New insights into the hypothalamic-pituitary-thyroid axis: a transcriptome and proteome-wide association study.

Introduction Thyroid hormones have systemic effects on the human body and play a key role in the development and function of virtually all tissues. They are regulated via the hypothalamic-pituitary-thyroid (HPT) axis and have a heritable component. Using genetic information, we applied tissue-specific transcriptome-wide association studies (TWAS) and plasma proteome-wide association studies (PWAS) to elucidate gene products related to thyrotropin (TSH) and free thyroxine (FT4) levels. Results TWAS identified 297 and 113 transcripts associated with TSH and FT4 levels, respectively (25 shared), including transcripts not identified by genome-wide association studies (GWAS) of these traits, demonstrating the increased power of this approach. Testing for genetic colocalization revealed a shared genetic basis of 158 transcripts with TSH and 45 transcripts with FT4, including independent, FT4-associated genetic signals within the CAPZB locus that were differentially associated with CAPZB expression in different tissues. PWAS identified 18 and 10 proteins associated with TSH and FT4, respectively (HEXIM1 and QSOX2 with both). Among these, the cognate genes of 5 TSH- and 7 FT4-associated proteins mapped outside significant GWAS loci. Colocalization was observed for 5 plasma proteins each with TSH and FT4. There were 10 TSH and one FT4-related gene(s) significant in both TWAS and PWAS. Of these, ANXA5 expression and plasma annexin A5 levels were inversely associated with TSH (PWAS: p=1.18×10-13, TWAS: p=7.61×10-12 [whole blood], p=6.40×10-13 [hypothalamus], p=1.57×10-15 [pituitary], p=4.27×10-15 [thyroid]), supported by colocalizations. Conclusions Our analyses revealed new thyroid function-associated genes and prioritized candidates in known GWAS loci, contributing to a better understanding of transcriptional regulation and protein levels relevant to thyroid function.

Polyelectrolyte Brushes with Protein-Like Nanocolloids.

Electrostatic interaction of ampholytic nanocolloidal particles (NPs), which mimic globular proteins, with polyelectrolyte brushes is analyzed within mean-field Poisson-Boltzmann approximation. In accordance with experimental findings, the theory predicts that an electrostatic driving force for the particle uptake by the brush may emerge when the net charge of the particle in the buffer and the charge of the brush are of the same sign. The origin of this driving force is change in the ionization state of weak cationic and anionic groups on the NP surface provoked by interaction with the brush. In experimental systems, the ionic interactions are complemented by excluded-volume, hydrophobic, and other types of interactions that all together control NP uptake by or expulsion from the brush. Here, we focus on the NP-brush ionic interactions. It is demonstrated that deviation between the buffer pH and the NP isoelectric point, considered usually as the key control parameter, does not uniquely determine the insertion free energy patterns. The latter depends also on the proportion of cationic and anionic groups in the NPs and their specific ionization constants as well as on salt concentration in the buffer. The analysis of the free energy landscape proves that a local minimum in the free energy inside the brush appears, provided the NP charge reversal occurs upon insertion into the brush. This minimum corresponds either to a thermodynamically stable or to a metastable state, depending on the pH offset from the IEP and salt concentration, and is separated from the bulk of the solution by a free energy barrier. The latter, being fairly independent of salt concentration in height, may strongly impede the NP absorption kinetically even when it is thermodynamically favorable. Hence, change reversal is a necessary but insufficient condition for the uptake of the NPs by similarly charged polyelectrolyte brushes.

Surface-Immobilized Interpolyelectrolyte Complexes Formed by Polyelectrolyte Brushes.

A scaling theory of interaction and complex formation between planar polyelectrolyte (PE) brush and oppositely charged mobile linear PEs is developed. Counterion release is found to be the main driving force for the complexation. An interpolyelectrolyte coacervate complex (IPEC) between the brush and oppositely charged mobile PEs is formed at moderate grafting density and low salt concentration. At higher grafting density mobile chains penetrate the brush, but the brush structure is controlled by the balance between entropic elasticity and nonelectrostatic short-range interactions, as happens in a neutral brush. An increase in salt concentration beyond the theoretically predicted threshold leads to the release of the guest polyions from the brush. For brushes with moderate grafting density, complexation with oppositely charged guest polyions is predicted to trigger lateral microphase separation and formation of the finite-size surface IPEC clusters. Power law dependencies for the cluster dimensions on the brush grafting density, PE length, and salt concentration are provided.

Interaction of Polyanionic and Polycationic Brushes with Globular Proteins and Protein-like Nanocolloids.

A large number of experimental studies have demonstrated that globular proteins can be absorbed from the solution by both polycationic and polyanionic brushes when the net charge of protein globules is of the same or of the opposite sign with respect to that of brush-forming polyelectrolyte chains. Here, we overview the results of experimental studies on interactions between globular proteins and polycationic or polyanionic brushes, and present a self-consistent field theoretical model that allows us to account for the asymmetry of interactions of protein-like nanocolloid particles comprising weak (pH-sensitive) cationic and anionic groups with a positively or negatively charged polyelectrolyte brush. The position-dependent insertion free energy and the net charge of the particle are calculated. The theoretical model predicts that if the numbers of cationic and anionic ionizable groups of the protein are approximately equal, then the interaction patterns for both cationic and anionic brushes at equal offset on the "wrong side" from the isoelectric point (IEP), i.e., when the particle and the brush charge are of the same sign, are similar. An essential asymmetry in interactions of particles with polycationic and polyanionic brushes is predicted when fractions of cationic and anionic groups differ significantly. That is, at a pH above IEP, the anionic brush better absorbs negatively charged particles with a larger fraction of ionizable cationic groups and vice versa.

Cylindrical brushes with ionized side chains: Scaling theory revisited.

We revisit the classic scaling model of a cylindrical polyelectrolyte (PE) brush focusing on molecular brushes with stiff backbones and dispersions of polymer-decorated nanorods. Based on the blob representation we demonstrate that similarly to the case of planar PE brushes, separation of intra- and intermolecular repulsions between charges leads to novel scaling regimes for cylindrical PE brushes in salt-added solution and a sharper decrease in its thickness versus salt concentration dependence. These theoretical predictions may inspire further comprehensive experimental research and computer simulations of synthetic and biopolyelectrolyte cylindrical brushes.

Analysis of 72,469 UK Biobank exomes links rare variants to male-pattern hair loss.

Male-pattern hair loss (MPHL) is common and highly heritable. While genome-wide association studies (GWAS) have generated insights into the contribution of common variants to MPHL etiology, the relevance of rare variants remains unclear. To determine the contribution of rare variants to MPHL etiology, we perform gene-based and single-variant analyses in exome-sequencing data from 72,469 male UK Biobank participants. While our population-level risk prediction suggests that rare variants make only a minor contribution to general MPHL risk, our rare variant collapsing tests identified a total of five significant gene associations. These findings provide additional evidence for previously implicated genes (EDA2R, WNT10A) and highlight novel risk genes at and beyond GWAS loci (HEPH, CEPT1, EIF3F). Furthermore, MPHL-associated genes are enriched for genes considered causal for monogenic trichoses. Together, our findings broaden the MPHL-associated allelic spectrum and provide insights into MPHL pathobiology and a shared basis with monogenic hair loss disorders.

Polyelectrolyte Cylindrical Brushes in Hairy Gels.

We considered dispersions of cylindrical polyelectrolyte (PE) brushes with stiff backbones, and polymer-decorated nanorods with tunable solubility of the brush-forming PE chains that affected thermodynamic stability of the dispersions. We focused on thermo-induced and deionization-induced conformational transition that provokes loss of aggregative dispersion stability of nanorods decorated with weakly ionized polyions. A comparison between theoretical predictions and experiments enabled rationalization and semi-quantitative interpretation of the experimental results.

Dissecting the genetic heterogeneity of gastric cancer.

BACKGROUND: Gastric cancer (GC) is clinically heterogenous according to location (cardia/non-cardia) and histopathology (diffuse/intestinal). We aimed to characterize the genetic risk architecture of GC according to its subtypes. Another aim was to examine whether cardia GC and oesophageal adenocarcinoma (OAC) and its precursor lesion Barrett's oesophagus (BO), which are all located at the gastro-oesophageal junction (GOJ), share polygenic risk architecture. METHODS: We did a meta-analysis of ten European genome-wide association studies (GWAS) of GC and its subtypes. All patients had a histopathologically confirmed diagnosis of gastric adenocarcinoma. For the identification of risk genes among GWAS loci we did a transcriptome-wide association study (TWAS) and expression quantitative trait locus (eQTL) study from gastric corpus and antrum mucosa. To test whether cardia GC and OAC/BO share genetic aetiology we also used a European GWAS sample with OAC/BO. FINDINGS: Our GWAS consisting of 5816 patients and 10,999 controls highlights the genetic heterogeneity of GC according to its subtypes. We newly identified two and replicated five GC risk loci, all of them with subtype-specific association. The gastric transcriptome data consisting of 361 corpus and 342 antrum mucosa samples revealed that an upregulated expression of MUC1, ANKRD50, PTGER4, and PSCA are plausible GC-pathomechanisms at four GWAS loci. At another risk locus, we found that the blood-group 0 exerts protective effects for non-cardia and diffuse GC, while blood-group A increases risk for both GC subtypes. Furthermore, our GWAS on cardia GC and OAC/BO (10,279 patients, 16,527 controls) showed that both cancer entities share genetic aetiology at the polygenic level and identified two new risk loci on the single-marker level. INTERPRETATION: Our findings show that the pathophysiology of GC is genetically heterogenous according to location and histopathology. Moreover, our findings point to common molecular mechanisms underlying cardia GC and OAC/BO. FUNDING: German Research Foundation (DFG).

Polyelectrolyte Brush Interacting with Ampholytic Nanoparticles as Coarse-Grained Models of Globular Proteins: Poisson-Boltzmann Theory.

The self-consistent field Poisson-Boltzmann framework is applied to analyze equilibrium partitioning of ampholytic nanoparticles (NPs) between buffer solution and polyelectrolyte (PE) polyanionic brush. We demonstrate that depending on pH and salt concentration in the buffer solution, interactions between ionizable (acidic and basic) groups on the NP surface and electrostatic field created by PE brush may either lead to the spontaneous uptake of NPs or create an electrostatic potential barrier, preventing the penetration of NPs inside PE brush. The capability of PE brush to absorb or repel NPs is determined by the shape of the insertion free energy that is calculated as a function of NP distance from the grafting surface. It is demonstrated that, at a pH value below or slightly above the isoelectric point (IEP), the electrostatic free energy of the particle is negative inside the brush and absorption is thermodynamically favorable. In the latter case, the insertion free energy exhibits a local maximum (potential barrier) at the entrance to the brush. An increase in pH leads to the shallowing of the free energy minimum inside the brush and a concomitant increase in the free energy maximum, which may result in kinetic hindering of NP uptake. Upon further increase in pH the insertion free energy becomes positive, making NP absorption thermodynamically unfavorable. An increase in salt concentration diminishes the depth of the free energy minimum inside the brush and eventually leads to its disappearance. Hence, in accordance with existing experimental data our theory predicts that an increase in salt concentration suppresses absorption of NPs (protein globules) by PE brush in the vicinity of IEP. The interplay between electrostatic driving force for NP absorption and osmotic repelling force (proportional to NP volume) indicates that for large NPs with relatively small number of ionizable groups osmotic repulsion overcomes electrostatic attraction preventing thereby absorption of NPs by PE brush.

Structure and Dynamics of Hybrid Colloid-Polyelectrolyte Coacervates.

We develop a scaling theory for the structure and dynamics of "hybrid" complex coacervates formed from linear polyelectrolytes (PEs) and oppositely charged spherical colloids, such as globular proteins, solid nanoparticles, or spherical micelles of ionic surfactants. At low concentrations, in stoichiometric solutions, PEs adsorb at the colloids to form electrically neutral finite-size complexes. These clusters attract each other through bridging between the adsorbed PE layers. Above a threshold concentration, macroscopic phase separation sets in. The coacervate internal structure is defined by (i) the adsorption strength and (ii) the ratio of the resulting shell thickness to the colloid radius, H/R. A scaling diagram of different coacervate regimes is constructed in terms of the colloid charge and its radius for Θ and athermal solvents. For high charges of the colloids, the shell is thick, H ≫ R, and most of the volume of the coacervate is occupied by PEs, which determine its osmotic and rheological properties. The average density of hybrid coacervates exceeds that of their PE-PE counterparts and increases with nanoparticle charge, Q. At the same time, their osmotic moduli remain equal, and the surface tension of hybrid coacervates is lower, which is a consequence of the shell's inhomogeneous density decreasing with the distance from the colloid surface. When charge correlations are weak, hybrid coacervates remain liquid and follow Rouse/reptation dynamics with a Q-dependent viscosity, η Rouse ∼ Q 4/5 and η rep ∼ Q 28/15 for a Θ solvent. For an athermal solvent, these exponents are equal to 0.89 and 2.68, respectively. The diffusion coefficients of colloids are predicted to be strongly decreasing functions of their radius and charge. Our results on how Q affects the threshold coacervation concentration and colloidal dynamics in condensed phases are consistent with experimental observations for in vitro and in vivo studies of coacervation between supercationic green fluorescent proteins (GFPs) and RNA.

Selective Colloid Transport across Planar Polymer Brushes.

Polymer brushes are attractive as surface coatings for a wide range of applications, from fundamental research to everyday life, and also play important roles in biological systems. How colloids (e.g., functional nanoparticles, proteins, viruses) bind and move across polymer brushes is an important yet under-studied problem. A mean-field theoretical approach is presented to analyze the binding and transport of colloids in planar polymer brushes. The theory explicitly considers the effect of solvent strength on brush conformation and of colloid-polymer affinity on colloid binding and transport. The position-dependent free energy of the colloid insertion into the polymer brush which controls the rate of colloid transport across the brush is derived. It is shown how the properties of the brush can be adjusted for brushes to be highly selective, effectively serving as tuneable gates with respect to colloid size and affinity to the brush-forming polymer. The most important parameter regime simultaneously allowing for high brush permeability and selectivity corresponds to a condition when the repulsive and attractive contributions to the colloid insertion free energy nearly cancel. This theory should be useful to design sensing and purification devices with enhanced selectivity and to better understand mechanisms underpinning the functions of biological polymer brushes.

Bovine Serum Albumin Interaction with Polyanionic and Polycationic Brushes: The Case Theoretical Study.

We apply a coarse-grained self-consistent field Poisson-Boltzmann framework to study interaction between Bovine Serum Albumin (BSA) and a planar polyelectropyte brush. Both cases of negatively (polyanionic) and positively (polycationic) charged brushes are considered. Our theoretical model accounts for (1) re-ionization free energy of the amino acid residues upon protein insertion into the brush; (2) osmotic force repelling the protein globule from the brush; (3) hydrophobic interactions between non-polar areas on the globule surface and the brush-forming chains. We demonstrate that calculated position-dependent insertion free energy exhibits different patterns, corresponding to either thermodynamically favourable BSA absorption in the brush or thermodynamically or kinetically hindered absorption (expulsion) depending on the pH and ionic strength of the solution. The theory predicts that due to the re-ionization of BSA within the brush, a polyanionic brush can efficiently absorb BSA over a wider pH range on the "wrong side" of the isoelectric point (IEP) compared to a polycationic brush. The results of our theoretical analysis correlate with available experimental data and thus validate the developed model for prediction of the interaction patterns for various globular proteins with polyelectrolyte brushes.

Hybrid Molecules Consisting of Lysine Dendrons with Several Hydrophobic Tails: A SCF Study of Self-Assembling.

In this article, we used the numerical self-consistent field method of Scheutjens-Fleer to study the micellization of hybrid molecules consisting of one polylysine dendron with charged end groups and several linear hydrophobic tails attached to its root. The main attention was paid to spherical micelles and the determination of the range of parameters at which they can appear. A relationship has been established between the size and internal structure of the resulting spherical micelles and the length and number of hydrophobic tails, as well as the number of dendron generations. It is shown that the splitting of the same number of hydrophobic monomers from one long tail into several short tails leads to a decrease in the aggregation number and, accordingly, the number of terminal charges in micelles. At the same time, it was shown that the surface area per dendron does not depend on the number of hydrophobic monomers or tails in the hybrid molecule. The relationship between the structure of hybrid molecules and the electrostatic properties of the resulting micelles has also been studied. It is found that the charge distribution in the corona depends on the number of dendron generations G in the hybrid molecule. For a small number of generations (up to G=3), a standard double electric layer is observed. For a larger number of generations (G=4), the charges of dendrons in the corona are divided into two populations: in the first population, the charges are in the spherical layer near the boundary between the micelle core and shell, and in the second population, the charges are near the periphery of the spherical shell. As a result, a part of the counterions is localized in the wide region between them. These results are of potential interest for the use of spherical dendromicelles as nanocontainers for drug delivery.

Implicit-Solvent Coarse-Grained Simulations of Linear-Dendritic Block Copolymer Micelles.

The design of nanoassemblies can be conveniently achieved by tuning the strength of the hydrophobic interactions of block copolymers in selective solvents. These block copolymer micelles form supramolecular aggregates, which have attracted great attention in the area of drug delivery and imaging in biomedicine due to their easy-to-tune properties and straightforward large-scale production. In the present work, we have investigated the micellization process of linear-dendritic block copolymers in order to elucidate the effect of branching on the micellar properties. We focus on block copolymers formed by linear hydrophobic blocks attached to either dendritic neutral or charged hydrophilic blocks. We have implemented a simple protocol for determining the equilibrium micellar size, which permits the study of linear-dendritic block copolymers in a wide range of block morphologies in an efficient and parallelizable manner. We have explored the impact of different topological and charge properties of the hydrophilic blocks on the equilibrium micellar properties and compared them to predictions from self-consistent field theory and scaling theory. We have found that, at higher degrees of branching in the corona and for short polymer chains, excluded volume interactions strongly influence the micellar aggregation as well as their effective charge.

Identification of de novo variants in nonsyndromic cleft lip with/without cleft palate patients with low polygenic risk scores.

BACKGROUND: Nonsyndromic cleft lip with/without cleft palate (nsCL/P) is a congenital malformation of multifactorial etiology. Research has identified >40 genome-wide significant risk loci, which explain less than 40% of nsCL/P heritability. Studies show that some of the hidden heritability is explained by rare penetrant variants. METHODS: To identify new candidate genes, we searched for highly penetrant de novo variants (DNVs) in 50 nsCL/P patient/parent-trios with a low polygenic risk for the phenotype (discovery). We prioritized DNV-carrying candidate genes from the discovery for resequencing in independent cohorts of 1010 nsCL/P patients of diverse ethnicities and 1574 population-matched controls (replication). Segregation analyses and rare variant association in the replication cohort, in combination with additional data (genome-wide association data, expression, protein-protein-interactions), were used for final prioritization. CONCLUSION: In the discovery step, 60 DNVs were identified in 60 genes, including a variant in the established nsCL/P risk gene CDH1. Re-sequencing of 32 prioritized genes led to the identification of 373 rare, likely pathogenic variants. Finally, MDN1 and PAXIP1 were prioritized as top candidates. Our findings demonstrate that DNV detection, including polygenic risk score analysis, is a powerful tool for identifying nsCL/P candidate genes, which can also be applied to other multifactorial congenital malformations.

GWAS meta-analysis of 16 790 patients with Barrett's oesophagus and oesophageal adenocarcinoma identifies 16 novel genetic risk loci and provides insights into disease aetiology beyond the single marker level.

OBJECTIVE: Oesophageal cancer (EC) is the sixth leading cause of cancer-related deaths. Oesophageal adenocarcinoma (EA), with Barrett's oesophagus (BE) as a precursor lesion, is the most prevalent EC subtype in the Western world. This study aims to contribute to better understand the genetic causes of BE/EA by leveraging genome wide association studies (GWAS), genetic correlation analyses and polygenic risk modelling. DESIGN: We combined data from previous GWAS with new cohorts, increasing the sample size to 16 790 BE/EA cases and 32 476 controls. We also carried out a transcriptome wide association study (TWAS) using expression data from disease-relevant tissues to identify BE/EA candidate genes. To investigate the relationship with reported BE/EA risk factors, a linkage disequilibrium score regression (LDSR) analysis was performed. BE/EA risk models were developed combining clinical/lifestyle risk factors with polygenic risk scores (PRS) derived from the GWAS meta-analysis. RESULTS: The GWAS meta-analysis identified 27 BE and/or EA risk loci, 11 of which were novel. The TWAS identified promising BE/EA candidate genes at seven GWAS loci and at five additional risk loci. The LDSR analysis led to the identification of novel genetic correlations and pointed to differences in BE and EA aetiology. Gastro-oesophageal reflux disease appeared to contribute stronger to the metaplastic BE transformation than to EA development. Finally, combining PRS with BE/EA risk factors improved the performance of the risk models. CONCLUSION: Our findings provide further insights into BE/EA aetiology and its relationship to risk factors. The results lay the foundation for future follow-up studies to identify underlying disease mechanisms and improving risk prediction.

A Polyelectrolyte Colloidal Brush Based on Cellulose: Perspectives for Future Applications.

This feature article is devoted to the evaluation of different techniques for producing colloidal polyelectrolyte brushes (CPEBs) based on cellulose nanofibers modified with grafted polyacrylates. The paper also reviews the potential applications of these CPEBs in designing electrode materials and as reinforcing additives. Additionally, we discuss our own perspectives on investigating composites with CPEBs. Herein, polyacrylic acid (PAA) was grafted onto the surface of cellulose nanofibers (CNFs) employing a "grafting from" approach. The effect of the PAA shell on the morphological structure of a composite with polypyrrole (PPy) was investigated. The performance of as-obtained CNF-PAA/PPy as organic electrode material for supercapacitors was examined. Furthermore, this research highlights the ability of CNF-PAA filler to act as an additional crosslinker forming a physical sub-network due to the hydrogen bond interaction inside chemically crosslinked polyacrylamide (PAAm) hydrogels. The enhancement of the mechanical properties of the material with a concomitant decrease in its swelling ratio compared to a pristine PAAm hydrogel was observed. The findings were compared with the recent theoretical foundation pertaining to other similar materials.