Identification of collaborative activities with oxidative phosphorylation in bipolar disorder

Association of abnormal NDUFB2 and UQCRH expression with venous thromboembolism in patients with liver cirrhosis

Venous thromboembolism (VTE) refers to abnormal coagulation of blood in veins, resulting in complete or incomplete occlusion of the blood vessels. Patients with liver cirrhosis are prone to blood clots. However, relationship between NDUFB2 and UQCRH and VTE is not clear. GSE19151 and GSE48000 profiles for venous thromboembolism were downloaded from gene expression omnibus (GEO) generated using GPL571 and GPL10558. Multiple datasets were merged and batched. The differentially expressed genes (DEGs) were screened and weighted gene co-expression network analysis (WGCNA) was performed. The construction and analysis of protein-protein interaction (PPI) network, functional enrichment analysis, Gene Set Enrichment Analysis (GSEA) were conducted. Gene expression heat map was drawn. Comparative toxicogenomics database (CTD) analysis were performed to find disease most related to the core genes. Western blotting (WB) experiments were further verified. TargetScan screened miRNAs that regulated central DEGs. 129 DEGs were identified. According to gene ontology (GO), DEGs were mainly enriched in mRNA metabolism, oxidative phosphorylation, nucleic acid binding and enzyme binding. The Kyoto Encyclopedia of Gene and Genome (KEGG) analysis showed that target cells were mainly enriched in ribosomes and oxidative phosphorylation. The intersection of enrichment items and GOKEGG enrichment items of DEGs is mainly enriched in oxidative phosphorylation, myocardial contraction and ribosome. In the metascape enrichment project, dna template transcription, cell stress response regulation and proton transport across the membrane can be seen in the GO enrichment project. The PPI network obtained 10 core genes (COX7C, NDUFB2, ATP5O, NDUFA4, NDUFAB1, ATP5C1, ATP5L, NDUFA7, NDUFA6, UQCRH). Gene expression heat map showed that 5 core genes (NDUFAB1, NDUFB2, UQCRH, COX7C, NDUFA4) were highly expressed in venous thromboembolism samples, and lowly expression in normal tissue samples, and 2 core genes (NDUFA7, NDUFA6) were lowly expressed in venous thromboembolism samples. CTD analysis showed that 5 genes (NDUFAB1, NDUFB2, UQCRH, COX7C, NDUFA4) were found to be associated with obesity, necrosis, inflammation and hepatomegaly. The result of WB showed that expression level of NDUFB2 and UQCR in venous thromboembolism was higher than that in control group. NDUFB2 and UQCRH are highly expressed in venous thromboembolism with liver cirrhosis, making them potential molecular targets for early diagnosis and precise treatment.

Single-Cell Sequencing Reveals Necroptosis-Related Prognostic Genes of Glioblastoma

Background

Glioblastoma (GBM) is one of the most malignant forms of brain cancer, with the extremely lower survival rate. Necroptosis (NCPS) is also one of the most wide types of cell death, and its clinical importance in GBM is not clear.

Methods

We first identified necroptotic genes in GBM by single-cell RNA sequencing analysis of our surgical samples and weighted coexpression network analysis (WGNCA) from TCGA GBM data. The cox regression model with least absolute shrinkage and selection operator (LASSO) was used to construct the risk model. Then, KM plot and reactive operation curve (ROC) analysis were used to assess the prediction ability of the model. At last, the infiltrated immune cells and gene mutation profiling were investigated between the high- and low-NCPS groups as well.

Result

The risk model including ten necroptosis-related genes was identified as an independent risk factor for the outcome. In addition, we found that the risk model is correlated with the infiltrated immune cells and tumor mutation burden in GBM. NDUFB2 is identified to be a risk gene in GBM with bioinformatical analysis and in vitro experiment validation.

Conclusion

This risk model of necroptosis-related genes might provide clinical evidence for GBM interventions.

Identification of key genes associated with sepsis patients infected by staphylococcus aureus through weighted gene co-expression network analysis

The prevention and treatment of staphylococcus aureus septicemia is one of the thorniest problems in modern medicine. However, as the underlying pathogenesis of sepsis is still unclear, there is currently no golden standard for clinical diagnosis. In this study, we used GSE33341 dataset for differentially expressed gene (DEG) analysis and screened out 857 differentially expressed genes associated with staphylococcus aureus infection. The module having the highest correlation with clinical features of sepsis was screened by weighted gene co-expression network analysis (WGCNA). The genes in the selected module and the differentially expressed genes were represented in Venn diagram, and 59 pathogenic genes at the intersection were obtained. GO and KEGG analysis showed that these genes were mainly related to aerobic respiration, cellular stress response, mitochondrial electron transport, mitochondrial transport, oxidative phosphorylation. Kaplan-Meier was used to analyze the influence of the top 10 key genes on the prognosis of sepsis patients. The results showed that the high expression of NDUFA4, NDUFB3, COX7A2, ATP5J and COX7C was significantly correlated with the poor overall survival (OS) in patients with bacterial sepsis. These findings may potentially provide a reference for the diagnosis and treatment of bacterial septicemia.

The Role of Mitonuclear Incompatibility in Bipolar Disorder Susceptibility and Resilience Against Environmental Stressors

It has been postulated that mitochondrial dysfunction has a significant role in the underlying pathophysiology of bipolar disorder (BD). Mitochondrial functioning plays an important role in regulating synaptic transmission, brain function, and cognition. Neuronal activity is energy dependent and neurons are particularly sensitive to changes in bioenergetic fluctuations, suggesting that mitochondria regulate fundamental aspects of brain function. Vigorous evidence supports the role of mitochondrial dysfunction in the etiology of BD, including dysregulated oxidative phosphorylation, general decrease of energy, altered brain bioenergetics, co-morbidity with mitochondrial disorders, and association with genetic variants in mitochondrial DNA (mtDNA) or nuclear-encoded mitochondrial genes. Despite these advances, the underlying etiology of mitochondrial dysfunction in BD is unclear. A plausible evolutionary explanation is that mitochondrial-nuclear (mitonuclear) incompatibility leads to a desynchronization of machinery required for efficient electron transport and cellular energy production. Approximately 1,200 genes, encoded from both nuclear and mitochondrial genomes, are essential for mitochondrial function. Studies suggest that mitochondrial and nuclear genomes co-evolve, and the coordinated expression of these interacting gene products are essential for optimal organism function. Incompatibilities between mtDNA and nuclear-encoded mitochondrial genes results in inefficiency in electron flow down the respiratory chain, differential oxidative phosphorylation efficiency, increased release of free radicals, altered intracellular Ca²⁺ signaling, and reduction of catalytic sites and ATP production. This review explores the role of mitonuclear incompatibility in BD susceptibility and resilience against environmental stressors.

Transcriptome analysis of Corynebacterium pseudotuberculosis-infected spleen of dairy goats

Caseous lymphadenitis is a chronic disease of goats caused by Corynebacterium pseudotuberculosis (C.pseudotuberculosis) which causes great harm to the dairy goats industry. In order to obtain detailed information about the pathogenesis and host immune response in C.pseudotuberculosis-infected goats, in this study, the gene expression difference of spleen tissue after infection with C.pseudotuberculosis was analyzed by high-throughput sequencing. Transcripts obtained over 412 700 462 clean reads after reassembly were 21 343 genes detected, of which 14 720 were known genes and 7623 new genes were predicted. There were 448 up-regulated and 519 down-regulated differentially expressed genes (DEGs). Gene Ontology (GO) analysis indicated that all of the DEGs were annotated into biological process, cellular component and molecular function. Most of these unigenes are annotated in cellular processes, the cell and binding. KEGG analysis of the DEGs showed that a total of 8733 DEGs unigenes were annotated into 459 pathways classified into 6 main categories. Most of these annotated unigenes were related to immune system response to the infectious diseases pathways. In addition, 14 DEGs were verified by quantitative real-time PCR. As the first, in vivo, RNAseq analysis of dairy goats and C.pseudotuberculosis infection, this study provides knowledge about the transcriptomics of spleen in C.pseudotuberculosis-infected goats, from which a complex molecular pathways and immune response mechanism are involved in C.pseudotuberculosis infection.

Candidate genes mediated by estrogen-related receptor γ in pancreatic β cells

Recent studies have established the importance of estrogen-related receptor γ (ERRγ) as a required participant for insulin secretion in pancreatic β cells. Key downstream genes of ERRγ remain unclear in the pancreatic β cell. To understand the molecular role of ERRγ and elucidate potential key candidate genes involved in pancreatic β cells, the eukaryotic expression plasmid containing mouse ERRγ was constructed and transfected into NIT-1 pancreatic β cells. Overexpression of ERRγ was confirmed by quantitative real-time reverse-transcription polymerase chain reaction and Western blot analyses. RNA-seq was conducted to get the gene expression profiling between the overexpression group cells and control cells. Differentially expressed genes (DEGs) were identified by edgR and subsequently analyzed by gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. We found that overexpression of ERRγ in pancreatic β cells enables regulation of the expression of certain genes involved in cell apoptosis and mitochondrial function, such as TFPT, Bcl7c, Dap, Thoc6, Ube2d3, ATP5H, MPV17, and NDUFA6. GO analysis revealed that the DEGs were mainly enriched in apoptotic process, cytoplasm, and protein binding. KEGG pathway analysis demonstrated that downregulated DEGs were mainly enriched in protein processing in endoplasmic reticulum, estrogen signaling pathway, and metabolic pathways. This study helps to further understand and reposition the molecular mechanisms of ERRγ in β cells.

Fine-mapping scan of bipolar disorder susceptibility loci in Latino pedigrees

We previously identified bipolar disorder (BD) susceptibility loci on 8q24, 14q32, and 2q12-14 in a genome-wide nonparametric linkage screen in a Latino cohort. We now perform a fine mapping analysis using a dense map of additional SNPs to identify BD susceptibility genes within these regions. One thousand nine hundred and thirty-eight individuals with Latino ancestry (880 individuals with BD Type I or Schizoaffective, Bipolar Type) from 416 Latino pedigrees from the United States, Mexico, Costa Rica, and Guatemala were genotyped with 3,074 SNPs to provide dense coverage of the 8q24 (11.5 cM), 14q32 (7.5 cM), and 2q12-14 (6.5 cM) chromosomal loci. Single-marker association tests in the presence of linkage were performed using the LAMP software. The top linkage peak (rs7834818; LOD = 5.08, p = 3.30E - 5) and associated single marker (rs2280915, p = 2.70E - 12) were located within FBXO32 on 8q24. On chromosome 2, the top linkage peak (rs6750326; LOD = 5.06, p = 3.50E - 5) and associated single marker (rs11887088, p = 2.90E - 6) were located in intragenic regions near ACTR3 and DPP10. None of the additional markers in the region around chromosome 14q32 met significance levels for linkage or association. We identified six SNPs on 2q12-q14 and one SNP in FBXO32 on 8q24 that were significantly associated with BD in this Latino cohort.

Mitochondrial respiratory chain complex abnormal expressions and fusion disorder are involved in fluoride-induced mitochondrial dysfunction in ovarian granulosa cells

Excessive fluoride intake has a strong female reproductive toxicity, which can result in follicular developmental dysplasia and decrease oocytes developmental potential. The underlying mechanisms of fluoride-induced mitochondrial dysfunction in ovarian granulosa cells remain largely unknown. In this study, the ultrastructure changes of mitochondria and DNA damage in ovarian granulosa cells were observed under transmission electron microscope and TUNEL staining. Then, the ATP content and ROS level in granulosa cells were measured. The expression of mitochondrial fusion proteins and mitochondrial respiratory chain complexes, including OPA1 and Mfn1, and NDUFV2, SDHA and CYC1, in the ovarian tissues were measured by immunohistochemistry, Western blot and Quantitative real-time PCR analyses. The expression of ATP5j and ATP5h in the ovarian tissues was also measured. Results show that fluoride treatment considerably damages mitochondrial ultrastructure and enhances the apoptosis of granulosa cells. The ATP content greatly decreased, whereas the ROS level increased after fluoride treatment. The expression level of Mfn1 in the ovarian tissue was up-regulated, whereas OPA1 expression had no significant change. The expression levels of NDUFV2, SDHA and CYC1 were considerably up-regulated, and the expression of ATP5j and ATP5h were down-regulated after fluoride treatment. In summary, the damage in the mitochondrial ultrastructure, ATP content decrease, ROS level increase and the abnormal expression of OPA1, Mfn1, NDUFV2, SDHA, CYC1, ATP5j and ATP5h in ovary tissue are closely associated with fluoride-induced mitochondrial dysfunction, which might be responsible for the follicular developmental dysplasia and the potential decrease in oocyte development induced by fluoride in female mice.

Association between one-carbon metabolism indices and DNA methylation status in maternal and cord blood

One-carbon metabolism is essential for multiple cellular processes and can be assessed by the concentration of folate metabolites in the blood. One-carbon metabolites serve as methyl donors that are required for epigenetic regulation. Deficiencies in these metabolites are associated with a variety of poor health outcomes, including adverse pregnancy complications. DNA methylation is known to vary with one-carbon metabolite concentration, and therefore may modulate the risk of adverse pregnancy outcomes. This study addresses changes in one-carbon indices over pregnancy and the relationship between maternal and child DNA methylation and metabolite concentrations by leveraging data from 24 mother-infant dyads. Five of the 13 metabolites measured from maternal blood and methylation levels of 993 CpG sites changed over the course of pregnancy. In dyads, maternal and fetal one-carbon concentrations were highly correlated, both early in pregnancy and at delivery. The 993 CpG sites whose methylation levels changed over pregnancy in maternal blood were also investigated for associations with metabolite concentrations in infant blood at delivery, where five CpG sites were associated with the concentration of at least one metabolite. Identification of CpG sites that change over pregnancy may result in better characterization of genes and pathways involved in maintaining a healthy, term pregnancy.

ATP5J and ATP5H Proactive Expression Correlates with Cardiomyocyte Mitochondrial Dysfunction Induced by Fluoride

To investigate the effect of excessive fluoride on the mitochondrial function of cardiomyocytes, 20 healthy male mice were randomly divided into 2 groups of 10, as follows: control group (animals were provided with distilled water) and fluoride group (animals were provided with 150 mg/L F^- drinking water). Ultrastructure and pathological morphological changes of myocardial tissue were observed under the transmission electron and light microscopes, respectively. The content of hydrolysis ATP enzyme was observed by ATP enzyme staining. The expression levels of ATP5J and ATP5H were measured by Western blot and quantitative real-time PCR. The morphology and ultrastructure of cardiomyocytes mitochondrial were seriously damaged by fluoride, including the following: concentration of cardiomyocytes and inflammatory infiltration, vague myofilaments, and mitochondrial ridge. The damage of mitochondrial structure was accompanied by the significant decrease in the content of ATP enzyme for ATP hydrolysis in the fluoride group. ATP5J and ATP5H expressions were significantly increased in the fluoride group. Thus, fluoride induced the mitochondrial dysfunction in cardiomyocytes by damaging the structure of mitochondrial and interfering with the synthesis of ATP. The proactive ATP5J and ATP5H expression levels were a good response to the mitochondrial dysfunction in cardiomyocytes.

Psychiatric disorders biochemical pathways unraveled by human brain proteomics

Approximately 25 % of the world population is affected by a mental disorder at some point in their life. Yet, only in the mid-twentieth century a biological cause has been proposed for these diseases. Since then, several studies have been conducted toward a better comprehension of those disorders, and although a strong genetic influence was revealed, the role of these genes in disease mechanism is still unclear. This led most recent studies to focus on the molecular basis of mental disorders. One line of investigation that has risen in the post-genomic era is proteomics, due to its power of revealing proteins and biochemical pathways associated with biological systems. Therefore, this review compiled and analyzed data of differentially expressed proteins, which were found in postmortem brain studies of the three most prevalent psychiatric diseases: schizophrenia, bipolar disorder and major depressive disorders. Overviewing both the proteomic methods used in postmortem brain studies, the most consistent metabolic pathways found altered in these diseases. We have unraveled those disorders share about 21 % of proteins affected, and though most are related to energy metabolism pathways deregulation, the main differences found are 14-3-3-mediated signaling in schizophrenia, mitochondrial dysfunction in bipolar disorder and oxidative phosphorylation in depression.

Consistently altered expression of gene sets in postmortem brains of individuals with major psychiatric disorders

The measurement of gene expression in postmortem brain is an important tool for understanding the pathogenesis of serious psychiatric disorders. We hypothesized that major molecular deficits associated with psychiatric disease would affect the entire brain, and such deficits may be shared across disorders. We performed RNA sequencing and quantified gene expression in the hippocampus of 100 brains in the Stanley Array Collection followed by replication in the orbitofrontal cortex of 57 brains in the Stanley Neuropathology Consortium. We then identified genes and canonical pathway gene sets with significantly altered expression in schizophrenia and bipolar disorder in the hippocampus and in schizophrenia, bipolar disorder and major depression in the orbitofrontal cortex. Although expression of individual genes varied, gene sets were significantly enriched in both of the brain regions, and many of these were consistent across diagnostic groups. Further examination of core gene sets with consistently increased or decreased expression in both of the brain regions and across target disorders revealed that ribosomal genes are overexpressed while genes involved in neuronal processes, GABAergic signaling, endocytosis and antigen processing have predominantly decreased expression in affected individuals compared to controls without a psychiatric disorder. Our results highlight pathways of central importance to psychiatric health and emphasize messenger RNA processing and protein synthesis as potential therapeutic targets for all three of the disorders.