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Introduction The burden of asthma morbidity with co-existing atopy among the racial/ethnic minorities in the socio-economically disadvantaged NYC borough of the Bronx is unusually high. The multidisciplinary Montefiore Asthma Center (MAC) provides guideline-based treatment to this high-risk population through the joint efforts of Allergists/Immunologists, Pulmonologists, and on-site health educators. Methods The objective of this prospective, observational study was to define the demographic and clinical characteristics of severe asthma, evaluate improvement in asthma severity and lung function through the course of treatment at the MAC, and describe the asthma phenotypes of the patients managed at the MAC. Adults with severe asthma receiving treatment at the MAC were followed from their first to their last visit at the MAC. Patient demographics, along with asthma severity and co-existing allergies, were assessed. Possible phenotypes were defined (based on presence or absence of atopy, age at asthma onset, and blood eosinophil counts). Results 227 patients were included in the final analysis, of which 55.5% were Hispanic and 33.9% identified as non-Hispanic Black. Ninety-one percent (91%) of our cohort was found to be atopic and allergic rhinoconjunctivitis (ARC) was the most commonly identified co-existing allergic condition (86.3%). Mean Asthma Control Test (ACT) scores improved from 11.1 (± 4.9) at the initial visit to 14.8 (± 6.1) at the last visit. The spirometric values did not improve despite treatment at MAC. Conclusion A multidisciplinary severe asthma center is an ideal setting to phenotype patients and offer personalized guideline-based management and education to adults with severe asthma.

Methods to experimentally alter and functionally evaluate cytosine methylation in a site-specific manner have proven elusive. We describe a site-specific DNA methylation method, using synthetically methylated primers and high fidelity PCR coupled with ligation of reporter constructs. We applied this method to introduce methylated cytosines into fragments of the respective DAPK and RASSF1A promoters that had been cloned into luciferase reporters. We found that methylation of 3-7 residue CpG clusters that were 5' adjacent to the transcription start site (TSS) of the DAPK gene produced up to a 54% decrease in promoter activity (p0.01). Similarly, for RASSF1A promoter reporter constructs, the methylation of either of two clusters of four CpGs each, but not an intervening cluster, produced a 63% decrease in promoter activity (p0.01), suggesting that precise mCpG position is crucial, and factors other than simple proximity to the TSS are at play. Chromatin immunoprecipitation analysis of these reporter constructs demonstrated that transcription factor Oct-1 and Sp1 preferentially bound the unmethylated vs. methylated DAPK or RASSF1A promoter reporter constructs at the functional CpG sites. Histone H1, hnRNP1, and MeCP2 showed preferential binding to methylated sequence at functional sites in these reporter constructs, as well as highly preferential (8-80-fold) binding to native methylated vs. unmethylated chromatin. These results suggest that: (1) site-specific, precision DNA methylation of a reporter construct can be used for functional analysis of commonly observed gene promoter methylation patterns; (2) the reporter system contains key elements of the endogenous chromatin machinery.

The number of predicted human microRNAs in Sanger miRBase currently stands at over a thousand, with each of these in turn predicted to target numerous mRNAs. However, those microRNAs for which mRNA targets have been evaluated, verified and reported in the literature are still in the minority and the bulk of microRNA/mRNA interactions are yet to be confirmed. Confirmation of microRNA interaction with predicted mRNA targets represents a considerable undertaking, made more complex by potential synergistic effects of multiple microRNAs and the three possible outcomes (translational repression, degradation or a mixture of both). In addition, contrasting results obtained when either stably expressing or transiently transfecting members of the miR-200 family illustrate limitations in the verification methods currently in use. In this article we suggest that instead of allowing computational predictions to drive investigation, it would be desirable, when possible, to systematically evaluate microRNA targets using inducible, stable, ectopic expression. The advantage of stable lines ectopically expressing microRNA(s) is that they allow an analysis of changes to both the proteome and the transcriptome. This would allow verification of targets, improve the design of prediction algorithms and greatly increase our understanding of the outcome of microRNA/mRNA interaction.

One in ten tobacco smokers develops bronchogenic carcinoma over a lifetime. The study of susceptibility of an individual and a population to lung cancer traditionally has been limited to the study of tobacco smoke dose and family history of cancer. New insights into lung carcinogenesis have made the study of molecular markers of risk possible in human populations in the emerging field of molecular epidemiology. This review summarizes data addressing the relationships of human lung cancer to polymorphisms of phase I procarcinogen-activating and phase II-deactivating enzymes and intermediate biomarkers of DNA mutation, such as DNA adducts, oncogene and tumor suppressor gene mutation, and polymorphisms. These parameters are reviewed as they relate to tobacco smoke exposure, procarcinogen metabolizing polymorphisms, and the presence of lung cancer. Problem areas in biomarker validation, such as cross-sectional data interpretation, tissue source, race, statistical power, and ethical implications are ad...