation in ER+ breast cancer, but the signature prognosticated independently of proliferation in multivariate analysis. Instead, the TSTSS was enriched for genes involved in cellular differentiation and movement, and ephrin was the top enriched signaling pathway. Ephrin knockdown in MCF10Ca1h cells led to increased migration, reduced apoptosis and differentiation and enhanced tumorigenesis. Our demonstration that a subset of breast cancer patients still has an active TGF-β tumor suppressor pathway at the time of surgery has important implications for patient stratification in ongoing clinical trials with TGF-β antagonists. Citation Format: Misako Sato, Mitsutaka Kadota, Binwu Tang, Yu-an Yang, Mengge Shan, Jia Weng, Michael Welsh, Yoshiko Nagano, Aleksandra Michalowski, Howard Yang, Robert Clifford, Maxwell Lee, Lalage Wakefield. Dissecting out the tumor suppressor aspect of TGF-β in breast cancer using integrated genomics. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr B029.

TGF-βs are pleiotropic growth factors with complex roles in tumorigenesis. Overexpression of TGF-β1 in many advanced human tumors correlates with metastasis and poor prognosis, and TGF-β antagonists are being developed for cancer therapy. Using a panel of syngeneic mouse transplant models of metastatic breast cancer, we found that an anti-TGF-β neutralizing antibody suppresses metastasis in several models, including the widely-used 4T1 model. However, as expected from the complexity of TGF-β action, responses were heterogeneous and anti-TGF-β antibody treatment had no effect or even stimulated metastasis in other models. This panel of models provides a powerful platform to identify candidate biomarkers for their ability predict therapeutic response to TGF-β antibodies. Previously we have shown that therapeutic outcome does not correlate with the expression of TGF-β ligands, the growth inhibitory response of the tumor model to TGF-β in vitro, the level of Six-1 expression, or the activation of non-canonical TGF-β signaling through formation of mixed Smad complexes. We next performed extensive histopathologic and immunohistochemical characterization of the tumor models to look for features that might correlate with therapeutic response. We found no obvious correlations between therapeutic response and a variety of markers, including estrogen receptor status, cytokeratin expression profile (luminal vs basal differentiation), p63 expression (basal marker), p53 expression or mutation status, smooth muscle actin expression or desmoplasia. There was also no correlation of response with tumor cell proliferation as assessed by quantitation of mitotic figures and Ki67, tumor cell apoptosis, extent of necrosis or histomorphology of the tumor cells (spindled vs polygonal). We then focused on mechanistic analysis of the undesirable stimulatory effect of anti-TGF-β antibodies in the Mvt-1 model in an attempt to generate new leads for biomarker analysis. We showed that the stimulatory effect of anti-TGF-β antibody treatment in the Mvt-1 model is still seen in SCID mice, suggesting that it does not involve T-cell mediated immune responses. Comparison of treated and untreated Mvt-1 tumors showed no effect of anti-TGF-β antibodies on tumor cell apoptosis, or infiltration by F480+ or CD11b+ immune cells. Tumor cell proliferation was actually decreased by the antibody treatment. In vitro assays showed that TGF-β had similar stimulatory effects on migration and invasion in both the 4T1 and Mvt-1 models, suggesting that the stimulatory effect of antibody therapy in the Mvt-1 model could not be explained by an anomalous invasion response to TGF-β. Thus the mechanism by which anti-TGF-β antibodies can stimulate metastasis in this model are unclear. Transcriptomic analyses of treated and untreated tumors are ongoing and results will be presented. Citation Format: Yu-an Yang, Jia Weng, Michael Welsh, Nancy Guan, Josh Webster, Kathy Flanders, Scott M. Lonning, John McPherson, Lalage M. Wakefield. Heterogeneity of response to anti-TGF-β antibody therapy in preclinical models. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5484. doi:10.1158/1538-7445.AM2013-5484

Transforming growth factor-βs (TGF-βs) have complex roles in tumorigenesis, with context-dependent effects that can either suppress or promote tumor progression. The dogma is that tumor suppressive effects are active in the early stages of carcinogenesis, but that later pro-progression effects come to dominate. Since TGF-β antagonists of various types are in early phase clinical trials in cancer, it is important to know whether the tumor suppressive effects of TGF-β are still intact in any tumors at the time of diagnosis and treatment. Existing TGF-β-related gene expression signatures were not designed a priori to discriminate the tumor suppressive from the tumor promoting activities. To address this question, we applied integrated ChIP-chip and transcriptomic approaches in the MCF10A-based model of breast cancer progression. We have previously shown that TGF-β has tumor suppressor activity in the less malignant cell lines of the series (MCF10A, MCF10AT1k, MCF10Ca1h), but that this effect is lost in the most malignant cell line (MCF10Ca1a). The tumor suppressor activity is dependent on the downstream signaling component Smad3. Using promoter-wide ChIP-chip, we found that the genomic landscape of TGF-β induced Smad3 binding differed dramatically between the four cell lines, despite their close genetic relatedness. Interestingly, TGF-β induced Smad3 binding only at genetic loci that were already transcriptionally active, suggesting that TGF-βs may primarily play a modulator rather than an instigator role in regulating transcription. This feature probably contributes significantly to the known contextuality of TGF-β activity. By focusing on the two malignant cell lines (MCF10CA1h and MCF10CA1a), we identified a core signature of 26 TGF-β/Smad3 regulated genes that were specifically associated with the tumor suppressor activity of TGF-β. Unexpectedly, the direction of regulation of 25% of these genes by TGF-β differed in vitro and in vivo, highlighting a further novel contribution to TGF-β contextuality, and emphasizing the importance of including in vivo data in this type of analysis. The in vivo weighted form of the TGF-β/Smad3 tumor suppressor signature was associated with good outcome in estrogen-receptor positive breast cancer patients, suggesting that TGF-β tumor suppressive pathways are still active and influencing disease outcome in a subset of patients’ tumors at the time of surgery. TGF-β is a potent growth inhibitor for most epithelial cells, but anti-proliferative effects made only a minor contribution to the tumor suppressor activity in the breast cancer cohorts. Instead, novel tumor suppressor effects of TGF-β captured by this approach included the restoration of tumor suppressive EphrinA signaling, leading to increased tumor cell differentiation. The results have important implications for patient stratification in ongoing clinical trials with TGF-β antagonists. Citation Format: Misako Sato, Mitsutaka Kadota, Binwu Tang, Yu-an Yang, Mengge Shan, Jia Weng, Michael Welsh, Aleksandra Michalowski, Howard Yang, Robert Clifford, Maxwell Lee, Lalage M. Wakefield. An integrated genomic approach specifically dissects out the tumor suppressor aspect of TGF-β in breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4310. doi:10.1158/1538-7445.AM2013-4310

TGF-betas are pleiotropic growth factors with complex roles in tumorigenesis. The TGF-betas have many activities that could promote metastasis, including the enhancement of invasion and migration, the promotion of angiogenesis, and the suppression of immune surveillance. Overexpression of TGF-beta in many advanced human tumors correlates with metastasis and poor prognosis, and there is now considerable interest in developing TGF-beta antagonists for cancer therapy. Indeed, a Phase I oncology trial using a fully humanized anti-TGF-beta monoclonal antibody was recently successfully completed. There is now an urgent need for good predictive biomarkers for patient stratification in future clinical trials. Using different syngeneic mouse transplant models of metastatic breast cancer, we have found that anti-TGF-beta antibodies suppress metastasis in several models, including the widely-used 4T1 model. However, TGF-beta antibody treatment has no effect or even stimulates metastasis in other models. This panel of mouse models with differing responses to anti-TGF-beta therapy represents a powerful experimental platform for the identification of predictive biomarkers. Based on existing knowledge, we have assessed a number of plausible candidates. Global gene expression analyses have defined several distinct molecular subtypes of breast cancer with different clinical characteristics. The “Claudin-low” subtype is a particularly poor prognosis subset of the triple negative ER-PR-HER2- breast cancers. By definition these tumors have low claudin and E-cadherin expression and a mesenchymal phenotype. Since TGF-betas are strong inducers of the mesenchymal phenotype, the claudin-low subtype may represent a particularly good target for anti-TGF-beta therapy. Similarly, overexpression of the homeobox protein Six-1 has recently been shown to cause TGF-beta to switch from tumor suppressor to pro-metastatic factor in breast cancer and might also be a predictor of a positive therapeutic response to TGF-beta antagonism. Here we have assessed the claudin-low status of a number of mouse mammary tumor models, by RTQ-PCR for key markers, using cells cultured in vitro. In addition, we determined nuclear Six1 levels by Western blot. Neither claudin-low status nor Six1 expression were predictive of response to anti-TGF-beta therapy. We are assessing additional candidate biomarkers and moving forward with discovery approaches. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1090. doi:10.1158/1538-7445.AM2011-1090