Illuminating ligand-induced dynamics in nuclear receptors through MD simulations.

Nuclear receptors (NRs) regulate gene expression in critical physiological processes, with their functionality finely tuned by ligand-induced conformational changes. While NRs may sometimes undergo significant conformational motions in response to ligand-binding, these effects are more commonly subtle and challenging to study by traditional structural or biophysical methods. Molecular dynamics (MD) simulations are a powerful tool to bridge the gap between static protein-ligand structures and dynamical changes that govern NR function. Here, we summarize a handful of recent studies that apply MD simulations to study NRs. We present diverse methodologies for analyzing simulation data with a detailed examination of the information each method can yield. By delving into the strengths, limitations and unique contributions of these tools, this review provides guidance for extracting meaningful data from MD simulations to advance the goal of understanding the intricate mechanisms by which ligands orchestrate a range of functional outcomes in NRs.

Nuclear receptor interdomain communication is mediated by the hinge with ligand specificity.

Nuclear receptors are ligand-induced transcription factors that bind directly to target genes and regulate their expression. Ligand binding initiates conformational changes that propagate to other domains, allosterically regulating their activity. The nature of this interdomain communication in nuclear receptors is poorly understood, largely owing to the difficulty of experimentally characterizing full-length structures. We have applied computational modeling approaches to describe and study the structure of the full length farnesoid X receptor (FXR), approximated by the DNA binding domain (DBD) and ligand binding domain (LBD) connected by the flexible hinge region. Using extended molecular dynamics simulations (> 10 microseconds) and enhanced sampling simulations, we provide evidence that ligands selectively induce domain rearrangement, leading to interdomain contact. We use protein-protein interaction assays to provide experimental evidence of these interactions, identifying a critical role of the hinge in mediating interdomain contact. Our results illuminate previously unknown aspects of interdomain communication in FXR and provide a framework to enable characterization of other full length nuclear receptors.

RGD density along with substrate stiffness regulate hPSC hepatocyte functionality through YAP signalling.

Human pluripotent stem cell-derived hepatocytes (hPSC-Heps) may be suitable for treating liver diseases, but differentiation protocols often fail to yield adult-like cells. We hypothesised that replicating healthy liver niche biochemical and biophysical cues would produce hepatocytes with desired metabolic functionality. Using 2D synthetic hydrogels which independently control mechanical properties and biochemical cues, we found that culturing hPSC-Heps on surfaces matching the stiffness of fibrotic liver tissue upregulated expression of genes for RGD-binding integrins, and increased expression of YAP/TAZ and their transcriptional targets. Alternatively, culture on soft, healthy liver-like substrates drove increases in cytochrome p450 activity and ureagenesis. Knockdown of ITGB1 or reducing RGD-motif-containing peptide concentration in stiff hydrogels reduced YAP activity and improved metabolic functionality; however, on soft substrates, reducing RGD concentration had the opposite effect. Furthermore, targeting YAP activity with verteporfin or forskolin increased cytochrome p450 activity, with forskolin dramatically enhancing urea synthesis. hPSC-Heps could also be successfully encapsulated within RGD peptide-containing hydrogels without negatively impacting hepatic functionality, and compared to 2D cultures, 3D cultured hPSC-Heps secreted significantly less fetal liver-associated alpha-fetoprotein, suggesting furthered differentiation. Our platform overcomes technical hurdles in replicating the liver niche, and allowed us to identify a role for YAP/TAZ-mediated mechanosensing in hPSC-Hep differentiation.

Higher Rate of Male Sexual Displays Correlates with Larger Ventral Posterior Amygdala Volume and Neuron Soma Volume in Wild-Caught Common Side-Blotched Lizards, Uta stansburiana.

Several areas of the vertebrate brain are involved in facilitating and inhibiting the production of sexual behaviors and displays. In the laboratory, a higher rate of sexual displays is correlated with a larger ventral posterior amygdala (VPA), an area of the brain involved in the expression of sexual display behaviors, as well as larger VPA neuronal somas. However, it remains unclear if individuals in the field reflect similar patterns, as there are likely many more selective pressures in the field that may also modulate the VPA architecture. In this study, we examined variation in VPA volume and neuron soma volume in wild-caught common side-blotched lizards (Uta stansburiana) from two different populations. In a population from Nevada, males experience high predation pressure and have decreased sexual display rates during the breeding season, whereas a population in Oregon has lower levels of predation and higher rates of male sexual displays. We found that wild-caught males from the population with lower display rates also exhibited decreased VPA volume and VPA neuron cell soma volume, which may suggest that decreased display rate, possibly due to increased predation rate, covaries with VPA attributes.

Selectively Cross-Linked Tetra-PEG Hydrogels Provide Control over Mechanical Strength with Minimal Impact on Diffusivity.

Synthetic hydrogels formed from poly(ethylene glycol) (PEG) are widely used to study how cells interact with their extracellular matrix. These in vivo-like 3D environments provide a basis for tissue engineering and cell therapies but also for research into fundamental biological questions and disease modeling. The physical properties of PEG hydrogels can be modulated to provide mechanical cues to encapsulated cells; however, the impact of changing hydrogel stiffness on the diffusivity of solutes to and from encapsulated cells has received only limited attention. This is particularly true in selectively cross-linked "tetra-PEG" hydrogels, whose design limits network inhomogeneities. Here, we used a combination of theoretical calculations, predictive modeling, and experimental measurements of hydrogel swelling, rheological behavior, and diffusion kinetics to characterize tetra-PEG hydrogels' permissiveness to the diffusion of molecules of biologically relevant size as we changed polymer concentration, and thus hydrogel mechanical strength. Our models predict that hydrogel mesh size has little effect on the diffusivity of model molecules and instead predicts that diffusion rates are more highly dependent on solute size. Indeed, our model predicts that changes in hydrogel mesh size only begin to have a non-negligible impact on the concentration of a solute that diffuses out of hydrogels for the smallest mesh sizes and largest diffusing solutes. Experimental measurements characterizing the diffusion of fluorescein isothiocyanate (FITC)-labeled dextran molecules of known size aligned well with modeling predictions and suggest that doubling the polymer concentration from 2.5% (w/v) to 5% produces stiffer gels with faster gelling kinetics without affecting the diffusivity of solutes of biologically relevant size but that 10% hydrogels can slow their diffusion. Our findings provide confidence that the stiffness of tetra-PEG hydrogels can be modulated over a physiological range without significantly impacting the transport rates of solutes to and from encapsulated cells.

ILC1 drive intestinal epithelial and matrix remodelling.

Organoids can shed light on the dynamic interplay between complex tissues and rare cell types within a controlled microenvironment. Here, we develop gut organoid cocultures with type-1 innate lymphoid cells (ILC1) to dissect the impact of their accumulation in inflamed intestines. We demonstrate that murine and human ILC1 secrete transforming growth factor ß1, driving expansion of CD44v6+ epithelial crypts. ILC1 additionally express MMP9 and drive gene signatures indicative of extracellular matrix remodelling. We therefore encapsulated human epithelial-mesenchymal intestinal organoids in MMP-sensitive, synthetic hydrogels designed to form efficient networks at low polymer concentrations. Harnessing this defined system, we demonstrate that ILC1 drive matrix softening and stiffening, which we suggest occurs through balanced matrix degradation and deposition. Our platform enabled us to elucidate previously undescribed interactions between ILC1 and their microenvironment, which suggest that they may exacerbate fibrosis and tumour growth when enriched in inflamed patient tissues.

Comparison of Reusable Models in Pericardiocentesis Simulation Training.

INTRODUCTION: Pericardiocentesis is a potentially life-saving procedure. We compared two low-cost models-an agar-based model and a novel model, Centesys-in terms of ultrasound image quality and realism, effectiveness of the model, and learners' confidence and satisfaction after training. METHODS: In this pilot randomised 2x2 crossover trial stratified by physician seniority, participants were assigned to undergo pericardiocentesis training either with the agar-based or Centesys model first, followed by the other model. Participants were asked to rate their confidence in performing ultrasound-guided pericardiocentesis, clarity and realism of cardiac structures on ultrasound imaging, and satisfaction on a 7-point Likert scale before and after training with each model. RESULTS: Twenty participants with median postgraduate year of 4 (interquartile range [IQR] 3.75-6) years were recruited. Pre-training, participants rated themselves a median score of 2.5 (IQR 2-4) for level of confidence in performing pericardiocentesis, which improved to 5 (IQR 4-6) post-training with Centesys (P=0.007). Centesys was recognised to be more realistic in simulating cardiac anatomy on ultrasound (median 5 [IQR 4-5] versus 3.5 [IQR 3-4], P=0.002) than the agar-based model. There was greater satisfaction with Centesys (median 5 [IQR 5-6] versus 4 [IQR 3.75-4], P<0.001). All 20 participants achieved successful insertion of a pericardial drain into the simulated pericardial sac with Centesys. CONCLUSION: Centesys achieved greater learner satisfaction as compared to the agar-based model, and was an effective tool for teaching ultrasound-guided pericardiocentesis and drain insertion.

Comparison of Reusable Models in Pericardiocentesis Simulation Training

INTRODUCTION@#Pericardiocentesis is a potentially life-saving procedure. We compared two low-cost models-an agar-based model and a novel model, Centesys-in terms of ultrasound image quality and realism, effectiveness of the model, and learners' confidence and satisfaction after training.@*METHODS@#In this pilot randomised 2x2 crossover trial stratified by physician seniority, participants were assigned to undergo pericardiocentesis training either with the agar-based or Centesys model first, followed by the other model. Participants were asked to rate their confidence in performing ultrasound-guided pericardiocentesis, clarity and realism of cardiac structures on ultrasound imaging, and satisfaction on a 7-point Likert scale before and after training with each model.@*RESULTS@#Twenty participants with median postgraduate year of 4 (interquartile range [IQR] 3.75-6) years were recruited. Pre-training, participants rated themselves a median score of 2.5 (IQR 2-4) for level of confidence in performing pericardiocentesis, which improved to 5 (IQR 4-6) post-training with Centesys (@*CONCLUSION@#Centesys achieved greater learner satisfaction as compared to the agar-based model, and was an effective tool for teaching ultrasound-guided pericardiocentesis and drain insertion.

Author Correction: Bi-directional cell-pericellular matrix interactions direct stem cell fate.

The original version of this Article contained an error in the author affiliations. The affiliation of Marjan Enayati with 'Ludwig Boltzmann Cluster for Cardiovascular Research at the Center for Biomedical Research, Medical University of Vienna, Austria' was inadvertently omitted. This has now been corrected in both the PDF and HTML versions of the Article.

Author Correction: Bi-directional cell-pericellular matrix interactions direct stem cell fate.

In the original version of this Article the dataset identifier in the Data Availability statement was incorrect. The correct dataset identifier is PXD009500. This has been corrected in the HTML and PDF versions of this Article.

Heterologous Hsp90 promotes phenotypic diversity through network evolution.

Biological processes in living cells are often carried out by gene networks in which signals and reactions are integrated through network hubs. Despite their functional importance, it remains unclear to what extent network hubs are evolvable and how alterations impact long-term evolution. We investigated these issues using heat shock protein 90 (Hsp90), a central hub of proteostasis networks. When native Hsp90 in Saccharomyces cerevisiae cells was replaced by the ortholog from hypersaline-tolerant Yarrowia lipolytica that diverged from S. cerevisiae about 270 million years ago, the cells exhibited improved growth in hypersaline environments but compromised growth in others, indicating functional divergence in Hsp90 between the two yeasts. Laboratory evolution shows that evolved Y. lipolytica-HSP90-carrying S. cerevisiae cells exhibit a wider range of phenotypic variation than cells carrying native Hsp90. Identified beneficial mutations are involved in multiple pathways and are often pleiotropic. Our results show that cells adapt to a heterologous Hsp90 by modifying different subnetworks, facilitating the evolution of phenotypic diversity inaccessible to wild-type cells.

Recent Progress in European Advanced Therapy Medicinal Products and Beyond.

Cell- and gene-based therapies form one of the pillars of regenerative medicine. They have the potential to transform quality of life and improve the health status of patients with genetic and cellular defects, including genetic diseases, neurodegenerative diseases and tissue malignancies, amongst others. Despite numerous challenges, in the last decade, tremendous unified efforts by research and clinical scientists in academic, translational and industry settings have resulted in tangible outcomes in the form of many marketing authorizations and approved commercial firsts, such as Glybera®, Kymriah®, YESCARTA®, Holoclar®, and Luxturna™. This report presents a succinct analysis of developments in the regenerative medicine landscape, including immuno-oncology, with a focus on the European Union and examples of clinical and commercial successes and failures. The factors that led to these exciting developments in immune-oncology are also considered. Concurrently, several key issues, spanning from the identification of unmet clinical need, associated challenges, economic evaluation to policy improvements are emphasized. Furthermore, industry insights encompassing the five-dimensional research and development framework for the focused development of medicine, pricing and reimbursement issues, technology adoption and permeation of innovative advanced therapy medicinal products in the clinical set up are reflected upon, following elaborate discussions that transpired in different thematic tracks of Tissue Engineering & Regenerative Medicine International Society European Chapter 2017 Industry Symposium.

Bi-directional cell-pericellular matrix interactions direct stem cell fate.

Modifiable hydrogels have revealed tremendous insight into how physical characteristics of cells' 3D environment drive stem cell lineage specification. However, in native tissues, cells do not passively receive signals from their niche. Instead they actively probe and modify their pericellular space to suit their needs, yet the dynamics of cells' reciprocal interactions with their pericellular environment when encapsulated within hydrogels remains relatively unexplored. Here, we show that human bone marrow stromal cells (hMSC) encapsulated within hyaluronic acid-based hydrogels modify their surroundings by synthesizing, secreting and arranging proteins pericellularly or by degrading the hydrogel. hMSC's interactions with this local environment have a role in regulating hMSC fate, with a secreted proteinaceous pericellular matrix associated with adipogenesis, and degradation with osteogenesis. Our observations suggest that hMSC participate in a bi-directional interplay between the properties of their 3D milieu and their own secreted pericellular matrix, and that this combination of interactions drives fate.

Neighboring cells override 3D hydrogel matrix cues to drive human MSC quiescence.

Physical properties of modifiable hydrogels can be tuned to direct stem cell differentiation in a role akin to that played by the extracellular matrix in native stem cell niches. However, stem cells do not respond to matrix cues in isolation, but rather integrate soluble and non-soluble signals to balance quiescence, self-renewal and differentiation. Here, we encapsulated single cell suspensions of human mesenchymal stem cells (hMSC) in hyaluronic acid-based hydrogels at high and low densities to unravel the contributions of matrix- and non-matrix-mediated cues in directing stem cell response. We show that in high-density (HD) cultures, hMSC do not rely on hydrogel cues to guide their fate. Instead, they take on characteristics of quiescent cells and secrete a glycoprotein-rich pericellular matrix (PCM) in response to signaling from neighboring cells. Preventing quiescence precluded the formation of a glycoprotein-rich PCM and forced HD cultures to differentiate in response to hydrogel composition. Our observations may have important implications for tissue engineering as neighboring cells may act counter to matrix cues provided by scaffolds. Moreover, as stem cells are most regenerative if activated from a quiescent state, our results suggest that ex vivo native-like niches that incorporate signaling from neighboring cells may enable the production of clinically relevant, highly regenerative cells.

Exploiting Advanced Hydrogel Technologies to Address Key Challenges in Regenerative Medicine.

Regenerative medicine aims to tackle a panoply of challenges from repairing focal damage to articular cartilage to preventing pathological tissue remodeling after myocardial infarction. Hydrogels are water-swollen networks formed from synthetic or naturally derived polymers and are emerging as important tools to address these challenges. Recent advances in hydrogel chemistries are enabling researchers to create hydrogels that can act as 3D ex vivo tissue models, allowing them to explore fundamental questions in cell biology by replicating tissues' dynamic and nonlinear physical properties. Enabled by cutting edge techniques such as 3D bioprinting, cell-laden hydrogels are also being developed with highly controlled tissue-specific architectures, vasculature, and biological functions that together can direct tissue repair. Moreover, advanced in situ forming and acellular hydrogels are increasingly finding use as delivery vehicles for bioactive compounds and in mediating host cell response. Here, advances in the design and fabrication of hydrogels for regenerative medicine are reviewed. It is also addressed how controlled chemistries are allowing for precise engineering of spatial and time-dependent properties in hydrogels with a look to how these materials will eventually translate to clinical applications.

Socioeconomic burden of psoriatic arthritis in Hong Kong: direct and indirect costs and the influence of disease pattern.

OBJECTIVE: To estimate the direct costs and indirect costs of patients with psoriatic arthritis (PsA) in Hong Kong. METHODS: A retrospective cost-of-illness study was performed on 125 patients with PsA. Participants completed questionnaires on demographics, employment status, and out of pocket expenses. Health resources consumption was recorded by chart review and patient self-report questionnaire. Patients were grouped according to disease pattern, i.e., peripheral and axial disease. Multiple regression was used to determine the predictors of the costs. RESULTS: The average annual direct costs were $4,141 (2006 US dollars) per patient. Costs of inpatient care accounted for 27% of direct costs, followed by costs of visits to healthcare providers (25%). The estimated average indirect costs were $3,127 per patient-year. Forty-eight (42%) patients had no indirect costs. Sixty percent of patients with peripheral disease were still employed, compared to 39% of patients with axial disease. Patients with axial disease had almost twice the indirect costs compared to those with peripheral disease (p = 0.005). Increased pain and poor function were independently associated with increased direct costs. Worse physical health status, determined by indirect costs borne by the patient, and poor function and old age predicted high costs. CONCLUSION: PsA imposes substantial economic burden. Pain and function are significantly associated with costs. Improvements in treatments to reduce pain and restore function are likely to reduce the costs incurred by these patients.

Identification of ten novel genes involved in human spermatogenesis by microarray analysis of testicular tissue.

OBJECTIVE: To identify novel genes that are down-regulated in the testicular tissue of infertile men. DESIGN: Prospective study. SETTING: University-based reproductive clinics and genetics laboratory. PATIENTS: Nine patients with normal spermatogenesis, and 15 patients with maturation arrest (MA) or Sertoli cell-only syndrome (SCOS). INTERVENTION: Testicular samples of patients with the same histology were pooled for complementary DNA (cDNA) microarray analysis. MAIN OUTCOME MEASURE: Novel, down-regulated genes. RESULTS: In total, 300 genes were significantly down-regulated in SCOS or MA samples, and 10 novel sterility-related genes were identified. Of the 10 novel genes, 6 genes (Hs.126780, Hs.553658, Hs.274135, Hs.268122, Hs.531701, and Hs.171130) encode proteins with predictable functional domains, and all these functional domains are believed to correlate with spermatogenesis and/or spermiogenesis. Conversely, the other 4 genes (Hs.351582, Hs.407480, Hs.552781, and Hs.355570) do not encompass known functional domains. Two genes (Hs.407480 and Hs.552781) lack mouse orthologues. Most novel genes showed a testis-specific expression pattern in both mice and humans. Reverse transcription-polymerase chain reaction (RT-PCR) showed three distinct types of developmental stage-dependent expressions of message ribonucleic acid (mRNA) for these novel genes in murine testes. CONCLUSION: These 10 novel genes provide targets to elucidate novel pathways involved in human spermatogenesis.