Biochemical Genetics最新文献

Angiotensin-converting enzyme 2 (ACE2) has been reported to exert a protective effect in acute lung injury (ALI), though its underlying mechanism remains incompletely understood. In this study, ACE2 expression was found to be upregulated in a mouse model of ALI induced by lipopolysaccharide (LPS) injection. ACE2 knockdown modulated the severity of ALI, the extent of autophagy, and the mTOR pathway in this model. ACE2 regulated liver kinase B1 (LKB1) gene expression by sequestering miR-326, thereby alleviating ALI severity through enhanced autophagy. In cell-based experiments, miR-326 was shown to regulate ACE2 and LKB1 expression and autophagy. Overexpression of ACE2 disrupted miR-326's regulatory effect on LKB1, suggesting that LKB1 may function as an endogenous sponge for miR-326. These findings imply that elevated ACE2 expression in lung could play enhance the autophagy via the consumption of miR-326.

The ornamental fish Poecilia velifera (Sail-fin molly, Poeciliidae) has spread widely to various non-native ecosystems around the world, far from its native habitat in the Yucatan Peninsula, Mexico. Despite the availability of some partial mitochondrial and nuclear genetic information, the complete mitogenomic structure and its variation remain unknown for this species, which is essential for a comprehensive genetic characterization and detailed phylogenetic investigation. This study applied next-generation sequencing to generate the de novo mitogenome of morphologically identified P. velifera from a non-native brackish water ecosystem in Banten Province, Indonesia. The resulting mitogenome was 16,627 bp in length and encompassed 13 protein-coding genes (PCGs), 22 transfer RNAs, two ribosomal RNAs, and a non-coding control region (CR). The result enhances our understanding of the genetic makeup of P. velifera compared to its congeners. Furthermore, the identified nucleotide variations within the conserved blocks of the CR region could provide insights into the functional role of this non-coding region. Bayesian phylogenetic inference using concatenated PCGs distinguished P. velifera from its congeners and showed monophyletic clustering of Poecilia in the family Poeciliidae, consistent with earlier evolutionary hypotheses. This first mitogenome of P. velifera paves the way for using multiple mitochondrial markers in species identification and understanding population structure in the near future. In addition, looking into the genetic evidence of this ornamental species in a non-native ecosystem, the study emphasizes the importance of strict quarantine regulations to protect Indonesia's native fish species.

Red algae are widely used as a source of health-promoting bioactive compounds and dietary fibers in health foods. The identification and classification of red algal species based on morphological and molecular characteristics is challenging because of the similarity of the thallus and its high degree of plasticity and because complete mitochondrial genomes have only been reported for a few species. In this study, the complete mitochondrial genome sequencing of the red macroalga Chondracanthus tenellus (Harvey) (Hommersand et al., Hydrobiologia 260:105-120, 1993)) (Rhodophyta, Gigartinales) was performed for the first time. Additionally, we aimed to reconstruct the phylogenetic relationships of the species within the order Gigartinales using complete mitochondrial genome sequences. Genomic DNA was extracted, analyzed by whole-genome sequencing (WGS), and assembled using NOVOPlasty. The mitochondrial genome sequence was annotated, and both a genome map and a phylogenetic tree were constructed using maximum likelihood analysis. The mitochondrial genome was 25,928 bp in length, had strongly biased [AT] content (72.08%), and comprised 3 rRNAs, 23 tRNAs, and 24 protein-coding genes (PCGs). In comparison with the mitochondrial genome of other red algae, that of C. tenellus lacks rpl5 and rpl20. Based on a phylogenetic study of the complete mitochondrial genome, C. tenellus belongs to the family Gigartinaceae and is monophyletic with other species of the order Gigartinales. This is the first report of C. tenellus complete mitochondrial genome; its characteristics are consistent with those of other red algae. The study of genomic data will be beneficial for future comparative genomics, phylogenetics, and evolutionary studies.

Ideonella and Thermobifida were the most promising bacterial candidates for degrading plastic polymers. A comparative pan- and phylogenomic analysis of 33 Ideonella and Thermobifida strains was done to determine their plastic degradation potential, niche adaptation and speciation. Our study disclosed that more accessory genes in the strains showed phenotypic plasticity, according to the BPGA data. Pan and core genes were employed for the phylogenetic reconstruction. Pathway enrichment analyses scrutinized the functional roles of the core and adaptive-associated genes. KEGG annotation revealed that most genes were associated with the metabolism of amino acids and carbohydrates. The detailed COG analysis disclosed that approximately 40% of the pan genes performed metabolic functions. The unique gene pool consisted of genes chiefly involved in "general function prediction" and "amino acid transport and metabolism". Our in silico study revealed that these strains could assist in agronomic applications in the future since they devour nitrogen compounds and their central metabolic pathways are involved in amino acid metabolism. The rational selection of strains of Ideonella is far more effective at depolymerising plastics than Thermobifida. A greater number of unique genes, 1701 and 692, were identified for Ideonella sakaiensis 201-F6 and Thermobifida alba DSM-43795, respectively. Furthermore, we examined the singletons involved in xenobiotic catabolism. The unique singleton data were used to construct a supertree. To characterize the conserved patterns, we used SMART and MEME to identify domain and transmembrane regions in the unique protein sequences. Therefore, our study unraveled the genomic insights into the ecology-driven speciation of Ideonella and Thermobifida.

Methotrexate (MTX) pharmacogenetics has been extensively investigated due to the high inter-individual variability in response to treatment. This wide variability can lead to treatment discontinuation or even death. Several genes involved in the pharmacodynamics and pharmacokinetics of MTX have been studied. However, there are still no guidelines for pharmacogenetics-guided MTX dosing. The FPGS rs1544105 and GGH rs3758149 gene polymorphisms were genotyped and their allele frequencies were determined. Their associations with MTX treatment response and toxicity in Uruguayan adults with haematological malignancies receiving high-dose MTX were analyzed. A worldwide systematic review of the association of these gene polymorphisms with response and toxicity to high-dose MTX treatment was also conducted. The allele frequencies of FPGS rs1544105 were 0.54 and 0.46 (C and T, respectively), and of GGH rs3758149 were 0.77 and 0.23 (C and T, respectively). Several associations were found between toxicity (gastrointestinal, hepatic and hematological) and the FPGS rs1544105 T allele (p = 0.01, p < 0.001 and p = 0.04, respectively) and between mucositis and the FPGS TT genotype (p < 0.001). The GGH rs375814 TT genotype was associated with gastrointestinal and hepatic toxicity (p = 0.01 and p < 0.001, respectively). Both the FPGS rs1544105 C allele and the GGH rs3758149 TT genotype were associated with remission (p < 0.001 and p = 0.04, respectively). The systematic review identified 247 publications and finally included 17 research articles. Few consistent data were found due to the lack of homogeneity between study groups.

Caspase-9 is crucial for initiating apoptosis, and its activity is tightly regulated through various mechanisms, especially phosphorylation by kinases activated by extracellular growth factors, osmotic stress, or during mitosis. Mass spectrometric analyses have shown that residues S302 and S307 in human caspase-9 are prone to phosphorylation. To investigate the effects of phosphorylation at these sites, three phosphomimetic variants of recombinant caspase-9 were created: S302D, S307D, and the combined S302D/S307D variant. The QuickChange method was employed to generate these mutant constructs, which were expressed in Escherichia coli (E. coli) and purified using affinity chromatography. For enzymatic assays, the chromogenic substrate Ac-LEHD-pNA was utilized, and the temperature profiles of enzyme activity were assessed. Computational modeling was used to predict the structures of the mutants, allowing for comparison with the native enzyme. The results indicated that both the S302D and S302D/S307D variants exhibited complete loss of enzyme activity. In contrast, the S307D variant demonstrated a 10-fold increase in the Michaelis constant (K_m) for the substrate and a 4-fold increase in the maximum reaction rate (V_max) compared to the wild-type enzyme. Notably, the k_cat/K_m value for wild-type caspase-9 was three times greater than that of the S307D variant. The optimal temperature for wild-type activity was between 30 and 37 °C, while for the S307D variant, it ranged from 37 to 45 °C. Importantly, the S302 residue is essential for caspase-9 function; introducing a negative charge at this position leads to complete inactivation of the enzyme.

Breast cancer is a prevalent and highly heterogeneous malignancy that continues to be a major global health concern. Voltage-gated sodium channels are primarily known for their role in neuronal excitability, but emerging evidence suggests their involvement in the pathogenesis of various cancers, including breast cancer. However, the effect of β-subunits on breast cancer cells is not yet studied. SCN3B, as a modulatory subunit, is of particular interest due to its less understood role in cancer biology. This research comprehensively investigates the clinical associations, diagnostic potential, and functional role of SCN3B in breast cancer, shedding light on its diverse implications from patient outcomes to molecular mechanisms. Our methods included clinical data analysis from The Cancer Genome Atlas (TCGA) breast cancer dataset, diagnostic analysis through ROC curves, differential gene expression analysis, SCN3B expression assessment in cell lines, overexpression experiments, and functional assays. Additionally, we constructed a protein-protein interaction network to explore potential mechanisms underlying SCN3B's impact. The study revealed significant clinical associations between SCN3B expression and various parameters such as tumor stage, race, age, histological type, molecular subtype, and hormone receptor status. SCN3B demonstrated strong diagnostic potential with an AUC of 0.95. It influenced the expression of over 800 genes, primarily associated with cell migration and extracellular matrix interactions. SCN3B exhibited distinct expression patterns between normal and breast cancer cell lines and successfully overexpressed in various breast cancer cell lines. This overexpression inhibited cell migration and invasion. Our research emphasizes SCN3B's clinical relevance, diagnostic potential, and influence on cell behavior in breast cancer, offering insights into its multifaceted role and therapeutic implications.

The tumor microenvironment has a significant input on prognosis and also for predicting clinical outcomes in various types of cancers. However, tumor tissue is not always available, thus, rendering peripheral blood a preferable alternative in the search for prognostic and predictive gene signatures. Head and neck squamous cell carcinoma (HNSCC) constitutes a quite heterogeneous disease characterized by poor prognosis. Therefore, the discovery of novel therapeutics based on prognostic gene signatures for effective disease governance is of paramount importance. In this study, we report for the first time an immune-gene signature identified in the peripheral blood of HNSCC patients comprising five genes (CLEC4C, IL23A, LCK, LY9, and CD19) which were more than threefold downregulated as compared to healthy individuals and were associated with poor prognosis. By performing analyses of HNSCC tumor samples from The Cancer Genome Atlas (TCGA) database, we discovered that decreased expression of these genes, both as single genes and as a 5-gene signature (5-GS), was significantly correlated with worse overall survival (OS). Our data show that the levels of expression of the 5-GS represent an immune profile predicting OS in patients with HNSCC.

Although DNA methyltransferase 1 (DNMT1) and RNA editor ADAR triplications exist in Down syndrome (DS), their specific roles remain unclear. DNMT methylates DNA, yielding S-adenosine homocysteine (SAH), subsequently converted to homocysteine (Hcy) and adenosine by S-adenosine homocysteine (Hcy) hydrolase (SAHH). ADAR converts adenosine to inosine and uric acid. We hypothesized that targeting epigenetic regulators and RNA editor, and inhibiting Hcy and adenosine, could alleviate DS phenotype including the congenital heart disease (CHD). DS and wild-type mice were treated with epigallocatechin gallate (EG), inhibitor of Hcy, and adenosine. Specific substrate gel zymography identified matrix metalloproteinases (MMPs)/A Disintegrin and Metalloproteinase with Thrombospondin motifs (ADAMTS) activities and MMP12/ADAMTS12 and MMP13/ADAMTS13 levels were assessed via gel zymography. Cardiac levels of DNMT1, ADAR, tissue inhibitor of metalloproteinase 1 (TIMP1), SAHH, and ten-eleven translocator (TET2), along with hydroxymethylation (a gene eraser), were measured. Calcium urate deposits in heart tissue suggested gout mechanism in DS. Robust amyloid fibers in DS mouse brain cortex were most likely dissolved by ADAMTS as its levels were elevated in tissues, with a corresponding decrease in TIMP1 in the EG group. It appears that triplication of down syndrome cell adhesion molecule (DSCAM) and cell adhesion molecule 1 (CAM1) fragment also help dissolve amyloid fibers, thus suggesting ADAMTS13/TIMP1 ratio could predict plaque dissolution. Our results indicate that cystathionine-β synthase (CBS) inhibitor as a potential therapy for amyloid dissolution.

BRD4, part of the bromodomain and extra terminal domain (BET) protein family, plays a pivotal role in gene transcription, DNA replication, and repair via transcription regulators. Despite its established involvement in various human diseases, its function in esophageal squamous cell carcinoma (ESCC) has not been fully explored. Our research investigated the association of BRD4 in ESCC and its underlying molecular mechanisms. The findings revealed that BRD4 knockdown notably diminished the cells' proliferation, migration, invasion capabilities and induced apoptosis and cell cycle arrest. Conversely, overexpression of BRD4 can reverse these phenotypes. Pearson correlation and enrichment analyses indicated that BRD4 expression was associated with the cell cycle and Wnt/β-catenin signaling pathway. Further validation confirmed that reduced BRD4 expression downregulates Cyclin D1 and c-Myc, and suppresses epithelial-to-mesenchymal transition (EMT) and Wnt/β-catenin signaling pathway. Furthermore, rescue experiments showed that overexpressing c-Myc significantly mitigated the inhibitory impact of BRD4. Moreover, by employing single-cell transcriptome sequencing, we explored the impact of the tumor microenvironment on BRD4 overexpression in ESCC cells. These insights confirmed BRD4's potential as a therapeutic target, suggesting that modulating its expression could yield promising strategies for ESCC treatment.