Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding.

A major challenge in obtaining a full molecular description of evolutionary adaptation is to characterize how transcription factor (TF) DNA-binding specificity can change. To identify mechanisms of TF diversification, we performed detailed comparisons of yeast C2H2 ZF proteins with identical canonical recognition residues that are expected to bind the same DNA sequences. Unexpectedly, we found that ZF proteins can adapt to recognize new binding sites in a modular fashion whereby binding to common core sites remains unaffected. We identified two distinct mechanisms, conserved across multiple Ascomycota species, by which this molecular adaptation occurred. Our results suggest a route for TF evolution that alleviates negative pleiotropic effects by modularly gaining new binding sites. These findings expand our current understanding of ZF DNA binding and provide evidence for paralogous ZFs utilizing alternate modes of DNA binding to recognize unique sets of noncanonical binding sites.

Underuse of statins for secondary prevention of atherosclerotic cardiovascular disease events among ambulatory surgical patients.

Although statins are highly effective for reducing cardiovascular disease events, prior studies demonstrate their significant underuse in the US population, including among those with known atherosclerotic disease. It is unknown whether this finding applies to the subset of patients who present for outpatient surgery, as such patients would be expected to have recent exposures to healthcare providers during the preoperative referral period. The primary aim of this manuscript was to ascertain the prevalence of statin underuse and associated risk-factors for such underuse among ambulatory surgical patients with documented atherosclerotic cardiovascular disease. This was a retrospective observational study of a random sample of 600 patients ages 40-75 years presenting for ambulatory surgery within a 6-month period in 2016, at one of three ambulatory surgical centers affiliated with a large, tertiary care hospital. Compilation and analysis of data occurred in 2018-2019. Of the 600 subjects, 117 (19.5%) had documented atherosclerotic cardiovascular disease. Within this high-risk group, only 71 (60.7%) carried a prescription for any statin, and only 30 (25.6%) were prescribed a recommended high intensity statin dose for secondary prevention. In a multivariable logistic regression analysis, older age, male sex, and treatment for hypertension were positively associated with statin use. In conclusion, statin underuse among ambulatory surgical patients is common and mirrors what has been observed in non-surgical populations. Future trials are needed to investigate the possible role of surgical teams to promote guideline-based statin therapy, including the role of preoperative screening interventions to impact long term cardiovascular morbidity and mortality.

Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients.

Sputum induction is a non-invasive method to evaluate the airway environment, particularly for asthma. RNA sequencing (RNA-seq) of sputum samples can be challenging to interpret due to the complex and heterogeneous mixtures of human cells and exogenous (microbial) material. In this study, we develop a pipeline that integrates dimensionality reduction and statistical modeling to grapple with the heterogeneity. LDA(Latent Dirichlet allocation)-link connects microbes to genes using reduced-dimensionality LDA topics. We validate our method with single-cell RNA-seq and microscopy and then apply it to the sputum of asthmatic patients to find known and novel relationships between microbes and genes.

Characterizing the DNA binding site specificity of NF-κB with protein-binding microarrays (PBMs).

NF-κB transcription factors control a wide array of important cellular and organismal processes in eukaryotes. All NF-κB transcription factors bind to DNA target sites as dimers. In vertebrates, there are five NF-κB subunits, p50, p52, RelA (p65), c-Rel, and RelB, that can form almost all combinations of homodimers and heterodimers, which recognize distinct, but overlapping, target sequences. In this chapter, we describe the use of protein-binding microarrays (PBMs), a high-throughput method to measure the binding of proteins to different DNA sequences. PBM datasets allow for sensitive comparisons of NF-κB dimer DNA-binding differences and can aid in the computational and experimental prediction of NF-κB target genes.