Genome-wide pathway-based association study implicates complement system in the development of Kashin-Beck disease in Han Chinese

The anaphylatoxin C5a: Structure, function, signaling, physiology, disease, and therapeutics

The complement system is one of the oldest known tightly regulated host defense systems evolved for efficiently functioning cell-based immune systems and antibodies. Essentially, the complement system acts as a pivot between the innate and adaptive arms of the immune system. The complement system collectively represents a cocktail of ∼50 cell-bound/soluble glycoproteins directly involved in controlling infection and inflammation. Activation of the complement cascade generates complement fragments like C3a, C4a, and C5a as anaphylatoxins. C5a is the most potent proinflammatory anaphylatoxin, which is involved in inflammatory signaling in a myriad of tissues. This review provides a comprehensive overview of human C5a in the context of its structure and signaling under several pathophysiological conditions, including the current and future therapeutic applications targeting C5a.

The alteration of urinary metabolomics profiles in Kashin-Beck disease in a three consecutive year study

Kashin-Beck disease (KBD) is a serious, endemic chronic osteochondral disease characterized by symmetrical enlargement of the phalanges, brachydactyly, joint deformity, and even dwarfism. To investigate the urinary metabolomic profiles of KBD patients, we performed an untargeted metabolomics approach using liquid chromatography coupled with mass spectrometry (LC-MS). Adult urinary specimens were collected from 39 patients with KBD and 19 healthy subjects; the children's urinary specimens were collected from 5 patients with KBD, 25 suspected KBD cases and 123 healthy subjects in the KBD endemic area during a three consecutive year study. We identified 10 upregulated and 28 downregulated secondary level metabolites highly associated with aetiology and pathogenesis of KBD between adult KBD and adult controls. A total of 163, 967 and 795 metabolites were significantly different in the urine among children with KBD, suspected children with KBD cases and healthy child controls, respectively, for each year in three consecutive years. HT-2 toxin, Se-adenosylselenomethionine (AdoSeMet), the toxin T2 tetrol, and many kinds of amino acids were identified as differential metabolites in this study. Amino sugar and nucleotide sugar metabolism, fructose and mannose metabolism, arachidonic acid metabolism, D-glutamine and D-glutamate metabolism, ubiquinone and other terpenoid-quinone biosynthesis, and D-glutamine and D-glutamate metabolism were perturbed pathways in adult and child KBD patients. Our study provides new insight into the underlying mechanisms of KBD, and suggests that we should pay more attention to these differences in small-molecule metabolites and metabolic pathways in the environmental aetiology and pathogenesis of KBD.

Network pharmacology and experimental validation-based approach to understand the effect and mechanism of Taohong Siwu Decoction against ischemic stroke

ETHNOPHARMACOLOGICAL RELEVANCE

Taohong Siwu Decoction (THSWD) is a classic prescription of traditional Chinese medicine that is mainly used for promoting blood circulation and alleviating blood stasis. THSWD is composed of Prunus persica (L.) Batsch, Carthamus tinctorius L., Ligusticum chuanxiong hort, Angelica sinensis (Oliv.) Diels, Rehmannia glutinosa (Gaertn.) DC, and Paeoniae Radix Alba. This prescription eliminates blood stasis, supplements blood, and dredges the body as an auxiliary treatment.

AIM OF THE STUDY

To investigate the mechanistic effects of THSWD in the treatment of cerebral ischemia.

MATERIALS AND METHODS

we downloaded 39 blood components for THSWD from the PharmMapper database for target prediction studies and identified the targets of cerebral ischemia. We identified the intersection between the components and targets, constructed a protein-protein interaction (PPI) network, carried out GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. a rat model of cerebral ischemia was established in rats, and the results of network pharmacology were verified by in vivo experiments.

RESULTS

Established a component-target-pathway network, further transcriptomics analysis identified a total of 11 target genes (Plau, Fabp4, Mmp9, Mmp12, Cfd, Lcn2, Trem1, Lgals3, Hmox1, Selp and Slc6a4), a total of seven pathways (focal adhesion, complement and coagulation cascades, Staphylococcus aureus infection, malaria, transcriptional dysregulation in cancer, progesterone-mediated oocyte maturation, and the PI3K-Akt signaling pathway), because both targets genes and the complement and coagulation cascade signaling pathways mediate inflammatory responses, the signaling pathways associated with the complement and coagulation cascades were selected for experimental verification. We detected inflammatory factors and several key proteins in the complement and coagulation cascade signaling pathway (C1qb, C1qc, C3ar1, C5ar1, and Cfd). Analysis showed that THSWD can reduce the release of inflammatory factors and inhibit activation of the complement signaling pathways, thereby protecting against ischemic stroke disease.

CONCLUSIONS

Our findings provide preliminary clarification of the predominant mechanism of action of THSWD when used to treat ischemic stroke.

Effects of Separate and Combined Exposure of Cadmium and Lead on the Endochondral Ossification in Bufo gargarizans

Cadmium (Cd) and lead (Pb) are ubiquitous in aquatic environments and most studies have examined the potential effects of Cd or Pb alone on aquatic organisms. In the present study, chronic effects of Cd and Pb, alone and in combination, on Bufo gargarizans were investigated by exposing embryos to these contaminants throughout metamorphosis. Significant reductions in body mass and snout-to-vent length were observed in B. gargarizans at Gosner stage 42 (Gs 42) and Gs 46 exposed to a Cd/Pb mixture. Single and combined exposure with Cd and Pb induced histological alterations of the thyroid gland characterized by reduced colloid area and thickness of epithelial cells. There was a significant decrease in the maximum jump distance of froglets exposed to Cd alone and the Cd/Pb mixture, and the jumping capacity showed a positive correlation with hind limb length and tibia/fibula. Moreover, single metals and their mixture induced reduction of endochondral bone formation in B. gargarizans. Transcriptomic and real-time quantitative polymerase chain reaction results showed that genes involved in skeletal ossification (TRα, TRβ, Dio2, Dio3, MMP9, MMP13, Runx1, Runx2, and Runx3) were transcriptionally dysregulated by Cd and Pb exposure alone or in combination. Our results suggested that despite the low concentration tested, the Cd/Pb mixture induced more severe impacts on B. gargarizans. In addition, the Cd/Pb mixture might reduce chances of survival for B. gargarizans froglets by decreasing size at metamorphosis, impaired skeletal ossification, and reduction in jumping ability, which might result from dysregulation of genes involved in thyroid hormone action and endochondral ossification. The findings obtained could add a new dimension to understanding of the mechanisms underpinning skeletal ossification response to heavy metals in amphibians. Environ Toxicol Chem 2022;41:1228-1245. © 2022 SETAC.

Identifying insomnia-related chemicals through integrative analysis of genome-wide association studies and chemical-genes interaction information

STUDY OBJECTIVES

Insomnia is a common sleep disorder and constitutes a major issue in modern society. We provide new clues for revealing the association between environmental chemicals and insomnia.

METHODS

Three genome-wide association studies (GWAS) summary datasets of insomnia (n = 113,006, n = 1,331,010, and n = 453,379, respectively) were driven from the UK Biobank, 23andMe, and deCODE. The chemical-gene interaction dataset was downloaded from the Comparative Toxicogenomics Database. First, we conducted a meta-analysis of the three datasets of insomnia using the METAL software. Using the result of meta-analysis, transcriptome-wide association studies were performed to calculate the expression association testing statistics of insomnia. Then chemical-related gene set enrichment analysis (GSEA) was used to explore the association between chemicals and insomnia.

RESULTS

For GWAS meta-analysis dataset of insomnia, we identified 42 chemicals associated with insomnia in brain tissue (p < 0.05) by GSEA. We detected five important chemicals such as pinosylvin (p = 0.0128), bromobenzene (p = 0.0134), clonidine (p = 0.0372), gabapentin (p = 0.0372), and melatonin (p = 0.0404) which are directly associated with insomnia.

CONCLUSION

Our study results provide new clues for revealing the roles of environmental chemicals in the development of insomnia.

Pathway-based network analyses and candidate genes associated with Kashin-Beck disease

To perform a comprehensive analysis focusing on the biological functions and interactions of Kashin-Beck disease (KBD)-related genes to provide information towards understanding the pathogenesis of KBD.A retrospective, integrated bioinformatics analysis was designed and conducted. First, by reviewing the literature deposited in PubMed, we identified 922 genes genetically associated with KBD. Then, biological function and network analyses were conducted with Cytoscape software. Moreover, KBD specific molecular network analysis was conducted by Cytocluster using the Molecular Complex Detection Algorithm (MCODE).The biological function enrichment analysis suggested that collagen catabolic process, protein activation cascade, cellular response to growth factor stimulus, skeletal system development, and extrinsic apoptosis played important roles in KBD development. The apoptosis pathway, NF-kappa B signaling pathway, and the glutathione metabolism pathway were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway network, suggesting that these pathways may play key roles in KBD occurrence and development. MCODE clusters showed that in top 3 clusters, 54 of KBD-related genes were included in the network and 110 candidate genes were discovered might be potentially related to KBD.The 110 candidate genes discovered in the current study may be related to the development of KBD. The expression changes of apoptosis and oxidative stress-related genes might serve as biomarkers for early diagnosis and treatment of KBD.

Identification of core genes and prediction of miRNAs associated with osteoporosis using a bioinformatics approach

Osteoporosis (OP) is an age-related disease, and osteoporotic fracture is one of the major causes of disability and mortality in elderly patients (>70 years old). As the pathogenesis and molecular mechanism of OP remain unclear, the identification of disease biomarkers is important for guiding research and providing therapeutic targets. In the present study, core genes and microRNAs (miRNAs) associated with OP were identified. Differentially expressed genes (DEGs) between human mesenchymal stem cell specimens from normal osseous tissues and OP tissues were detected using the GEO2R tool of the Gene Expression Omnibus database and Morpheus. Network topological parameters were determined using NetworkAnalyzer. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using the Database for Annotation, Visualization and Integrated Discovery, and ClueGO. Cytoscape with the Search Tool for the Retrieval of Interacting Genes and Molecular Complex Detection plug-in was used to visualize protein-protein interactions (PPIs). Additionally, miRNA-gene regulatory modules were predicted using CyTargetLinker in order to guide future research. In total, 915 DEGs were identified, including 774 upregulated and 141 downregulated genes. Enriched GO terms and pathways were determined, including 'nervous system development', 'regulation of molecular function', 'glutamatergic synapse pathway' and 'pathways in cancer'. The node degrees of DEGs followed power-law distributions. A PPI network with 541 nodes and 1,431 edges was obtained. Overall, 3 important modules were identified from the PPI network. The following 10 genes were identified as core genes based on high degrees of connectivity: Albumin, PH domain leucine-rich repeat-containing protein phosphatase 2 (PHLPP2), DNA topoisomerase 2-α, kininogen 1 (KNG1), interleukin 2 (IL2), leucine-rich repeats and guanylate kinase domain containing, phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit γ (PIK3CG), leptin, transferrin and RNA polymerase II subunit A (POLR2A). Additionally, 15 miRNA-target interactions were obtained using CyTargetLinker. Overall, 7 miRNAs co-regulated IL2, 3 regulated PHLPP2, 3 regulated KNG1, 1 regulated PIK3CG and 1 modulated POLR2A. These results indicate potential biomarkers in the pathogenesis of OP and therapeutic targets.

A Novel Prioritization Method in Identifying Recurrent Venous Thromboembolism-Related Genes

Identifying the genes involved in venous thromboembolism (VTE) recurrence is important not only for understanding the pathogenesis but also for discovering the therapeutic targets. We proposed a novel prioritization method called Function-Interaction-Pearson (FIP) by creating gene-disease similarity scores to prioritize candidate genes underling VTE. The scores were calculated by integrating and optimizing three types of resources including gene expression, gene ontology and protein-protein interaction. As a result, 124 out of top 200 prioritized candidate genes had been confirmed in literature, among which there were 34 antithrombotic drug targets. Compared with two well-known gene prioritization tools Endeavour and ToppNet, FIP was shown to have better performance. The approach provides a valuable alternative for drug targets discovery and disease therapy.