Mitochondrial outer membrane protein Samm50 protects against hypoxia-induced cardiac injury by interacting with Shmt2.

Cardiac remodeling is a critical process following myocardial infarction (MI), potentially leading to heart failure if untreated. The significance of mitochondrial homeostasis in MI remains insufficiently understood. Samm50 is an essential component of mitochondria. Our study aimed to investigate its role in hypoxia-induced cardiac injury and the underlying mechanisms. First, we observed that Samm50 was dynamically downregulated in mice with MI compared to the control mice. In vitro, Samm50 was also downregulated in oxygen-glucose-deprived neonatal rat cardiomyocytes and fibroblasts. Overexpression and knockdown of Samm50 mitigated and exacerbated cardiac apoptosis and fibrosis, while also improving and worsening mitochondrial homeostasis, respectively. Protein interactions with Samm50 during the protective process were identified via immune-coprecipitation/mass spectroscopy. Mechanistically, serine hydroxymethyltransferase 2 (Shmt2) interacted with Samm50, acting as a crucial element in the protective process by hindering the transfer of Bax from the cytoplasm to the mitochondria and subsequent activation of caspase-3. Inhibition of Shmt2 diminished the protective effect of Samm50 overexpression against cardiac injury. Finally, Samm50 overexpression in vivo mitigated cardiac remodeling and enhanced cardiac function in both acute and chronic MI. In conclusion, Samm50 overexpression mitigated hypoxia-induced cardiac remodeling by inhibiting apoptosis and fibrosis, with Shmt2 acting as a key regulator in this protective process. The Samm50/Shmt2 axis represents a newly discovered mitochondria-related pathway for mitigating hypoxia-induced cardiac injury.

URI alleviates tyrosine kinase inhibitors-induced ferroptosis by reprogramming lipid metabolism in p53 wild-type liver cancers.

The clinical benefit of tyrosine kinase inhibitors (TKIs)-based systemic therapy for advanced hepatocellular carcinoma (HCC) is limited due to drug resistance. Here, we uncover that lipid metabolism reprogramming mediated by unconventional prefoldin RPB5 interactor (URI) endows HCC with resistance to TKIs-induced ferroptosis. Mechanistically, URI directly interacts with TRIM28 and promotes p53 ubiquitination and degradation in a TRIM28-MDM2 dependent manner. Importantly, p53 binds to the promoter of stearoyl-CoA desaturase 1 (SCD1) and represses its transcription. High expression of URI is correlated with high level of SCD1 and their synergetic expression predicts poor prognosis and TKIs resistance in HCC. The combination of SCD1 inhibitor aramchol and deuterated sorafenib derivative donafenib displays promising anti-tumor effects in p53-wild type HCC patient-derived organoids and xenografted tumors. This combination therapy has potential clinical benefits for the patients with advanced HCC who have wild-type p53 and high levels of URI/SCD1.

A circRNA-miRNA-mRNA network analysis underlying pathogenesis of human heart failure.

BACKGROUND: The molecular mechanisms of heart failure (HF) are still poorly understood. Circular RNA (circRNA) has been discovered in the heart in increasing numbers of studies. The goal of this research is to learn more about the potential roles of circRNAs in HF. METHODS & RESULTS: We used RNA sequencing data to identify the characteristics of circRNAs expressed in the heart and discovered that the majority of circRNAs screened were less than 2000 nt. Additionally, chromosomes One and Y had the most and least number of circRNAs, respectively. After excluding duplicate host genes and intergenic circRNAs, a total of 238 differentially expressed circRNAs (DECs) and 203 host genes were discovered. However, only four of the 203 host genes of DECs were examined in HF differentially expressed genes. Another study used Gene Oncology analysis of DECs host genes to elucidate the underlying pathogenesis of HF, and it found that binding and catalytic activity accounted for a large portion of DECs. Immune system, metabolism, and signal transduction pathways were significantly enriched. Furthermore, 1052 potentially regulated miRNAs from the top 40 DECs were collected to build a circRNA-miRNA network, and it was discovered that 470 miRNAs can be regulated by multiple circRNAs, while others are regulated by a single circRNA. In addition, a comparison of the top 10 mRNAs in HF and their targeted miRNAs revealed that DDX3Y and UTY were regulated by the most and least circRNA, respectively. CONCLUSION: These findings demonstrated circRNAs have species and tissue specific expression patterns; while circRNA expression is independent on host genes, the same types of genes in DECs and DEGs worked in HF. Our findings would contribute to a better understanding of the critical roles of circRNAs and lay the groundwork for future studies of HF molecular functions.

Tertiary lymphoid structures predict the prognosis and immunotherapy response of cholangiocarcinoma.

Introduction: Cholangiocarcinoma (CCA) is a malignant tumor of the biliary epithelium with a poor prognosis. The lack of biomarkers to predict therapeutic response and prognosis is one of the major challenges for CCA treatment. Tertiary lymphoid structures (TLS) provide a local and pivotal microenvironment for tumor immune responses. The prognostic value and clinical relevance of TLS in CCA remain unclear. We aimed to explore the characteristics and clinical significance of TLS in CCA. Methods: We investigated the prognostic value and clinical relevance of TLS in CCA using a surgery cohort containing 471 CCA patients (cohort 1) and an immunotherapy cohort containing 100 CCA patients (cohort 2). Hematoxylin and eosin (H&E) and immunohistochemical (IHC) staining were used to evaluate the maturity of TLS. Multiplex IHC (mIHC) was employed to characterize the composition of TLS. Results: Different maturity of TLS were observed in CCA tissue sections. Strong staining of the four-gene signature including PAX5, TCL1A, TNFRSF13C, and CD79A were found in TLS regions. A high density of intra-tumoral TLS (T-score high) were significantly correlated with longer overall survival (OS) both in CCA cohort 1 (p = 0.002) and cohort 2 (p = 0.01), whereas a high density of peri-tumoral TLS (P-score high) were associated with shorter OS in these two cohorts (p = 0.003 and p = 0.03, respectively). Conclusion: The established four-gene signature efficiently identified the TLS in CCA tissues. The abundance and spatial distribution of TLS were significantly correlated with the prognosis and immune checkpoint inhibitors (ICIs) immunotherapy response of CCA patients. The presence of intra-tumoral TLS are positive prognostic factors for CCA, which provide a theoretical basis for the future diagnosis and treatment of CCA.

Bioinformatic analysis and validation of cardiac hypertrophy-related genes.

In this study, we have screened genes involved in myocardial hypertrophy (MH) using a mice model for compensatory stress overload (transverse aortic constriction, TAC) and bioinformatics. Microarrays were downloaded, and according to the Venn diagram, three groups of data intersections were obtained. Gene function was analyzed by Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), whereas protein-protein interactions (PPI) were analyzed using the STRING database. A mouse aortic arch ligation model was established to verify and screen the expression of hub genes. A total of 53 (DEGs) and 32 PPI genes were screened out. GO analysis showed DEGs mainly involved in cytokine and peptide inhibitor activity. KEGG analysis focused on ECM receptor interaction and osteoclast differentiation. Expedia co-expression gene network analysis showed that Serpina3n, Cdkn1a, Fos, Col5a2, Fn1 and Timp1 participated in the occurrence and development of MH. RT-qPCR verified that all the other 9 hub genes except Lox were highly expressed in TAC mice. This study lays a foundation for further study on the molecular mechanism of MH and for screening of molecular markers.

Insights into peptide profiling of sturgeon myofibrillar proteins with low temperature vacuum heating.

BACKGROUND: Protein oxidation during food processing causes changes in the balance of protein-molecular interactions and protein-water interactions, ultimately leading to protein denaturation, which results in the loss of a range of functional properties. Therefore, how to control the oxidative modification of proteins during processing has been the focus of research. RESULTS: In the present study, the intrinsic fluorescence value of the myofibrillar proteins (MP) decreased and the surface hydrophobicity value increased, indicating that the heat treatment caused a significant change in the conformation of the MP. With an increase in heating temperature, protein carbonyl content increased, total sulfhydryl content decreased, and protein secondary structure changed from α-helix to ß-sheet, indicating that protein oxidation and aggregation occurred. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that heat treatment can lead to the degradation of proteins, especially myosin heavy chain, although actin had a certain thermal stability. In total, 733 proteins were identified by proteomics, and the protein oxidation caused by low temperature vacuum heating (LTVH) was determined to be mild oxidation dominated by malondialdehyde and 4-hydroxynonenal by oxidation site division. CONCLUSION: The present study has revealed the effect of LTVH treatment on the protein oxidation modification behavior of sturgeon meat, and explored the effect mechanism of LTVH treatment on the processing quality of sturgeon meat from the perspective of protein oxidation. The results may provide a theoretical basis for the precise processing of aquatic products. © 2023 Society of Chemical Industry.

PTEN Deficiency Facilitates Exosome Secretion and Metastasis in Cholangiocarcinoma by Impairing TFEB-mediated Lysosome Biogenesis.

BACKGROUND & AIMS: In eukaryotes, the ubiquitin-proteasome system and the autophagy-lysosome pathway are essential for maintaining cellular proteostasis and associated with cancer progression. Our previous studies have demonstrated that phosphatase and tensin homolog (PTEN), one of the most frequently mutated genes in human cancers, limits proteasome abundance and determines chemosensitivity to proteasome inhibitors in cholangiocarcinoma (CCA). However, whether PTEN regulates the lysosome pathway remains unclear. METHODS: We tested the effects of PTEN on lysosome biogenesis and exosome secretion using loss- and gain-of-function strategies in CCA cell lines. Using in vitro dephosphorylation assays, we explored the regulatory mechanism between PTEN and the key regulator of lysosome biogenesis, transcription factor EB (TFEB). Using the migration assays, invasion assays, and trans-splenic liver metastasis mouse models, we evaluated the function of PTEN deficiency, TFEB-mediated lysosome biogenesis, and exosome secretion on tumor metastasis. Moreover, we investigated the clinical significance of PTEN expression and exosome secretion by retrospective analysis. RESULTS: PTEN facilitated lysosome biogenesis and acidification through its protein phosphatase activity to dephosphorylate TFEB at Ser211. Notably, PTEN deficiency increased exosome secretion by reducing lysosome-mediated degradation of multi-vesicular bodies, which further facilitated the proliferation and invasion of CCA. TFEB agonist curcumin analog C1 restrained the metastatic phenotype caused by PTEN deficiency in mouse models, and we highlighted the correlation between PTEN deficiency and exosome secretion in clinical cohorts. CONCLUSIONS: In CCA, PTEN deficiency impairs lysosome biogenesis to facilitate exosome secretion and cancer metastasis in a TFEB phosphorylation-dependent manner.

A novel synergistic covalence and complexation bridging strategy based on multi-functional biomass-derived aldehydes and Al(III) for engineering high-quality eco-leather.

To get rid of the chrome pollution faced by the leather industry, we explored a novel engineering high-quality eco-leather technology based on the synergistic interactions between biomass-based aldehydes and Al(III). Firstly, dialdehyde xanthan gum (DXG) was prepared to covalently crosslink with the collagen fibers (CFs) via Schiff-base linkages under alkaline conditions, endowing the leather with a shrinkage temperature (Ts) of 80 °C and opening channels for the subsequent penetration of Al species (AL). Secondly, and for this latter purpose, the DXG-tanned leather was acidified to release part of the DXG from the leather according to the dynamic nature of the Schiff-base. Containing suitable oxygen-containing groups (OGs) with excellent complexation capabilities, the released DXG served as masking agents for AL, facilitating the penetration of AL into the inner CFs network for further complexation crosslinking. Consequently, a denser crosslinking network was constructed in the leather, and the crust leather exhibited higher Ts (82.2 °C), improved mechanical (tensile strength: 13.4 N/mm2, tear strength: 53.3 N/mm) and organoleptic properties than those of the DXG crust or AL crust leathers. This demonstrates that this synergistic covalence and complexation bridging strategy is a sustainable option to substitute highly restricted chrome tanning agent for eco-leather production.

Purification and characterization of a chitinase from Aeromonas media CZW001 as a biocatalyst for producing chitinpentaose and chitinhexaose.

Developing chitinase suitable for the bioconversion of chitin to chitin oligosaccharides has attracted significant attention due to its benefits in environmental protection. In this study, chitinase from Aeromonas media CZW001 (AmChi) was purified and characterized. The molecular weight of AmChi was approximately 40 kDa. AmChi exhibited maximum catalytic activity at pH 8.0 with an optimum temperature of 55°C and showed broad stability between 15 and 65°C and between pH 5.0 and 9.0. AmChi was activated by Mg2+ , Na+ , and K+ and inhibited by Hg+ , Co2+ , Fe2+ , Ca2+ , Ag+ , Zn2+ , and EDTA. The main products of AmChi on colloidal chitin were chitinhexaose and chitinpentaose. AmChi had better substrate specificity for powdered chitin than colloidal chitin and had a higher catalytic efficiency toward (GlcNAc)5 than colloidal chitin. AmChi inhibited fungal growth in a dose-dependent manner. These results suggest that AmChi could be used for the enzymatic degradation of chitin to produce chitinhexaose and chitinpentaose, which have several industrial applications.

TAK1 Activation by NLRP3 Deficiency Confers Cardioprotection Against Pressure Overload-Induced Cardiomyocyte Pyroptosis and Hypertrophy.

A comprehensive view of the role of NLRP3/caspase-1/GSDMD-mediated pyroptosis in pressure overload cardiac hypertrophy is presented in this study. Furthermore, mitigation of NLRP3 deficiency-induced pyroptosis confers cardioprotection against pressure overload through activation of TAK1, whereas this salutary effect is abolished by inhibition of TAK1 activity, highlighting a previously unrecognized reciprocally regulatory role of NLRP3-TAK1 governing inflammation-induced cell death and hypertrophic growth. Translationally, this study advocates strategies based on inflammation-induced cell death might be exploited therapeutically in other inflammatory and mechanical overload disorders, such as myocardial infarction and mitral regurgitation.

Interaction and binding mechanism of lipid oxidation products to sturgeon myofibrillar protein in low temperature vacuum heating conditions: Multispectroscopic and molecular docking approaches.

In this work, the binding mechanism of myofibrillar protein (MP) with malondialdehyde and 4-hydroxy-2-nonenal under low temperature vacuum heating was investigated via multispectroscopic and molecular docking. The results showed that binding interaction and increasing temperature caused significant changes in the conformations as well as a decrease in the value of protein intrinsic fluorescence, surface hydrophobicity, and fluorescence excitation-emission matrix spectra. Furthermore, the decrease in α-helix and ß-turn, increase in ß-sheet and a random coil of MP, imply the MP molecules to be more unfolded. Isothermal titration calorimetry and molecular docking results showed that main driving force for binding with MP was hydrogen bond, and the binding ability of malondialdehyde was superior to that of 4-hydroxy-2-nonenal. Moreover, increasing the heating temperature was beneficial to the binding reaction and intensified the conformational transition of MP. These results will provide a reference for further studies on the lipid and protein interaction of sturgeon.

The therapeutic effect of KSP inhibitors in preclinical models of cholangiocarcinoma.

Cholangiocarcinoma (CCA) is an epithelial malignancy with a dismal prognosis owing to limited treatment options. Here, we identified several compound candidates against CCA using a high-throughput drug screen with approved or emerging oncology drugs, among which kinesin spindle protein (KSP) inhibitors showed potent cytotoxic effects on CCA cells. Treatment with KSP inhibitors SB743921 and ARRY520 caused significant tumor suppression in CCA xenograft models in vivo. Mechanistically, KSP inhibitors led to the formation of abnormal monopolar spindles, which further resulted in the mitotic arrest and cell death of CCA cells both in vivo and in vitro. KEGG pathway analysis of transcriptional data confirmed this finding. Moreover, our clinical data as well as the TCGA database showed KIF11 expression was abundant in most CCA tumor specimens and associated with poor outcomes of CCA patients. Our results demonstrate that the therapeutic regimen of KSP inhibitors could be a promising treatment strategy in CCA.

Gankyrin and TIGAR cooperatively accelerate glucose metabolism toward the PPP and TCA cycle in hepatocellular carcinoma.

Oncogene-derived metabolic reprogramming is important for anabolic growth of cancer cells, which is now considered to be not simply rely on glycolysis. Pentose phosphate pathway and tricarboxylic acid cycle also play pivotal roles in helping cancer cells to meet their anabolic and energy demands. The present work focused on gankyrin, a relatively specific oncogene in hepatocellular carcinoma (HCC), and its impact on glycolysis and mitochondrial homeostasis. Metabolomics, RNA-seq analysis, and subsequent conjoint analysis illustrated that gankyrin regulated the pentose phosphate pathway (PPP), tricarboxylic acid (TCA) cycle, and mitochondrial function and homeostasis, which play pivotal roles in tumor development. Mechanistically, gankyrin was found to modulate HCC metabolic reprogramming via TIGAR. Gankyrin positively regulated the transcription of TIGAR through Nrf2, which bound to the antioxidant response elements (AREs) in the promoter of TIGAR. Interestingly, TIGAR feedback regulated the transcription of Nrf2 and subsequently gankyrin by promoting nuclear importation of PGC1α. The loop between gankyrin, Nrf2, and TIGAR accelerated glucose metabolism toward the PPP and TCA cycle, which provided vital building blocks, such as NADPH, ATP, and ribose of tumor and further facilitated the progression of HCC.

The HBV Specially-Related Long Noncoding RNA HBV-SRL Involved in the Pathogenesis of Hepatocellular Carcinoma.

Hepatitis B virus (HBV) is one of the major risk factors for HCC (hepatocellular carcinoma) occurrence with a diverse role in the pathogenesis of HCC. More works need to be performed to elucidate a more thorough understanding of the molecular mechanisms involving in HBV-induced HCC, although some mechanisms such as genome integration have been reported. In the present study, aberrantly expressed lncRNAs were identified between HCC tumor tissues with or without HBV infection. Among these molecules, HBV specially-related long noncoding RNA (HBV-SRL) was further found to correlate with poor prognosis and a shorter overall survival time in HCC patients with HBV infection. Additionally, HBV-SRL was found function as oncogene by upregulating the NF-κB2 expression. These data suggest that HBV infection altered gene expression pattern in liver cells which contributed to HBV-related HCC development, and HBV-SRL may serve as a new molecular marker or potential therapeutic target of HBV-related HCC.

Identification of Differential Expression Genes between Volume and Pressure Overloaded Hearts Based on Bioinformatics Analysis.

Volume overload (VO) and pressure overload (PO) are two common pathophysiological conditions associated with cardiac disease. VO, in particular, often occurs in a number of diseases, and no clinically meaningful molecular marker has yet been established. We intend to find the main differential gene expression using bioinformatics analysis. GSE97363 and GSE52796 are the two gene expression array datasets related with VO and PO, respectively. The LIMMA algorithm was used to identify differentially expressed genes (DEGs) of VO and PO. The DEGs were divided into three groups and subjected to functional enrichment analysis, which comprised GO analysis, KEGG analysis, and the protein-protein interaction (PPI) network. To validate the sequencing data, cardiomyocytes from AR and TAC mouse models were used to extract RNA for qRT-PCR. The three genes with random absolute values of LogFC and indicators of heart failure (natriuretic peptide B, NPPB) were detected: carboxylesterase 1D (CES1D), whirlin (WHRN), and WNK lysine deficient protein kinase 2 (WNK2). The DEGs in VO and PO were determined to be 2761 and 1093, respectively, in this study. Following the intersection, 305 genes were obtained, 255 of which expressed the opposing regulation and 50 of which expressed the same regulation. According to the GO and pathway enrichment studies, DEGs with opposing regulation are mostly common in fatty acid degradation, propanoate metabolism, and other signaling pathways. Finally, we used Cytoscape's three techniques to identify six hub genes by intersecting 255 with the opposite expression and constructing a PPI network. Peroxisome proliferator-activated receptor (PPARα), acyl-CoA dehydrogenase medium chain (ACADM), patatin-like phospholipase domain containing 2 (PNPLA2), isocitrate dehydrogenase 3 (IDH3), heat shock protein family D member 1 (HSPD1), and dihydrolipoamide S-acetyltransferase (DLAT) were identified as six potential genes. Furthermore, we predict that the hub genes PPARα, ACADM, and PNPLA2 regulate VO myocardial changes via fatty acid metabolism and acyl-Coa dehydrogenase activity, and that these genes could be employed as basic biomarkers for VO diagnosis and treatment.

Insight into the molecular mechanism of texture improvement of sturgeon fillets treated by low temperature vacuum heating technology using label-free quantitative proteomics.

Label-free quantitative proteomics and weighted protein co-expression network (WPCNA) strategy was used to determine the molecular mechanisms about how did the low temperature vacuum heating (LTVH) improve the texture quality of sturgeon fillets compared to traditional cooking (TC). Results showed that LTVH can reduce the accumulation of lactate and malondialdehyde (MDA) in sturgeon fillets, and decrease the degradation of myofibrillar protein. 594 proteins were identified, 26 and 10 key differentially abundant proteins (KDAPs) were observed in LTVH50-15 vs TC100-15 and LTVH60-15 vs TC100-15 groups, respectively. Most of KDAPs were structural proteins, metabolic enzymes, and oxidoreductase enzymes. They were primarily implicated in the structures of myofibrillar proteins and cytoskeleton, glycolysis/gluconeogenesis and oxidative phosphorylation pathways. In contrast to TC, LTVH can better preserve the structure of myofibrillar proteins and cytoskeleton, reduce lactate accumulation induced by glycolysis/gluconeogenesis, and limit the oxidative damage caused by oxidative phosphorylation, thereby improving the texture of sturgeon fillets.

Monitoring the lipid oxidation and flavor of Russian sturgeon fillets treated with low temperature vacuum heating: formation and relationship.

BACKGROUND: Sturgeon is one of the most precious fish resources worldwide. Low temperature vacuum heating (LTVH) has been confirmed as a good way of maintaining food quality. However, there is a lack of in-depth studies assessing the impact of LTVH on lipid oxidation and flavor formation. RESULTS: The present study compared the effect of LTVH and traditional cooking on lipid oxidation and flavor of sturgeon fillets. In total, 13 fatty acids were detected, of which polyunsaturated fatty acids content was the highest (P < 0.05). LTVH prevented the formation of conjugated diene and thiobarbituric acid reactive substances (P < 0.05), as manifested by an increased signal intensity of free radicals of electron spin resonance. The characteristic peaks intensity of lipid by Raman at 970 cm-1 , 1080 cm-1 and 1655 cm-1 were reduced, whereas peaks at 1068 cm-1 and 1125 cm-1 displayed the opposite trend. Confocal fluorescence microscopy showed that the lipids particles were reduced and distributed more evenly with an increase in heating temperature. Principal component analysis of electronic nose cannot effectively separate all groups; however, gas chromatography-ion migration spectrometry showed that the volatile flavor compounds were relatively stable during LTVH. Correlation analysis of all the above lipid oxidation indices and characteristic flavor substances showed that each treatment group was located in different quadrants and demonstrated great differentiation. CONCLUSION: Overall, the results of the present study support the view that LTVH is a healthier way of cooking. © 2022 Society of Chemical Industry.

Deduction and exploration of the evolution and function of vertebrate GFPT family.

BACKGROUND: Glutamine-fructose-6-phosphate aminotransferase (GFPT) is a key factor in the hexosamine metabolism pathway. It regulates the downstream factor O-GlcNAc to change cell function and plays an important role in the metabolism and immune process of tissues and organs. However, the evolutionary relationship of GFPT family proteins in vertebrates has not been elucidated. OBJECTIVE: To deduce and explore the evolution and function of vertebrate GFPT family. METHODS: 18 GFPT sequences were obtained from Homo sapiens (H. sapiens), Trachypithecus francoisi (T. francoisi), Mus musculus (M. musculus), Rattus norvegicus (R. norvegicus), Gallus gallus (G. gallus), Zootoca vivipara (Z. vivipara), Xenopus tropicalis (X. tropicalis), Danio rerio (D. rerio), Rhincodon typus (R. typus), Plasmodium relictum from National Center for Biotechnology Information (NCBI). The physical and chemical characteristics and molecular evolution of GFPT family proteins and nucleic acid sequences were analyzed by ClustalX2, Gene Doc, MEGA-X, SMART, Datamonkey, R etc. RESULTS: Based on the neighbor-joining (NJ) phylogenetic tree and evolution fingerprints, GFPT family members of vertebrates can be divided into two groups: the GFPT1 group and the GFPT2 group. Seven positive selection sites were identified by IFEL and integrated methods mixed effects model of evolution (MEME) and fixed effects likelihood (REL). Finally, we predicted 28 phosphorylation sites and 18 ubiquitousness sites in the human GFPT1 sequence, 10 phosphorylation sites, and five ubiquitousness sites in GFPT2. Gene ontology (GO) analyzes the protein molecules and KEGG signaling pathways of vertebrates interacting with GFPT family proteins. CONCLUSIONS: Our work confirmed that higher animals GFPT family may have differentiated GFPT1 and GFPT2, which meets their own functional needs. This knowledge answers the question what the origin and evolution of GFPT family in vertebrates and provided the basis for disease treatment and function research of GFPT protein.

Potential biomarkers of acute myocardial infarction based on co-expression network analysis.

Acute myocardial infarction (AMI) is a common cause of death in numerous countries. Understanding the molecular mechanisms of the disease and analyzing potential biomarkers of AMI is crucial. However, specific diagnostic biomarkers have thus far not been fully established and candidate regulatory targets for AMI remain to be determined. In the present study, the AMI gene chip dataset GSE48060 comprising blood samples from control subjects with normal cardiac function (n=21) and patients with AMI (n=26) was downloaded from Gene Expression Omnibus. The differentially expressed genes (DEGs) between the AMI and control groups were identified with the online tool GEO2R. The co-expression network of DEGs was analyzed by calculating the Pearson correlation coefficient of all gene pairs, mutual rank screening and cutoff threshold screening. Subsequently, the Gene Ontology (GO) database was used to analyze the genes' functions and pathway enrichment of genes in the most important modules was performed. Kyoto Encyclopedia of Genes and Genomes (KEGG) Disease and BioCyc were used to analyze the hub genes in the module to determine important sub-pathways. In addition, the expression of hub genes was confirmed by reverse transcription-quantitative PCR in AMI and control specimens. In the present study, 52 DEGs, including 26 upregulated and 26 downregulated genes, were identified. As key hub genes, three upregulated genes (AKR1C3, RPS24 and P2RY12) and three downregulated genes (ACSL1, B3GNT5 and MGAM) were identified from the co-expression network. Furthermore, GO enrichment analysis of all AMI co-expression network genes revealed functional enrichment mainly in 'RAGE receptor binding' and 'negative regulation of T cell cytokine production'. In addition, KEGG Disease and BioCyc analysis indicated functional enrichment of the genes RPS24 and P2RY12 in 'cardiovascular diseases', of AKR1C3 in 'cardenolide biosynthesis', of MGAM in 'glycogenolysis', of B3GNT5 in 'glycosphingolipid biosynthesis' and of ACSL1 in 'icosapentaenoate biosynthesis II'. In conclusion, the hub genes AKR1C3, RPS24, P2RY12, ACSL1, B3GNT5 and MGAM are potential markers of AMI, and have potential application value in the diagnosis of AMI.

Quantitative proteomics reveals the relationship between protein changes and off-flavor in Russian sturgeon (Acipenser gueldenstaedti) fillets treated with low temperature vacuum heating.

This study aimed to reveal the molecular mechanisms associated with off-flavor generation in sturgeon fillets treated by low temperature vacuum heating (LTVH). Label-free quantitative proteomics was used to identify 120 favor-related proteins, 27 proteins were screened as differentially expressed for bioinformatics analysis. 17 of KEGG pathways were identified. Particularly, proteins involved in proteasome and peroxisome were highly correlated with off-flavor formation. They were primarily implicated in the structures of proteins, including binding and proteasome pathways. The results indicated that the LTVH reduced the binding sites by down-regulating protease and superoxide dismutase expression. LTVH increased the myofibrillar protein and sulfhydryl content and decreased the total volatile basic nitrogen and thiobarbituric acid reactive substance, which confirmed that protein oxidation was related to off-flavor. This proteomics study provided new insights into the off-flavor of sturgeon with LTVH, and proposed potential link between biological processes and off-flavor formation.