Meta-analysis of airway epithelium gene expression in asthma

Differential gene expression in the airway epithelium of patients with asthma versus controls has been reported in several studies. However, there is no consensus on which genes are reproducibly affected in asthma. We sought to identify a consensus list of differentially expressed genes (DEGs) using a meta-analysis approach. We identified eight studies with data that met defined inclusion criteria. These studies comprised 355 cases and 193 controls and involved sampling either bronchial or nasal epithelium. We conducted study-level analyses, followed by a meta-analysis. Likewise, we applied a meta-analysis framework to the results of study-level pathway enrichment. We identified 1273 DEGs, 431 of which had not been identified in previous studies. 450 DEGs exhibited large effect sizes and were robust to study population differences in age, sex, race/ethnicity, medication use, smoking status and exacerbations. The magnitude of differential expression of these 450 genes was highly similar in bronchial and nasal airway epithelia. Meta-analysis of pathway enrichment revealed a number of consistently dysregulated biological pathways, including putative transcriptional and post-transcriptional regulators. In total, we identified a set of genes that is consistently dysregulated in asthma, that links to known and novel biological pathways, and that will inform asthma subtype identification

Direct CP, T and/or CPT violations in the K^0-\bar{K^0} system - Implications of the recent KTeV results on 2π2\pi decays -

The recent results on the CP violating parameters Re(e'/e) and \Delta\phi = \phi_{00}-\phi_{+-} reported by the KTeV Collaboration are analyzed with a view to constrain CP, T and CPT violations in a decay process. Combining with some relevant data compiled by the Particle Data Group, we find Re(e_2-e_0) = (0.85 +- 3.11)*10^{-4} and Im(e_2-e_0) = (3.2 +- 0.7)*10^{-4}, where Re(e_I) and Im(e_I) represent respectively CP/CPT and CP/T violations in decay of K^0 and \bar{K^0} into a 2\pi state with isospin I.Comment: 7 pages, No figure

Coherent dynamics and decoherence in a superconducting weak link

We demonstrate coherent dynamics of quantized magnetic fluxes in a superconducting loop with a weak link - a nanobridge patterned from the same thin NbN film as the loop. The bridge is a short rounded shape constriction, close to 10 nm long and 20 - 30 nm wide, having minimal width at its center. Quantum state control and coherent oscillations in the driven time evolution of the tunnel-junctionless system are achieved. Decoherence and energy relaxation in the system are studied using a combination of microwave spectroscopy and direct time-domain techniques. The effective flux noise behavior suggests inductance fluctuations as a possible cause of the decoherence.Comment: 5 pages, 3 figure

Electromagnetically induced transparency on a single artificial atom

We present experimental observation of electromagnetically induced transparency (EIT) on a single macroscopic artificial “atom” (superconducting quantum system) coupled to open 1D space of a transmission line. Unlike in an optical media with many atoms, the single-atom EIT in 1D space is revealed in suppression of reflection of electromagnetic waves, rather than absorption. The observed almost 100% modulation of the reflection and transmission of propagating microwaves demonstrates full controllability of individual artificial atoms and a possibility to manipulate the atomic states. The system can be used as a switchable mirror of microwaves and opens a good perspective for its applications in photonic quantum information processing and other fields

Utility of TERT Promoter Mutations for Cutaneous Primary Melanoma Diagnosis

Telomerase reverse transcriptase (TERT) promoter mutations are commonly found in malignant melanomas but rare in melanocytic nevi. To assess its potential diagnostic utility for the distinction of melanoma from nevus, we determined the TERT promoter mutation status of 86 primary melanomas, 72 melanocytic nevi, and 40 diagnostically problematic melanocytic proliferations. Of the 86 melanomas, 67 (77.9%) were TERT-positive, defined as harboring a hotspot TERT promoter mutation at positions -124C>T, -124_125CC>TT, -138_139CC>TT, or -146C>T. Of the 72 nevi, only 1 (1.4%) was TERT-positive. Of the 40 diagnostically uncertain melanocytic proliferations, 2 (5.0%) were TERT-positive. TERT positivity as a test for melanoma versus nevus had an accuracy of 87.3% [95% confidence interval (CI), 81.1-92.1], a sensitivity of 77.9% (95% CI, 68.9-85.4), a specificity of 98.6% (95% CI, 95.8-100), a positive predictive value of 98.5% (95% CI, 95.6-100), and a negative predictive value of 78.9% (95% CI, 72.6-85.4). Our results indicate that hotspot TERT promoter mutation status may be a useful ancillary parameter for the diagnosis of melanoma. In particular, the high specificity of these mutations for melanoma indicates the presence of a TERT promoter mutation in a melanocytic neoplasm associated with diagnostic controversy, or uncertainty should increase concern for a melanoma

An integrated model for predicting KRAS dependency

The clinical approvals of KRAS G12C inhibitors have been a revolutionary advance in precision oncology, but response rates are often modest. To improve patient selection, we developed an integrated model to predict KRAS dependency. By integrating molecular profiles of a large panel of cell lines from the DEMETER2 dataset, we built a binary classifier to predict a tumor's KRAS dependency. Monte Carlo cross validation via ElasticNet within the training set was used to compare model performance and to tune parameters α and λ. The final model was then applied to the validation set. We validated the model with genetic depletion assays and an external dataset of lung cancer cells treated with a G12C inhibitor. We then applied the model to several Cancer Genome Atlas (TCGA) datasets. The final "K20" model contains 20 features, including expression of 19 genes and KRAS mutation status. In the validation cohort, K20 had an AUC of 0.94 and accurately predicted KRAS dependency in both mutant and KRAS wild-type cell lines following genetic depletion. It was also highly predictive across an external dataset of lung cancer lines treated with KRAS G12C inhibition. When applied to TCGA datasets, specific subpopulations such as the invasive subtype in colorectal cancer and copy number high pancreatic adenocarcinoma were predicted to have higher KRAS dependency. The K20 model has simple yet robust predictive capabilities that may provide a useful tool to select patients with KRAS mutant tumors that are most likely to respond to direct KRAS inhibitors

Histone deacetylase 11 inhibition promotes breast cancer metastasis from lymph nodes

Lymph node (LN) metastases correspond with a worse prognosis in nearly all cancers, yet the occurrence of cancer spreading from LNs remains controversial. Additionally, the mechanisms explaining how cancers survive and exit LNs are largely unknown. Here, we show that breast cancer patients frequently have LN metastases that closely resemble distant metastases. In addition, using a microsurgical model, we show how LN metastasis development and dissemination is regulated by the expression of a chromatin modifier, histone deacetylase 11 (HDAC11). Genetic and pharmacologic blockade of HDAC11 decreases LN tumor growth, yet substantially increases migration and distant metastasis formation. Collectively, we reveal a mechanism explaining how HDAC11 plasticity promotes breast cancer growth as well as dissemination from LNs and suggest caution with the use of HDAC inhibitors

Identification of a Robust Methylation Classifier for Cutaneous Melanoma Diagnosis

Early diagnosis improves melanoma survival, yet the histopathological diagnosis of cutaneous primary melanoma can be challenging, even for expert dermatopathologists. Analysis of epigenetic alterations, such as DNA methylation, that occur in melanoma can aid in its early diagnosis. Using a genome-wide methylation screening, we assessed CpG methylation in a diverse set of 89 primary invasive melanomas, 73 nevi, and 41 melanocytic proliferations of uncertain malignant potential, classified based on interobserver review by dermatopathologists. Melanomas and nevi were split into training and validation sets. Predictive modeling in the training set using ElasticNet identified a 40-CpG classifier distinguishing 60 melanomas from 48 nevi. High diagnostic accuracy (area under the receiver operator characteristic curve = 0.996, sensitivity = 96.6%, and specificity = 100.0%)was independently confirmed in the validation set (29 melanomas, 25 nevi)and other published sample sets. The 40-CpG melanoma classifier included homeobox transcription factors and genes with roles in stem cell pluripotency or the nervous system. Application of the 40-CpG melanoma classifier to the diagnostically uncertain samples assigned melanoma or nevus status, potentially offering a diagnostic tool to assist dermatopathologists. In summary, the robust, accurate 40-CpG melanoma classifier offers a promising assay for improving primary melanoma diagnosis

Resonance fluorescence of a single artificial atom

An atom in open space can be detected by means of resonant absorption and reemission of electromagnetic waves, known as resonance fluorescence, which is a fundamental phenomenon of quantum optics. We report on the observation of scattering of propagating waves by a single artificial atom. The behavior of the artificial atom, a superconducting macroscopic two-level system, is in a quantitative agreement with the predictions of quantum optics for a pointlike scatterer interacting with the electromagnetic field in one-dimensional open space. The strong atom-field interaction as revealed in a high degree of extinction of propagating waves will allow applications of controllable artificial atoms in quantum optics and photonics