Oxidative Phosphorylation Pathway Research Articles

Pyruvate Dehydrogenase Kinase 1 inhibition mediated oxidative phosphorylation enhancement in cartilage promotes osteoarthritis progression

Osteoarthritis (OA) is a common disease characterized by cartilage degradation. Growing evidence showed that glucose metabolism impacts joint homeostasis and an imbalance between glycolysis and oxidative phosphorylation (OXPHOS) may exacerbate OA progression, however, a definitive link is yet to be established. Here, we report that pyruvate metabolism and oxidative phosphorylation pathway is enriched in OA cartilage through gene set enrichment analysis (GSEA) and expression of Pyruvate Dehydrogenase Kinase 1 (PDK1), an enzyme that can phosphorylate Pyruvate Dehydrogenase (PDH), and inhibit pyruvate fluxes into the tricarboxylic acid (TCA) cycle and to OXPHOS, in articular cartilage is notably reduced through destabilization of medial meniscus (DMM). Moreover, by inhibiting PDK1, cartilage loss is markedly accelerated in DMM-induced OA through extracellular matrix (ECM) degradation and apoptosis of chondrocytes. These results indicate that PDK1 is involved in the progression of OA through accelerating cartilage matrix degradation and synovium inflammation to ameliorate cartilage degeneration.

Procine recombinant NK-lysin inhibits hepatocellular carcinoma metastasis by downregulating FKBP3 and inhibiting oxidative phosphorylation and glycolysis: a proteomic analysis

To investigate the potential mechanisms that mediate the inhibitory effect of porcine recombinant NKlysin (prNK-lysin) against liver cancer cell metastasis. HPLC-tandem mass spectrometry was used to identify the differentially expressed proteins in prNK-lysin-treated hepatocellular carcinoma SMMOL/LC-7721 cells in comparison with the control and PBS-treated cells. GO functional annotation and KEGG pathway analysis of the differentially expressed proteins were performed using GO and KEGG databases. RT-qPCR was used to determine the mRNA expression levels of polypeptide-N-acetylgalactosaminotransferase 13 (GALNT13), transmembrane protein 51 (TMEM51) and FKBP prolyl isomerase 3 (FKBP3) in the cells, and the protein expression of FKBP3 was verified using Western blotting. Proteomic analysis identified 1989 differentially expressed proteins in prNK-lysin-treated cells compared with the control cells, and 2753 compared with PBS-treated cells. Fifteen proteins were differentially expressed between PBS-treated and the control cells, and 1909 were differentially expressed in prNK- lysin group compared with both PBS and control groups. These differentially expressed proteins were involved mainly in the viral process, translational initiation and RNA binding and were enriched mainly in ribosome, protein process in endoplasmic reticulum, and RNA transport pathways. RT-qPCR showed that compared with the control group, prNK-lysin treatment significantly increased the mRNA expressions of GALNT13 (P < 0.05) and TMEM51 (P < 0.01) and lowered FKBP3 mRNA expression (P < 0.05). Western blotting also showed a significantly decreased expression of FKBP3 protein in prNK-lysin-treated cells (P < 0.001). Treatment with prNK-lysin causes significant changes in protein expression profile of SMMOL/LC-7721 cells and inhibits hepatocellular carcinoma metastasis by downregulating FKBP3 protein and affecting the cellular oxidative phosphorylation and glycolysis pathways.

Congenital cataracts affect the retinal visual cycle and mitochondrial function: A multi-omics study of GJA8 knockout rabbits

Congenital cataracts are a threat to visual development in children, and the visual impairment persists after surgical treatment; however, the mechanisms involved remain unclear. Previous clinical studies have identified the effect of congenital cataracts on retinal morphology and function. To further understand the molecular mechanisms by which congenital cataracts affect retinal development, we analyzed retina samples from 7-week-old GJA8-knockout rabbits with congenital cataracts and controls by four-dimensional label-free quantification proteomics and untargeted metabolomics. Bioinformatics analysis of proteomic data showed that retinol metabolism, oxidative phosphorylation, and fatty acid degradation pathways were downregulated in the retinas of rabbits with congenital cataracts, indicating that their visual cycle and mitochondrial function were affected. Additional validation of differentially abundant proteins related to the visual cycle and mitochondrial function was performed using Parallel reaction monitoring and western blot experiments. Untargeted metabolome analysis showed significant upregulation of the antioxidant glutathione and ascorbic acid in the retinas of rabbits with congenital cataracts, indicating that their oxidative stress balance was not dysregulated. SignificanceCongenital cataracts in children can alter retinal structure and function, yet the mechanisms are uncertain. Here is the first study to use proteomics and metabolomics approaches to investigate the effects of congenital cataracts on retinal development in the early postnatal period. Our findings suggest that congenital cataracts have an impact on the retinal visual cycle and mitochondrial function. These findings give insight on the molecular pathways behind congenital cataract-induced visual function impairment in the early postnatal period.

Exploring biomarkers of premature ovarian insufficiency based on oxford nanopore transcriptional profile and machine learning

Premature ovarian insufficiency (POI) is a reproductive endocrine disorder characterized by infertility and perimenopausal syndrome, with a highly heterogeneous genetic etiology and its mechanism is not fully understood. Therefore, we utilized Oxford Nanopore Technology (ONT) for the first time to characterize the full-length transcript profile, and revealed biomarkers, pathway and molecular mechanisms for POI by bioinformatics analysis and machine learning. Ultimately, we identified 272 differentially expressed genes, 858 core genes, and 25 hub genes by analysis of differential expression, gene set enrichment, and protein–protein interactions. Seven candidate genes were identified based on the intersection features of the random forest and Boruta algorithm. qRT-PCR results indicated that COX5A, UQCRFS1, LCK, RPS2 and EIF5A exhibited consistent expression trends with sequencing data and have potential as biomarkers. Additionally, GSEA analysis revealed that the pathophysiology of POI is closely associated with inhibition of the PI3K-AKT pathway, oxidative phosphorylation and DNA damage repair, as well as activation of inflammatory and apoptotic pathways. Furthermore, we emphasize that downregulation of respiratory chain enzyme complex subunits and inhibition of oxidative phosphorylation pathways play crucial roles in the pathophysiology of POI. In conclusion, our utilization of long-read sequencing has refined the annotation information within the POI transcriptional profile. This valuable data provides novel insights for further exploration into molecular regulatory networks and potential biomarkers associated with POI.

Growth, biochemical indices and transcriptomic profile of Chinese mitten crab (Eriocheir sinensis) respond to different ratios of dietary carbohydrates to lipids

IntroductionAlthough carbohydrates and lipids are important energy substances for Chinese mitten crab (Eriocheir sinensis), little is known about their synergistic effect on the growth, energy utilization characteristics and mechanisms involved in this process.MethodsA 58-d feeding experiment was conducted to investigate the effects of dietary carbohydrate to lipid ratio (C/L) on the growth performance, biochemical indices, and metabolism-related differential gene expression of juvenile E. sinensis in both intermolt (InM) and premolt (PrM) stages. Five experimental diets were formulated with increasing dietary C/L (1.34, 2.39, 3.59, 5.52 and 9.42).ResultsThe results showed that the weight growth rate of juvenile E. sinensis was highest in dietary C/L3.59 group, which was significantly higher than that in the other groups. As dietary C/L increased, the hepatic glycogen contents increased, but triglyceride contents decreased in the hepatopancreas of E. sinensis in the InM. In both two molting stages, the activities of glycogen synthase and fatty acid synthase paralleled with their contents, respectively. Crabs in the InM showed higher contents of triglyceride and the activities of glycolytic rate-limiting enzymes but lower contents of hepatic glycogen than those in the PrM, especially in the C/L 1.34 and C/L 3.59 groups. In all dietary groups, the activities and transcription of gluconeogenesis and fatty acid synthesis related enzymes were significantly higher in the InM than those in the PrM. KEGG analysis showed that differential genes were enriched in fatty acid biosynthesis, fatty acid metabolism, oxidative phosphorylation pathway, pentose phosphate pathway, pyruvate metabolism and steroid biosynthesis between different dietary groups and molting stages.DiscussionTo conclude, the optimal dietary C/L was estimated to be 3.59 for juvenile E. sinensis based on the survival and growth performance. Compared to PrM, E. sinensis in the InM was more active in the carbohydrate metabolism (glycolysis and gluconeogenesis) and fatty acid synthesis, with more triglyceride and less glycogen accumulated in the hepatopancreas.This study could contribute to better understanding the carbohydrate and lipid metabolism between different molting stages, and optimizing the precise feed formulation for juvenile E. sinensis.

Transcriptome and hypoxia-responsive gene expression analyses reveal the physiological reaction to acute hypoxia and reoxygenation in Epinephelus coioides

Dissolved oxygen (DO) is crucial for fish farming, and when fish experience hypoxic stress, negative effects such as the disruption of normal physiological activities, a decline in aerobic swimming ability, and feeding restriction will occur. In this study, healthy Epinephelus coioides individuals were subjected to hypoxic (DO = 0.6 ± 0.1 mg/L) and reoxygenation treatments (DO = 6.0 ± 0.1 mg/L), with a normoxic group (DO = 6.0 ± 0.1 mg/L) set as the control. Transcriptome sequencing (RNA-seq) was performed on the brains of E. coioides in hypoxia-sensitive (EBW), hypoxia-tolerant (EBS), and normoxic control (CB) groups. In total, 1174 differentially expressed genes (DEGs) were screened from the three groups. KEGG analysis revealed several pathways, including the HIF-1 signaling pathway, and immune-related pathways such as MAPK signaling, microRNAs (miRNAs), and oxidative phosphorylation pathways enriched in the EBS group, and cAMP signaling pathway enriched in the EBW group. Moreover, a variety of significant hypoxia-responsive DEGs involved in energy metabolism and immune reactions were identified in the EBS and EBW groups. qRTPCR analysis showed that the key DEGs HIF-1α, LDH-A, PPARα, PNP, RAB13, DDIT4, TNF-1, and ALDOA were significantly upregulated in the brain tissues of E. coioides under acute hypoxic stress and that their expression returned to normoxic levels after reoxygenation, indicating that they provided energy to the organism and regulated severe damage and lesions appearing in the brains of E. coioides during hypoxic stress to prolong the survival time of the organism. Altogether, these results suggest that hypoxia disrupts the expression patterns of multiple genes in E. coioides and that these genes may participate in resistance and adaptation to hypoxia in the organisms by regulating apoptosis, proliferation, differentiation, and energy metabolism.

METTL5 serves as a diagnostic and prognostic biomarker in hepatocellular carcinoma by influencing the immune microenvironment

Despite the abnormal expression of 18S rRNA m6A methyltransferase METTL5 being reported in some types of human malignancies, but its effect on hepatocellular carcinoma (HCC) remains to be unclear. This study aims to elucidate the influences of METTL5 on the carcinogenesis and progression of HCC. Expressions of METTL5 gene, transcript, protein, and promoter methylation in HCC were examined through multiple databases, c-BioPortal was used to confirm the genomic alterations of METTL5, the biological functions, target networks of kinases and microRNAs of METTL5, and its interactive differential genes were investigated through LinkedOmics. The possible correlation of METTL5 with the tumor-related infiltration of immune cells for HCC were explored comprehensively by using the online tools of TIMER and TISIDB. Expressions of METTL5 gene, mRNA, and protein were considerably overexpressed in HCC samples in comparison with healthy samples. The high methylation of the METTL5 promoter was observed in HCC tissues. Elevated METTL5 expression exhibited unfavorable survival outcomes in HCC patients. METTL5 expression were enriched in the signaling pathways of ribosome and oxidative phosphorylation, mismatch repair, and spliceosome through the involvement of several cancer-related kinases and miRNAs. The METTL5 expression has a positive correlation with the infiltration degree of B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells in HCC. Marker genes of tumor immune-infiltrated cells have strong connection with METTL5. Furthermore, the upregulation of METTL5 was strongly correlated with the immune regulation of immunomodulators, chemokines, and chemokine receptors in the immune microenvironment. The oncogenesis and development of HCC are closely related to METTL5 expression, and the overexpression of METTL5 resulted in the poor survival outcome of HCC patients by regulating tumor immune microenvironment.

Machine learning reveals common transcriptomic signatures across rat brain and placenta following developmental organophosphate ester exposure.

Toxicogenomics is a critical area of inquiry for hazard identification and to identify both mechanisms of action and potential markers of exposure to toxic compounds. However, data generated by these experiments are highly dimensional and present challenges to standard statistical approaches, requiring strict correction for multiple comparisons. This stringency often fails to detect meaningful changes to low expression genes and/or eliminate genes with small but consistent changes particularly in tissues where slight changes in expression can have important functional differences, such as brain. Machine learning offers an alternative analytical approach for "omics" data that effectively sidesteps the challenges of analyzing highly dimensional data. Using 3 rat RNA transcriptome sets, we utilized an ensemble machine learning approach to predict developmental exposure to a mixture of organophosphate esters (OPEs) in brain (newborn cortex and day 10 hippocampus) and late gestation placenta of male and female rats, and identified genes that informed predictor performance. OPE exposure had sex specific effects on hippocampal transcriptome, and significantly impacted genes associated with mitochondrial transcriptional regulation and cation transport in females, including voltage-gated potassium and calcium channels and subunits. To establish if this holds for other tissues, RNAseq data from cortex and placenta, both previously published and analyzed via a more traditional pipeline, were reanalyzed with the ensemble machine learning methodology. Significant enrichment for pathways of oxidative phosphorylation and electron transport chain was found, suggesting a transcriptomic signature of OPE exposure impacting mitochondrial metabolism across tissue types and developmental epoch. Here we show how machine learning can complement more traditional analytical approaches to identify vulnerable "signature" pathways disrupted by chemical exposures and biomarkers of exposure.

Ldlr-/-.Leiden mice develop neurodegeneration, age-dependent astrogliosis and obesity-induced changes in microglia immunophenotype which are partly reversed by complement component 5 neutralizing antibody.

Obesity has been linked to vascular dysfunction, cognitive impairment and neurodegenerative diseases. However, experimental models that recapitulate brain pathology in relation to obesity and vascular dysfunction are still lacking. In this study we performed the histological and histochemical characterization of brains from Ldlr-/-.Leiden mice, an established model for obesity and associated vascular disease. First, HFD-fed 18 week-old and 50 week-old Ldlr-/-.Leiden male mice were compared with age-matched C57BL/6J mice. We then assessed the effect of high-fat diet (HFD)-induced obesity on brain pathology in Ldlr-/-.Leiden mice and tested whether a treatment with an anti-complement component 5 antibody, a terminal complement pathway inhibitor recently shown to reduce vascular disease, can attenuate neurodegeneration and neuroinflammation. Histological analyses were complemented with Next Generation Sequencing (NGS) analyses of the hippocampus to unravel molecular pathways underlying brain histopathology. We show that chow-fed Ldlr-/-.Leiden mice have more severe neurodegeneration and show an age-dependent astrogliosis that is not observed in age-matched C57BL/6J controls. This was substantiated by pathway enrichment analysis using the NGS data which showed that oxidative phosphorylation, EIF2 signaling and mitochondrial dysfunction pathways, all associated with neurodegeneration, were significantly altered in the hippocampus of Ldlr-/-.Leiden mice compared with C57BL/6J controls. Obesity-inducing HFD-feeding did not aggravate neurodegeneration and astrogliosis in Ldlr-/-.Leiden mice. However, brains from HFD-fed Ldlr-/-.Leiden mice showed reduced IBA-1 immunoreactivity and increased CD68 immunoreactivity compared with chow-fed Ldlr-/-.Leiden mice, indicating alteration of microglial immunophenotype by HFD feeding. The systemic administration of an anti-C5 treatment partially restored the HFD effect on microglial immunophenotype. In addition, NGS data of hippocampi from Ldlr-/-.Leiden mice showed that HFD feeding affected multiple molecular pathways relative to chow-fed controls: HFD notably inactivated synaptogenesis and activated neuroinflammation pathways. The anti-C5 treatment restored the HFD-induced effect on molecular pathways to a large extent. This study shows that the Ldlr-/-.Leiden mouse model is suitable to study brain histopathology and associated biological processes in a context of obesity and provides evidence of the potential therapeutic value of anti-complement therapy against obesity-induced neuroinflammation.

Identification and Analysis of DNA Methylation Inflammation-Related Key Genes in Intracerebral Hemorrhage.

Inflammation and DNA methylation have been reported to play key roles in intracerebral hemorrhage (ICH). This study aimed to investigate new diagnostic biomarkers associated with inflammation and DNA methylation using a comprehensive bioinformatics approaches. GSE179759 and GSE125512 were collected from the Gene Expression Omnibus database, and 3222 inflammation-related genes (IFRGs) were downloaded from the Molecular Signatures Database. Key differentially expressed methylation-regulated and inflammation-related genes (DE-MIRGs) were identified by overlapping methylation-regulated differentially expressed genes (MeDEGs) between patients with ICH and control samples, module genes from weighted correlation network analysis, and IFRGs. Functional annotation of DE-MIRGs was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). A protein-protein interaction (PPI) network was constructed to clarify the interrelationships between different DE-MIRGs. The key genes were categorized by least absolute shrinkage selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE), and gene set enrichment analysis (GSEA). A total of 22 DE-MIRGs were acquired from 451 MeDEGs, 3222 IFRGs, and 302 module genes, and were mainly enriched in the GO terms of wound healing, blood coagulation, and hemostasis; and the KEGG pathways of PI3K/Akt signaling, focal adhesion, and regulation of actin cytoskeleton. A PPI network with 22 nodes and 87 edges was constructed based on the 22 DE-MIRGs, 11 of which were selected for key gene selection. Two 2 key genes (SELP and S100A4) were identified using LASSO and SVM-RFE. Finally, SELP was mainly enriched in cell morphogenesis involved in differentiation, cytoplasmic translation, and actin binding of GO terms, and the KEGG pathway including endocytosis, focal adhesion, and platelet activation. S100A4 was mainly enriched in GO terms including mitochondrial inner membrane; mitochondrial respirasome and lysosomal membrane; and the KEGG pathway of oxidative phosphorylation, regulation of actin cytoskeleton, and chemical carcinogenesis-reactive oxygen species. Twenty-two DE-MIRGs-associated inflammation and DNA methylation were identified between patients with ICH and normal controls, and two key genes (SELP and S100A4) were identified and regarded as biomarkers for ICH, which could provide the research foundation for further investigation of the pathological mechanism of ICH.

5-OR: Adipocyte ANGPTL8 Regulates Insulin Sensitivity and Thermogenic Programing

ANGPTL8 (A8), expressed mainly in the liver and adipocytes, regulates lipoprotein lipase (LPL) and lipid metabolism. Hepatic A8 and ANGPTL3 form a complex that inhibits LPL. However, the precise intracellular role of A8 in adipocytes is yet to be explored. We observed that RNAi-knockdown of A8 in mouse primary subcutaneous (SC) pre-adipocytes reduces adipocyte differentiation, glycerol, and fatty acid release at day 7 post-differentiation. RNAseq analysis of A8 siRNA or control siRNA transfected SC pre-adipocytes on days 0, 2, 4 and 7 of differentiation showed that A8 silencing impeded adipogenic and oxidative phosphorylation pathways and reduced expression of insulin signaling pathway genes IRS1, IRS2, PPARG, mTOR, early during differentiation, suggesting a role for A8 in the regulation of insulin sensitivity. Next, we investigated the functional role of adipose A8 by generating conditional adipocyte-specific A8 Knockout (AT-A8-KO) mice. AT-A8-KO mice on 45% high fat diet (HFD) with 30% fructose for 20 weeks showed a decrease in body weight gain, glycemia, brown fat mass, plasma TG and smaller cell size of SC adipocytes, while increased rectal temperature compared to controls. Interestingly, OGTT revealed AT-A8-KO mice in control diet or in HFD have significantly lower insulinemia. ITT results confirmed significant improvement of insulin sensitivity of AT-A8-KO mice on HFD. In addition, upon exposure to 6°C for 24h, AT-A8-KO mice exhibited elevated body temperature and energy expenditure compared to control mice, indicating that adipose tissue A8 negatively modulates cold-induced thermogenesis. Our results reveal that A8 regulates in vitro adipocyte differentiation, probably by modulating insulin signaling and mitochondrial respiration, and that deletion of adipocyte A8 in mice enhances insulin sensitivity, cold induced body temperature and energy expenditure. Therefore, targeting adipose specific A8 may be beneficial in promoting insulin sensitivity and preventing obesity. Disclosure A.Ghosh: None. I.Al-khairi: None. J.Abubaker: None. F.Al-mulla: None. M.Abu-farha: None. M.Prentki: None. Y.H.Leung: None. J.C.Y.Yu: None. R.M.Sladek: None. I.Chenier: None. A.Oppong: None. M.Peyot: None. M.Madiraju: None. Funding Dasman Diabetes Institute (731)

Induce male sterility by CRISPR/Cas9-mediated mitochondrial genome editing in tobacco.

Genome editing has become more and more popular in animal and plant systems following the emergence of CRISPR/Cas9 technology. However, target sequence modification by CRISPR/Cas9 has not been reported in the plant mitochondrial genome, mtDNA. In plants, a type of male sterility known as cytoplasmic male sterility (CMS) has been associated with certain mitochondrial genes, but few genes have been confirmed by direct mitochondrial gene-targeted modifications. Here, the CMS-associated gene (mtatp9) in tobacco was cleaved using mitoCRISPR/Cas9 with a mitochondrial localization signal. The male-sterile mutant, with aborted stamens, exhibited only 70% of the mtDNA copy number of the wild type and exhibited an altered percentage of heteroplasmic mtatp9 alleles; otherwise, the seed setting rate of the mutant flowers was zero. Transcriptomic analyses showed that glycolysis, tricarboxylic acid cycle metabolism and the oxidative phosphorylation pathway, which are all related to aerobic respiration, were inhibited in stamens of the male-sterile gene-edited mutant. In addition, overexpression of the synonymous mutations dsmtatp9 could restore fertility to the male-sterile mutant. Our results strongly suggest that mutation of mtatp9 causes CMS and that mitoCRISPR/Cas9 can be used to modify the mitochondrial genome of plants.

ChIP-Seq Analysis of SlAREB1 Downstream Regulatory Network during Tomato Ripening.

SlAREB1, a member of the abscisic acid (ABA) response element-binding factors (AREB/ABFs) family, was reported to play a crucial role in the expression of ABA-regulated downstream genes and affect the ripening of tomato fruit. However, the downstream genes of SlAREB1 are still unclear. Chromatin immunoprecipitation (ChIP) is a powerful tool and a standard method for studying the interactions between DNA and proteins at the genome-wide level. In the present study, SlAREB1 was proved to continually increase until the mature green stage and then decrease during the ripening period, and a total of 972 gene peaks were identified downstream of SlAREB1 by ChIP-seq analysis, mainly located in the intergenic and promoter regions. Further gene ontology (GO) annotation analysis revealed that the target sequence of SlAREB1 was the most involved in biological function. Kyoto Encylopaedia of Genes and Genomes (KEGG) pathway analysis showed that the identified genes were mainly involved in the oxidative phosphorylation and photosynthesis pathways, and some of them were associated with tomato phytohormone synthesis, the cell wall, pigment, and the antioxidant characteristic of the fruit as well. Based on these results, an initial model of SlAREB1 regulation on tomato fruit ripening was constructed, which provided a theoretical basis for further exploring the effects of the regulation mechanism of SlAREB1 and ABA on tomato fruit ripening.

XRT-02. SINGLE-CELL RNA SEQUENCING IDENTIFIES FUNCTIONAL MACROPHAGE SUBSETS THAT ARE ENRICHED IN RESPONSE TO DIFFERENTIAL PHAGOCYTOSIS INDUCTION AGAINST GLIOMA

Abstract Pediatric diffuse midline gliomas (DMGs), are fatal brain tumors of childhood arising in the ventral pons. Currently, radiation therapy (RT) is the mainstay treatment for DIPG. However, RT is not a curative treatment and provides only temporary relief for most patients. Recent advances in immunotherapy have yielded some fantastic opportunities to effectively treat patients with high-grade pediatric brain tumors. In this study, we demonstrate that fractionated RT (4Gy X 3) induces immunogenic cell death and activates multiple damage-associated molecular patterns (DAMPs) on DMG/DIPG cells. Furthermore, combining 4Gy X 3 with anti-CD47 therapy enhances the in vitro phagocytosis of DIPG/DMG cells by peripheral blood mononuclear cell-derived macrophages. Next, using single-cell RNA sequencing (scRNA-seq), we investigated the transcriptomic profile of macrophages that were co-cultured with irradiated or non-irradiated DMG cells in the presence of anti-CD47 monoclonal antibodies for 24 hours. Our findings identified eleven distinct macrophage clusters displaying different gene expression patterns in all the treatment conditions. However, PBS treatment led to a marked increase in macrophages expressing antigen-presentation genes (HLA-DR and HLA-DQB1). 4Gy X 3 treatment led to the enrichment of macrophages expressing genes related to the oxidative phosphorylation pathway, whereas anti-CD47 treatment led to the enrichment of macrophages expressing genes related to interferon-gamma response and ERK-signaling pathway. Lastly, mice intracranially transplanted with DMG/DIPG that received 4Gy X 3 and anti-CD47 therapy showed a significant decrease in tumor growth and an increase in survival rate than those receiving either monotherapy alone. We are currently performing scRNA-seq validation studies on tumors obtained from orthotopic and syngeneic models of DMG. In summary, our results highlight the functional heterogeneity of macrophages and suggest that combining fractionated RT with anti-CD47 therapy has distinct anti-tumor effects and can be used as a therapeutic approach for treating DIPG patients.

Examination of the effects of dry storage stress on mitochondrial energy synthesis in the scallop Mizuhopecten yessoensis

Postharvest dry storage was simulated by storing scallops at 4 °C for different durations. The quantification of 40 energy metabolites related to the glycolysis, tricarboxylic acid (TCA) cycle and oxidative phosphorylation pathways in the scallop adductor muscle was performed by LC–MS/MS. The results showed that during the early stage (0–6 h), 6-phosphofructokinase-2 (PFK-2) in glycolysis was inhibited, and the TCA cycle was maintained at a low level. Concurrently, the aspartate pathway and opine pathway were initiated, and alanine and opines were the early metabolites found during this stage. During the middle and late stages (6–12 h) of dry storage, muscle pH decreased. Phosphoenolpyruvate carboxy kinase (PEPCK) was activated, leading to the competitive inhibition of pyruvate synthesis by PEPCK. Phosphoenolpyruvate enters the reverse TCA cycle via the phosphoenolpyruvate → malate pathway to produce succinate. The increase in succinate further induced the succinyl-CoA → propionate pathway, and the end products were acetate and propionate. Alteration of the metabolic pathway was observed, leading to a change in the NADH level. Subsequently, a fluctuating mitochondrial membrane potential was observed. Reimmersion after 6 h of dry storage promoted the recovery of the muscle TCA cycle. Nevertheless, after long-term dry storage (24 h), reimmersion storage did not restore the succinate → oxaloacetate metabolism in the TCA cycle. High-intensity air exposure had a long-term and irreversible effect on mitochondrial energy metabolism. Therefore, it is concluded that the dynamics of mitochondrial metabolism may be sensitive to dry exposure during postharvest operations.

The conditional mitochondrial protein complexome in the Arabidopsis thaliana root and shoot

Protein complexes are important for almost all biological processes. Hence, to fully understand how cells work, it is also necessary to characterize protein complexes and their dynamics in response to various cellular cues. Moreover, the dynamics of protein interaction play crucial roles in regulating the (dis)association of protein complexes and, in turn, regulating biological processes such as metabolism. Here, mitochondrial protein complexes were investigated by blue native PAGE and size-exclusion chromatography under conditions of oxidative stress in order to monitor their dynamic (dis)associations. Rearrangements of enzyme interactions and changes in protein complex abundance were observed in response to oxidative stress induced by menadione treatment. These included changes in enzymatic protein complexes involving γ-amino butyric acid transaminase (GABA-T), Δ-ornithine aminotransferase (Δ-OAT), or proline dehydrogenase 1 (POX1) that are expected to affect proline metabolism. Menadione treatment also affected interactions between several enzymes of the tricarboxylic acid (TCA) cycle and the abundance of complexes of the oxidative phosphorylation pathway. In addition, we compared the mitochondrial complexes of roots and shoots. Considerable differences between the two tissues were observed in the mitochondrial import/export apparatus, the formation of super-complexes in the oxidative phosphorylation pathway, and specific interactions between enzymes of the TCA cycle that we postulate may be related to the metabolic/energetic requirements of roots and shoots.

Dammarane-type saponins from Gynostemma pentaphyllum and their anti-aging activities via up-regulating mitochondria related proteins

The importance of mitochondria in regulation of aging has been extensively recognized and confirmed. Gynostemma pentaphyllum (Thunb.) Makino, a homology of medicine and food, has been widely utilized as dietary supplement. In this study, the transcriptome of normal cells (wild type mouse embryo fibroblasts) regulated by the 30% aqueous EtOH extract of G. pentaphyllum was firstly evaluated by RNA sequencing and the results revealed that the G. pentaphyllum could up-regulate the genes involved in oxidative phosphorylation (OXPHOS) and sirtuin (SIRT) signaling pathways, indicating its effect in promoting cell viability might be attributed to the role of improving mitochondrial functions. To further discover the bioactive compounds, sixteen undescribed dammarane-type saponins along with twenty-eight known analogues were isolated from the active extract of G. pentaphyllum. Their structures were elucidated by means of comprehensive analysis of NMR and HRMS spectroscopic data. All isolates were evaluated for the regulatory effects on SIRT3 and translocase of the outer membrane 20 (TOM20), and thirteen of them exhibited satisfactory agonist activities on both SIRT3 and TOM20 at 5 μM. Furthermore, the preliminary structure-activity relationships analysis demonstrated the additional hydroxymethyl and carbonyl groups or less sugar residues in saponins could contribute positively to the up-regulatory effect on SIRT3 and TOM20. These findings encouraged the potential roles of G. pentaphyllum and its bioactive saponins in the development of natural drugs for the treatment of aging-related diseases.

Different microplastics in anaerobic paddy soils: Altering methane emissions by influencing organic matter composition and microbial metabolic pathways

Microplastics are widespread in farmland and threaten soil ecology. However, how different microplastics affect methane emission in paddy soil are still unclear. To address this knowledge gap, three typical microplastics, polyethylene, polypropylene, and polyvinyl chloride were added to paddy soil with different doses (0.01%, 0.1%, and 1%), and a 50-day incubation experiment was conducted. Compared with polyethylene and polypropylene microplastics, 1% of polyvinyl chloride microplastic resulted in the highest increase in methane production. According to the integrated liquid phase analysis, all three microplastics contributed to the accumulation of humus in the soil solution. Differential microbial taxa analysis indicated that some denitrifying bacteria such as Gemmatimonadetes and Omnitrophicaeota were significantly enriched in 1% polyethylene and polypropylene microplastics groups on day 30, and Rice Cluster I methanogens archaea were enriched specially in the 1% polyvinyl chloride microplastic group. The predicted soil metabolic functions suggested that polyethylene and polyvinyl chloride microplastics enhanced oxidative phosphorylation and amino acid reduction pathways. Macromolecular humus induced by microplastics may play a critical role in the dynamic equilibrium of anaerobic systems in paddy soils. These findings highlighted the threat of microplastics in agricultural fields greenhouse gas emissions. The identified quinone reductive metabolic pathways may provide potential strategies to reduce methane emissions.

Transcriptomic Analysis of Three Differentially Senescing Maize (Zea mays L.) Inbred Lines upon Heat Stress.

Maize, one of the world's major food crops, is facing the challenge of rising temperature. Leaf senescence is the most significant phenotypic change of maize under heat stress at the seedling stage, but the underlying molecular mechanism is still unknown. Here, we screened for three inbred lines (PH4CV, B73, and SH19B) that showed differentially senescing phenotypes under heat stress. Among them, PH4CV showed no obviously senescing phenotype under heat stress, while SH19B demonstrated a severely senescing phenotype, with B73 being between the two extremes. Subsequently, transcriptome sequencing showed that differentially expressed genes (DEGs) were generally enriched in response to heat stress, reactive oxygen species (ROS), and photosynthesis in the three inbred lines under heat treatment. Notably, ATP synthesis and oxidative phosphorylation pathway genes were only significantly enriched in SH19B. Then, the expression differences of oxidative phosphorylation pathways, antioxidant enzymes, and senescence-related genes in response to heat stress were analyzed in the three inbred lines. In addition, we demonstrated that silencing ZmbHLH51 by virus-induced gene silencing (VIGS) inhibits the heat-stress-induced senescence of maize leaves. This study helps to further elucidate the molecular mechanisms of heat-stress-induced leaf senescence at the seedling stage of maize.

Sevoflurane inhibited reproductive function in male mice by reducing oxidative phosphorylation through inducing iron deficiency.

Sevoflurane (Sev) is one of the commonly used inhalation anesthetic chemicals in clinics. It has great impact on spermatogenesis and fertilization in male animals. The underlying mechanism remains largely unexplored. Based on our previous research, we hypothesized that Sev induced iron metabolism disturbance in the testis and epididymis and inhibited the spermatogenesis. In this study, two-month-old C57BL/6 male mice were treated with 3% Sev for 6h, and their fertility (including sperm concentration, sperm mobility, and the number of offspring) was evaluated. Mice testis, epididymis, and sperm were harvested and subjected to Western blot analysis and immunofluorescence analysis. Iron levels were reflected by the gene expression of iron metabolism-related proteins (including ferritin, TfR1, and FpN1) and ICP-MS and Perl's iron staining. Electron transport and oxidative phosphorylation levels were measured by Oxygraph-2k and ATP contents. The activity of ribonucleotide reductase was evaluated by assay kit. DNA synthesis status in testis and/or epididymis was marked with BrdU. Cell proliferation was evaluated by double immunofluorescence staining of specific protein marker expression. Our results revealed that the mice exposed to Sev showed damaged testicular and epididymis structure and significantly reduced the sperm concentration, sperm motility, and fertility. Sev decreases the iron levels through down-regulating the expression of H-ferritin, L-ferritin, and FpN1, and up-regulating the expression of TfR1 in the testis and epididymis. Iron levels also significantly reduced in germ cells which decrease the number of germ cells, including sperm, Sertoli cells, and primary spermatocyte. Iron deficiency not only decreases electron transport, oxidative phosphorylation level, and ATP production but also suppresses the activity of ribonucleotide reductase and the expression of Ki67, DDX4, GATA1, and SCP3, indicating that Sev affects the spermatogenesis and development. Meanwhile, Sev impaired the blood-testis barrier by decreasing the ZO1 expression in the testis and epididymis. The damage effect induced by Sev can be significantly ameliorated by iron supplementation. In conclusion, our study illustrates a new mechanism by which Sev inhibits spermatogenesis and fertility through an oxidative phosphorylation pathway due to iron deficiency of epididymis and testis or sperm. Furthermore, the damaging effects could be ameliorated by iron supplementation.