An immunogenetic basis for lung cancer risk.

Cancer risk is influenced by inherited mutations, DNA replication errors, and environmental factors. However, the influence of genetic variation in immunosurveillance on cancer risk is not well understood. Leveraging population-level data from the UK Biobank and FinnGen, we show that heterozygosity at the -II loci is associated with reduced lung cancer risk in smokers.

Pan-cancer proteogenomics characterization of tumor immunity.

Despite the successes of immunotherapy in cancer treatment over recent decades, less than <10%-20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten different cancers using CPTAC pan-cancer proteogenomic data.

Sustained CD28 costimulation is required for self-renewal and differentiation of TCF-1 PD-1 CD8 T cells.

During persistent antigen stimulation, such as in chronic infections and cancer, CD8 T cells differentiate into a hypofunctional programmed death protein 1-positive (PD-1) exhausted state. Exhausted CD8 T cell responses are maintained by precursors (Tpex) that express the transcription factor T cell factor 1 (TCF-1) and high levels of the costimulatory molecule CD28. Here, we demonstrate that sustained CD28 costimulation is required for maintenance of antiviral T cells during chronic infection.

A proteogenomic portrait of lung squamous cell carcinoma.

Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a deeper exposition of LSCC biology with potential therapeutic implications. We identify NSD3 as an alternative driver in FGFR1-amplified tumors and low-p63 tumors overexpressing the therapeutic target survivin.

Ancestral reconstruction reveals mechanisms of ERK regulatory evolution.

Protein kinases are crucial to coordinate cellular decisions and therefore their activities are strictly regulated. Previously we used ancestral reconstruction to determine how CMGC group kinase specificity evolved (Howard et al., 2014).

ImmuneRegulation: a web-based tool for identifying human immune regulatory elements.

Humans vary considerably both in their baseline and activated immune phenotypes. We developed a user-friendly open-access web portal, ImmuneRegulation, that enables users to interactively explore immune regulatory elements that drive cell-type or cohort-specific gene expression levels. ImmuneRegulation currently provides the largest centrally integrated resource on human transcriptome regulation across whole blood and blood cell types, including (i) ∼43,000 genotyped individuals with associated gene expression data from ∼51,000 experiments, yielding genetic variant-gene expression associations on ∼220 million eQTLs; (ii) 14 million transcription factor (TF)-binding region hits extracted from 1945 ChIP-seq studies; and (iii) the latest GWAS catalog with 67,230 published variant-trait associations.

A New Mixed All-Atom/Coarse-Grained Model: Application to Melittin Aggregation in Aqueous Solution.

We introduce a new mixed resolution, all-atom/coarse-grained approach (AACG), for modeling peptides in aqueous solution and apply it to characterizing the aggregation of melittin. All of the atoms in peptidic components are represented, while a single site is used for each water molecule. With the full flexibility of the peptide retained, our AACG method achieves speedups by a factor of 3-4 for CPU time reduction and another factor of roughly 7 for diffusion.

Applications of a general random-walk theory for confined diffusion.

A general random walk theory for diffusion in the presence of nanoscale confinement is developed and applied. The random-walk theory contains two parameters describing confinement: a cage size and a cage-to-cage hopping probability. The theory captures the correct nonlinear dependence of the mean square displacement (MSD) on observation time for intermediate times.

Toward a predictive understanding of water and charge transport in proton exchange membranes.

An analytical model for water and charge transport in highly acidic and highly confined systems such as proton exchange membranes of fuel cells is developed and compared to available experimental data. The model is based on observations from both experiment and multiscale simulation. The model accounts for three factors in the system including acidity, confinement, and connectivity.

A reactive molecular dynamics study of the thermal decomposition of perfluorodimethyl ether.

Classical reactive molecular dynamics (RMD) simulation is used to model the thermal decomposition of perfluorodimethyl ether (CF(3)OCF(3)), which is relevant as a simple molecule containing the necessary architectural elements to study the chemical stability of perfluoropolyether lubricants. The RMD algorithm employs nonreactive interaction potentials for the reactants and products. The reactivity is implemented through a coarse-grained simulation algorithm, incorporating elements from both the quantum and macroscopic descriptions of the reaction.

Comparison of the hydration and diffusion of protons in perfluorosulfonic acid membranes with molecular dynamics simulations. scui@utk.edu.

Classical molecular dynamics (MD) simulations were performed to determine the hydrated morphology and hydronium ion diffusion coefficients in two different perfluorosulfonic acid (PFSA) membranes as functions of water content. The structural and transport properties of 1143 equivalent weight (EW) Nafion, with its relatively long perfluoroether side chains, are compared to the short-side-chain (SSC) PFSA ionomer at an EW of 977. The separation of the side chains was kept uniform in both ionomers consisting of -(CF 2) 15- units in the backbone, and the degree of hydration was varied from 5 to 20 weight % water.

A molecular dynamics study of a nafion polyelectrolyte membrane and the aqueous phase structure for proton transport.

A molecular dynamics simulation study of hydrated Nafion at water contents ranging from 5 to 20 wt % was performed to examine the structure and dynamics of the hydrated polyelectrolyte system. The simulations show that the system forms segregated hydrophobic regions consisting primarily of the polymer backbone and hydrophilic regions with an inhomogeneous water distribution. We find that the water clustering strongly depends on the water content.