Gene set correlation enrichment analysis for interpreting and annotating gene expression profiles.

Pathway analysis, including nontopology-based (non-TB) and topology-based (TB) methods, is widely used to interpret the biological phenomena underlying differences in expression data between two phenotypes. By considering dependencies and interactions between genes, TB methods usually perform better than non-TB methods in identifying pathways that include closely relevant or directly causative genes for a given phenotype. However, most TB methods may be limited by incomplete pathway data used as the reference network or by difficulties in selecting appropriate reference networks for different research topics. Here, we propose a gene set correlation enrichment analysis method, Gscore, based on an expression dataset-derived coexpression network to examine whether a differentially expressed gene (DEG) list (or each of its DEGs) is associated with a known gene set. Gscore is better able to identify target pathways in 89 human disease expression datasets than eight other state-of-the-art methods and offers insight into how disease-wide and pathway-wide associations reflect clinical outcomes. When applied to RNA-seq data from COVID-19-related cells and patient samples, Gscore provided a means for studying how DEGs are implicated in COVID-19-related pathways. In summary, Gscore offers a powerful analytical approach for annotating individual DEGs, DEG lists, and genome-wide expression profiles based on existing biological knowledge.

SWEET: a single-sample network inference method for deciphering individual features in disease.

Recently, extracting inherent biological system information (e.g. cellular networks) from genome-wide expression profiles for developing personalized diagnostic and therapeutic strategies has become increasingly important. However, accurately constructing single-sample networks (SINs) to capture individual characteristics and heterogeneity in disease remains challenging. Here, we propose a sample-specific-weighted correlation network (SWEET) method to model SINs by integrating the genome-wide sample-to-sample correlation (i.e. sample weights) with the differential network between perturbed and aggregate networks. For a group of samples, the genome-wide sample weights can be assessed without prior knowledge of intrinsic subpopulations to address the network edge number bias caused by sample size differences. Compared with the state-of-the-art SIN inference methods, the SWEET SINs in 16 cancers more likely fit the scale-free property, display higher overlap with the human interactomes and perform better in identifying three types of cancer-related genes. Moreover, integrating SWEET SINs with a network proximity measure facilitates characterizing individual features and therapy in diseases, such as somatic mutation, mut-driver and essential genes. Biological experiments further validated two candidate repurposable drugs, albendazole for head and neck squamous cell carcinoma (HNSCC) and lung adenocarcinoma (LUAD) and encorafenib for HNSCC. By applying SWEET, we also identified two possible LUAD subtypes that exhibit distinct clinical features and molecular mechanisms. Overall, the SWEET method complements current SIN inference and analysis methods and presents a view of biological systems at the network level to offer numerous clues for further investigation and clinical translation in network medicine and precision medicine.

Hyperphosphorylation-Mimetic TDP-43 Drives Amyloid Formation and Possesses Neuronal Toxicity at the Oligomeric Stage.

TDP-43 proteinopathies cover a range of neurodegenerative diseases, including frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Hyperphosphorylated TDP-43 was found within the inclusion bodies in disease lesions; however, the role of hyperphosphorylation and the toxic species are still ambiguous. To characterize the hyperphosphorylation effect of TDP-43, here, we employed five serine mutations implicated in the diseases at serine locations 379, 403, 404, 409, and 410 in the C-terminus to aspartate (S5D) and to alanine (S5A). We systematically characterized the conformation, liquid-liquid phase separation, oligomerization, and fibrillization of TDP-43 variants. Results revealed that the recombinant TDP-43 variants readily formed structurally similar spherical oligomers, as evidenced by circular dichroism spectroscopy, fluorescence spectroscopy, the TDP-43 oligomer-specific antibody assay, dynamic light scattering, and transmission electron microscopy. After incubation, only the phosphor-mimic S5D TDP-43 formed thioflavin-positive amyloid fibrils, whereas wild-type and S5A TDP-43 formed amorphous aggregates. We also examined membrane disruption, the cytotoxicity of human neuroblastoma, and the synaptic loss of primary neurons induced by oligomers and large aggregates of TDP-43. The results showed that all oligomeric TDP-43 variants were toxic regardless of hyperphosphorylation, but the fibrils and amorphous aggregates were not. Overall, our results demonstrated the hyperphosphorylation effect on fibril formation and the toxicity attributed from TDP-43 oligomers. This study facilitates the understanding and therapeutic development for TDP-43 proteinopathies.

Recombinant thrombomodulin lectin-like domain attenuates Porphyromonas gingivalis lipopolysaccharide-induced osteoclastogenesis and periodontal bone resorption.

BACKGROUND: Evidence demonstrates that the thrombomodulin (TM) lectin domain (TMD1) exerts anti-inflammatory functions. Lipopolysaccharides derived from Porphyromonas gingivalis (Pg-LPS) are considered a major pathogenic factor for chronic periodontitis, promoting inflammation, osteoclastogenesis and alveolar bone resorption. Herein, we aimed to evaluate the potential therapeutic effect of recombinant TMD1 (rTMD1) in suppression of Pg-LPS-induced osteoclastogenesis and periodontal bone loss. METHODS: In vitro, the effects of Pg-LPS, tumor necrosis factor (TNF)-α and rTMD1 on osteoclast differentiation were investigated using receptor activator of nuclear factor-κB ligand (RANKL)-stimulated RAW 264.7 macrophages. In vivo, the effects of rTMD1 treatment were evaluated in a model of experimental periodontitis induced by direct injection of Pg-LPS into the vestibular gingiva. RESULTS: Administration of Pg-LPS to RANKL-stimulated RAW 264.7 macrophages resulted in upregulation of CD86 and osteoclast marker (eg, Dc-stamp and Trap) gene expression and increase of pro-inflammatory cytokine production (e.g., TNF-α) during osteoclast differentiation, and rTMD1 can attenuate these effects. Also, rTMD1 inhibited Pg-LPS-enhanced in vitro bone resorption in a dose-dependent manner. Moreover, TNF-α promoted phosphorylation of p38 and ERK during osteoclast differentiation, and the signal activation can be inhibited by rTMD1. Finally, treatment with rTMD1 hindered Pg-LPS-induced alveolar bone loss in experimental periodontitis in mice. CONCLUSION: Our study demonstrated that rTMD1 attenuates Pg-LPS-enhanced M1 macrophage polarization, osteoclastogenesis and periodontal bone resorption and thus holds therapeutic promise for periodontitis.

Thrombomodulin Functional Domains Support Osteoblast Differentiation and Bone Healing in Diabetes in Mice.

Thrombomodulin (TM) is a transmembrane glycoprotein that contains five functional domains. Soluble TM (sTM), comprising extracellular domains TMD1 (lectin-like), TMD2 (epidermal growth factor [EGF]-like repeat containing), and TMD3 (serine-threonine rich), can be shed from cells by the intramembrane protease rhomboid-like-2 (RHBDL2). TM is expressed by osteoblasts, yet its role there has not been determined. Herein we aimed to investigate the properties of TM and its domains in osteoblast function and bone repair following injury in diabetes. In response to a scratch injury of cultured osteoblast-like MG63 cells, expression of TM and RHBDL2 was enhanced, with increased release of sTM. Conditioned media from the injured cells promoted osteoblast migration, an effect that was lacking with conditioned media from MG63 cells in which TM was silenced by shRNA. Exogenous recombinant TMD1 had no effect on osteoblast activities or on bone repair in vivo. However, TM domains 2 and 3 (TMD2/3), induced MG63 cell migration, proliferation and mineralization in vitro, and when locally administered in mice, improved in vivo healing of injured calvarium. This beneficial effect of TMD2/3, mediated via fibroblast growth factor receptor (FGFR)/ERK signaling pathways, was also observed in vitro under high glucose conditions where endogenous TM expression was reduced, and in vivo in diabetic mice following tibia fracture or calvarium injury, where the osteoblastic response and healing were otherwise dampened. Taken together, osteoblast TM participates in bone healing, and recombinant TMD2/3 holds promise as a novel therapy for diabetic bone defect healing. © 2020 American Society for Bone and Mineral Research.

Water-oxidation catalysis by manganese in a geochemical-like cycle.

Water oxidation in all oxygenic photosynthetic organisms is catalysed by the Mn4CaO4 cluster of Photosystem II. This cluster has inspired the development of synthetic manganese catalysts for solar energy production. A photoelectrochemical device, made by impregnating a synthetic tetranuclear-manganese cluster into a Nafion matrix, has been shown to achieve efficient water oxidation catalysis. We report here in situ X-ray absorption spectroscopy and transmission electron microscopy studies that demonstrate that this cluster dissociates into Mn(II) compounds in the Nafion, which are then reoxidized to form dispersed nanoparticles of a disordered Mn(III/IV)-oxide phase. Cycling between the photoreduced product and this mineral-like solid is responsible for the observed photochemical water-oxidation catalysis. The original manganese cluster serves only as a precursor to the catalytically active material. The behaviour of Mn in Nafion therefore parallels its broader biogeochemistry, which is also dominated by cycles of oxidation into solid Mn(III/IV) oxides followed by photoreduction to Mn²âº.

Confirmation of the electrostatic self-assembly of nanodiamonds.

A reliable explanation for the underlying mechanism responsible for the persistent aggregation and self-assembly of colloidal 5 nm diamond nanoparticles is critical to the development of nanodiamond-based technologies. Although a number of mechanisms have been proposed, validation has been hindered by the inherent difficulty associated with the identification and characterisation of the inter-particle interfaces. In this paper we present results of high resolution aberration corrected electron microscopy and complementary computer simulations to explicate the features involved, and confirm the electrostatic interaction mechanism as the most probable cause for the formation of agglutinates and agglomerates of primary particles.

Resolving the structure of active sites on platinum catalytic nanoparticles.

Accurate understanding of the structure of active sites is fundamentally important in predicting catalytic properties of heterogeneous nanocatalysts. We present an accurate determination of both experimental and theoretical atomic structures of surface monatomic steps on industrial platinum nanoparticles. This comparison reveals that the edges of nanoparticles can significantly alter the atomic positions of monatomic steps in their proximity, which can lead to substantial deviations in the catalytic properties compared with the extended surfaces.

Low-dose aberration corrected cryo-electron microscopy of organic specimens.

Spherical aberration (C(s)) correction in the transmission electron microscope has enabled sub-angstrom resolution imaging of inorganic materials. To achieve similar resolution for radiation-sensitive organic materials requires the microscope to be operated under hybrid conditions: low electron dose illumination of the specimen at liquid nitrogen temperature and low defocus values. Initial images from standard inorganic and organic test specimens have indicated that under these conditions C(s)-correction can provide a significant improvement in resolution (to less than 0.16nm) for direct imaging of organic samples.

High-resolution TEM and the application of direct and indirect aberration correction.

Aberration correction leads to a substantial improvement in the directly interpretable resolution of transmission electron microscopes. Correction of the aberrations has been achieved electron-optically through a hexapole-based corrector and also indirectly by computational analysis of a focal or tilt series of images. These direct and indirect methods are complementary, and a combination of the two offers further advantages. Materials characterization has benefitted from the reduced delocalization and higher resolution in the corrected images. It is now possible, for example, to locate atomic columns at surfaces to higher accuracy and reliability. This article describes the JEM-2200FS in Oxford, which is equipped with correctors for both the image-forming and probe-forming lenses. Examples of the use of this instrument in the characterization of nanocrystalline catalysts are given together with initial results combining direct and indirect methods. The double corrector configuration enables direct imaging of the corrected probe, and a potential confocal imaging mode is described. Finally, modifications to a second generation instrument are outlined.

Local measurement and computational refinement of aberrations for HRTEM.

Methods for accurate and automated determination of the coefficients of the wave aberration function are compared with particular emphasis on measurements of higher order coefficients in corrected instruments. Experimental applications of aberration measurement to the determination of illumination isoplanicity and high precision local refinement of restored exit waves are also described.

Comparisons of linear and nonlinear image restoration.

Exit wave restoration using focus series of images has become a widely used technique to improve image resolution and interpretation. To understand the effects of the imaging approximations used, we have critically compared the specimen exit wave functions restored using the efficient linear Wiener filter, with a general nonlinear maximum likelihood method.

Calculations of spherical aberration-corrected imaging behaviour.

Different optimal operating conditions for a C3-corrected transmission electron microscope were compared for both conventional field emission sources and for the next generation of monochromated instruments. In particular, the contrast transfer functions and corresponding wave aberration functions for two previously proposed optimal conditions in which C3 is adjusted to compensate, respectively, C5 or Cc are critically compared. The results indicate that in the presence of a small positive C5 the former provides flat transfer to the information limit whereas the latter shows oscillatory transfer at high spatial frequencies, which is more pronounced for the monochromated instrument. The effects of this behaviour were further investigated through multislice simulations of Si [110] and diamond [110] under the C5-limited condition. These confirm that for the former structure with an interatomic separation of 0.14 nm this aberration has little influence, but that for the latter with a sub-0.1 nm interatomic separation its presence leads to a restricted defocus range over which the structure is faithfully resolved.