Targeted transcriptional downregulation of MYC using epigenomic controllers demonstrates antitumor activity in hepatocellular carcinoma models.

Dysregulation of master regulator c-MYC (MYC) plays a central role in hepatocellular carcinoma (HCC) and other cancers but remains an elusive target for therapeutic intervention. MYC expression is epigenetically modulated within naturally occurring DNA loop structures, Insulated Genomic Domains (IGDs). We present a therapeutic approach using an epigenomic controller (EC), a programmable epigenomic mRNA medicine, to precisely modify MYC IGD sub-elements, leading to methylation of MYC regulatory elements and durable downregulation of MYC mRNA transcription.

A Financial Incentives Program to Promote Smoking Cessation Among Recently Hospitalized Individuals: Feasibility and Acceptability Study.

Background: Hospitalization is an opportunity to engage underserved individuals in tobacco treatment who may not otherwise have access to it. Tobacco treatment interventions that begin during hospitalization and continue for at least 1 postdischarge month are effective in promoting smoking cessation. However, there is low usage of postdischarge tobacco treatment services.

Drugging the epigenome in the age of precision medicine.

Background: Modulating the epigenome has long been considered a potential opportunity for therapeutic intervention in numerous disease areas with several approved therapies marketed, primarily for cancer. Despite the overall promise of early approaches, however, these drugs have been plagued by poor pharmacokinetic and safety/tolerability profiles due in large part to off-target effects and a lack of specificity.

Results: Recently, there has been marked progress in the field on a new generation of epigenomic therapies which address these challenges directly by targeting defined loci with highly precise, durable, and tunable approaches.

A mixed methods study to inform and evaluate a longitudinal nurse practitioner/community health worker intervention to address social determinants of health and chronic obstructive pulmonary disease self-management.

Background: Individuals with low socioeconomic status experience higher prevalence and worse outcomes of chronic obstructive pulmonary disease (COPD). We undertook a quality improvement initiative at our safety net hospital in which a nurse practitioner (NP)/community health worker (CHW) team followed patients with COPD, frequent admissions, and unmet SDOH needs from hospitalization through one month post-discharge. We report our mixed methods approach to inform development and preliminary evaluation of this intervention.

Rapid Cycle Evaluation and Adaptation of an Inpatient Tobacco Treatment Service at a U.S. Safety-Net Hospital.

Background: To address disparities in smoking rates, our safety-net hospital implemented an inpatient tobacco treatment intervention: an "opt-out" electronic health record (EHR)-based Best Practice Alert + order-set, which triggers consultation to a Tobacco Treatment Consult (TTC) service for all hospitalized patients who smoke cigarettes. We report on development, implementation, and adaptation of the intervention, informed by a pre-implementation needs assessment and two rapid-cycle evaluations guided by the Consolidated Framework for Implementation Research (CFIR) and Expert Recommendations for Implementing Change (ERIC) compilation.

Methods: We identified stakeholders affected by implementation and conducted a local needs assessment starting 6 months-pre-launch.

Effectiveness of an Opt-Out Electronic Heath Record-Based Tobacco Treatment Consult Service at an Urban Safety Net Hospital.

Background: To address the burden of tobacco use in underserved populations, our safety net hospital developed a tobacco treatment intervention consisting of an "opt-out" electronic health record-based best practice alert + order set, which triggers consultation to an inpatient tobacco treatment consult (TTC) service for all hospitalized smokers.

Research Question: We sought to understand if the intervention would increase patient-level outcomes (receipt of tobacco treatment during hospitalization and at discharge; 6-month smoking abstinence) and improve hospital-wide performance on tobacco treatment metrics.

Design And Methods: We conducted two retrospective quasi-experimental analyses to examine effectiveness of the TTC service.

Feasibility, Acceptability, and Adoption of an Inpatient Tobacco Treatment Service at a Safety-Net Hospital: A Mixed-Methods Study.

Hospitalization is an opportunity to engage smokers who may not seek tobacco treatment. Our safety-net hospital developed and implemented an inpatient intervention consisting of an "opt-out" electronic health record-based Best Practice Alert (BPA)+order-set, designed to trigger referral to the Tobacco Treatment Consult (TTC) service (a team staffed by tobacco treatment specialists) for all hospitalized smokers, regardless of motivation to quit. We performed a sequential explanatory mixed-methods study to evaluate the feasibility, acceptability, and adoption of the TTC service.

A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface.

HLA-G, a nonclassical HLA molecule uniquely expressed in the placenta, is a central component of fetus-induced immune tolerance during pregnancy. The tissue-specific expression of HLA-G, however, remains poorly understood. Here, systematic interrogation of the HLA-G locus using massively parallel reporter assay (MPRA) uncovered a previously unidentified cis-regulatory element 12 kb upstream of HLA-G with enhancer activity, Enhancer L Strikingly, clustered regularly-interspaced short palindromic repeats (CRISPR)/Cas9-mediated deletion of this enhancer resulted in ablation of HLA-G expression in JEG3 cells and in primary human trophoblasts isolated from placenta.

Experimental and mathematical analysis of in vitro Pitavastatin hepatic uptake across species.

1. To investigate the non-linear kinetics of in vitro hepatocyte uptake across species, the OATP substrate Pitavastatin was used as a probe. 2.

Simultaneous alignment and folding of protein sequences.

Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We present partiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm's complexity is polynomial in time and space. Algorithmically, partiFold-Align exploits sparsity in the set of super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time for simultaneous pairwise alignment and folding.

MARIS: method for analyzing RNA following intracellular sorting.

Transcriptional profiling is a key technique in the study of cell biology that is limited by the availability of reagents to uniquely identify specific cell types and isolate high quality RNA from them. We report a Method for Analyzing RNA following Intracellular Sorting (MARIS) that generates high quality RNA for transcriptome profiling following cellular fixation, intracellular immunofluorescent staining and FACS. MARIS can therefore be used to isolate high quality RNA from many otherwise inaccessible cell types simply based on immunofluorescent tagging of unique intracellular proteins.

Differentiated human stem cells resemble fetal, not adult, β cells.

Human pluripotent stem cells (hPSCs) have the potential to generate any human cell type, and one widely recognized goal is to make pancreatic β cells. To this end, comparisons between differentiated cell types produced in vitro and their in vivo counterparts are essential to validate hPSC-derived cells. Genome-wide transcriptional analysis of sorted insulin-expressing (INS(+)) cells derived from three independent hPSC lines, human fetal pancreata, and adult human islets points to two major conclusions: (i) Different hPSC lines produce highly similar INS(+) cells and (ii) hPSC-derived INS(+) (hPSC-INS(+)) cells more closely resemble human fetal β cells than adult β cells.

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape.

We describe protein interaction quantitation (PIQ), a computational method for modeling the magnitude and shape of genome-wide DNase I hypersensitivity profiles to identify transcription factor (TF) binding sites. Through the use of machine-learning techniques, PIQ identified binding sites for >700 TFs from one DNase I hypersensitivity analysis followed by sequencing (DNase-seq) experiment with accuracy comparable to that of chromatin immunoprecipitation followed by sequencing (ChIP-seq). We applied PIQ to analyze DNase-seq data from mouse embryonic stem cells differentiating into prepancreatic and intestinal endoderm.

Design and optimization of pyrazinecarboxamide-based inhibitors of diacylglycerol acyltransferase 1 (DGAT1) leading to a clinical candidate dimethylpyrazinecarboxamide phenylcyclohexylacetic acid (AZD7687).

A new series of pyrazinecarboxamide DGAT1 inhibitors was designed to address the need for a candidate drug with good potency, selectivity, and physical and DMPK properties combined with a low predicted dose in man. Rational design and optimization of this series led to the discovery of compound 30 (AZD7687), which met the project objectives for potency, selectivity, in particular over ACAT1, solubility, and preclinical PK profiles. This compound showed the anticipated excellent pharmacokinetic properties in human volunteers.

A global sampling approach to designing and reengineering RNA secondary structures.

The development of algorithms for designing artificial RNA sequences that fold into specific secondary structures has many potential biomedical and synthetic biology applications. To date, this problem remains computationally difficult, and current strategies to address it resort to heuristics and stochastic search techniques. The most popular methods consist of two steps: First a random seed sequence is generated; next, this seed is progressively modified (i.

STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions.

The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Previous work has demonstrated that probability-based prediction of discrete β-strand pairs can offer insight into these structures.

Discovery, optimisation and in vivo evaluation of novel GPR119 agonists.

GPR119 is increasingly seen as an attractive target for the treatment of type II diabetes and other elements of the metabolic syndrome. During a programme aimed at developing agonists of the GPR119 receptor, we identified compounds that were potent with reduced hERG liabilities, that had good pharmacokinetic properties and that displayed excellent glucose-lowering effects in vivo. However, further profiling in a GPR119 knock-out (KO) mouse model revealed that the biological effects were not exclusively due to GPR119 agonism, highlighting the value of transgenic animals in drug discovery programs.

Efficient traversal of beta-sheet protein folding pathways using ensemble models.

Molecular dynamics (MD) simulations can now predict ms-timescale folding processes of small proteins; however, this presently requires hundreds of thousands of CPU hours and is primarily applicable to short peptides with few long-range interactions. Larger and slower-folding proteins, such as many with extended β-sheet structure, would require orders of magnitude more time and computing resources. Furthermore, when the objective is to determine only which folding events are necessary and limiting, atomistic detail MD simulations can prove unnecessary.

Opposing effects of glutamine and asparagine govern prion formation by intrinsically disordered proteins.

Sequences rich in glutamine (Q) and asparagine (N) residues often fail to fold at the monomer level. This, coupled to their unusual hydrogen-bonding abilities, provides the driving force to switch between disordered monomers and amyloids. Such transitions govern processes as diverse as human protein-folding diseases, bacterial biofilm assembly, and the inheritance of yeast prions (protein-based genetic elements).

A method for probing the mutational landscape of amyloid structure.

Motivation: Proteins of all kinds can self-assemble into highly ordered β-sheet aggregates known as amyloid fibrils, important both biologically and clinically. However, the specific molecular structure of a fibril can vary dramatically depending on sequence and environmental conditions, and mutations can drastically alter amyloid function and pathogenicity. Experimental structure determination has proven extremely difficult with only a handful of NMR-based models proposed, suggesting a need for computational methods.

3-Chlorotyrosine in sputum of COPD patients: relationship with airway inflammation.

The airways of patients with chronic obstructive pulmonary disease (COPD) are associated with increased numbers of inflammatory cells, in particular neutrophils and macrophages. Contained within the primary granules of neutrophils is the heme enzyme called myeloperoxidase (MPO) that has been used as a biomarker of neutrophilic inflammation in COPD and other inflammatory diseases. MPO is the only enzyme in the body that produces hypochlorous acid (HOCl), which effectively chlorinates tyrosine residues in proteins.

Adherence to ventilator-associated pneumonia bundle and incidence of ventilator-associated pneumonia in the surgical intensive care unit.

Objective: To examine the impact of adherence to a ventilator-associated pneumonia (VAP) bundle on the incidence of VAP in our surgical intensive care units (SICUs).

Design: Prospectively collected data were retrospectively examined from our Infection Control Committee surveillance database of SICU patients over a 38-month period. Cost of VAP was estimated at $30,000 per patient stay.

The accuracy of the central venous blood gas for acid-base monitoring.

Background: Routine use of central venous blood gases (VBGs) may reduce complications from prolonged arterial cannulation. We investigated the reliability of the VBG as a substitute for arterial blood gas (ABG) in multiple care settings.

Methods: We developed a VBG adjustment rule of ABG pH = VBG pH + 0.

Modeling ensembles of transmembrane beta-barrel proteins.

Transmembrane beta-barrel (TMB) proteins are embedded in the outer membrane of gram-negative bacteria, mitochondria, and chloroplasts. Despite their importance, very few nonhomologous TMB structures have been determined by X-ray diffraction because of the experimental difficulty encountered in crystallizing transmembrane proteins. We introduce the program partiFold to investigate the folding landscape of TMBs.

Learning biophysically-motivated parameters for alpha helix prediction.

Background: Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using parameterizable cost functions representing biological "pseudo-energies". Machine learning methods are applied to estimate the values of the parameters to correctly predict known protein structures.