DNA and cell biology最新文献

Long noncoding RNAs (lncRNAs) play crucial roles in liver fibrosis (LF). We previously showed that the key lncRNA Gm17586 is involved in LF, but its molecular mechanism remains unclear. Primary hepatic stellate cells (HSCs) were isolated from LF mice. Real-time quantitative PCR and Western blotting were used to detect the expression of lncRNA Gm17586, Sirtuin 1 (SIRT1), and Smad homolog 3 (Smad3). Cell counting kit-8 and flow cytometry were used to detect the cell viability and cell cycle of the HSCs. Finally, immunofluorescence (IF) and fluorescence in situ hybridization (FISH) were used to observe the cellular colocalization of lncRNA Gm17586 and SIRT1. In HSCs from LF mice, the expression of the lncRNA Gm17586 was significantly reduced and negatively correlated with the expression of the HSCs activation markers α-smooth muscle actin (α-SMA) and collagen I. Overexpression of the lncRNA Gm17586 suppressed α-SMA and collagen I expression, as well as HSCs proliferation. Bioinformatics analysis and FISH experiments revealed that the lncRNA Gm17586 has potential binding sites on SIRT1 mRNA and shares a common subcellular localization. Notably, overexpression of the lncRNA Gm17586 led to marked increases in SIRT1 mRNA and protein levels. Further studies on the role of SIRT1 as a deacetylase revealed that overexpression of SIRT1 significantly reduced Smad3 mRNA and protein levels. Importantly, SIRT1 overexpression also markedly decreased Smad3 protein acetylation, suggesting that a mechanism exists by which Smad3 is regulated via deacetylation in HSCs. The results of this study suggested that downregulation of lncRNA Gm17586 expression reduced the expression of SIRT1, leading to decreased Smad3 deacetylation and promoting HSCs activation. The lncRNA Gm17586 may be a novel therapeutic target for the diagnosis and treatment of LF.

Extracellular vesicles (EVs) have been investigated due to their natural biocompatibility and targeting capabilities. The specific approach of combining EVs with liposomes to create hybrid nanoparticles (ELNPs) for the delivery of the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas9) system for deletion of the HGF gene in stem cells, but their effectiveness in encapsulating large nucleic acids is limited due to their small size. This study aimed to knock out the HGF gene by the CRISPR/Cas9 system by ELNPs, and it was expected that the efficiency of the CRISPR/Cas9 system transfer would increase compared to the usual methods of using lipofectamine in stem cells from apical papilla (SCAPs). In this study, gRNA suitable for the HGF gene is designed first, and after insertion into the CRISPR/Cas9 vector, it enters Lipofectamine 2000. In the next step, ELNPs are prepared after collecting EVs and hybridizing them with liposomes containing CRISPR/Cas9 vector. Then, these integrated nanoparticles were presented to SCAPs, and the removal of HGF gene expression was evaluated at the level of RNA and protein. This study showed that the CRISPR/Cas9 system can be efficiently transferred to SCAP cells using ELNPs. Genomic DNA sequencing analyses of SCAP cells showed a unique pattern of mutation, highly likely mediated through EVs. Quantitative PCR and protein staining further showed a decrease in HGF gene expression in the knockout cells. Moreover, cell proliferation analysis showed a decrease in cell proliferation in KO-HGF adipose cells compared to the nonedited counterpart. In summary, this study highlights the supportive role of EVs in facilitating cell transfection and promoting a dominant DNA repair pattern, likely through an RNA-mediated mechanism, rather than the random insertions and deletions typically induced during CRISPR editing of the HGF gene in SCAPs.

Osteoclasts, as the only cells capable of resorbing bone, play a significant role in all processes that take place at the level of bone tissue and are involved in the development of the skeleton, maintenance of its integrity, repair, and regeneration of bones. Therefore, it is not surprising that even small deviations from their normal functioning result in diseases that not only affect skeletal system but also the entire organism. There are a number of rare genetic bone diseases associated with mutations in osteoclast genes that govern their differentiation and function. Specifically, they are known as osteoclast-related diseases, and their main hallmark is either decreased or increased bone resorption. To understand the impact of osteoclast gene mutations on the course of these diseases, it is also necessary to know the cellular and molecular mechanisms underlying osteoclast development and function. Moreover, identification of specific gene mutations as potential therapeutic targets would be an important step in creating personalized gene therapies in the future.

We summarize recent findings on the conformational differences of chromatin fibers in immature versus mature retina cells due to different nucleosome linker length values and distributions, as revealed by cryo-electron microscopy and modeling studies, emphasizing implications to chromatin organization and epigenetic regulation broadly.

Probiotics sourced from host-adapted microbes represent a sustainable innovation in aquaculture nutrition, aiming to replace antibiotics and enhance fish health. However, studies evaluating indigenous probiotic strains specifically adapted to the gut environment of target species remain limited. In this study, an indigenous Bacillus subtilis strain was isolated from common carp (Cyprinus carpio) intestine, PCR-authenticated via dual endoglucanase amplicons (545 and 1311 bp), formulated as a powdered feed additive, and tested at 1, 10, and 100 mg/kg against commercial Nutri-Fish®, Infloran Bio®, vitamin C, and a supplemented control in an 8-week feeding trial with (n = 126) carp. The 10 mg/kg dose significantly (p < 0.05) enhanced growth performance, producing the highest weight gain (133.27 ± 4.56 g), specific growth rate (2.59 ± 0.12% per day), and relative growth rate (43.09 ± 1.23%), along with improved feed conversion ratio (3.51 ± 0.09%), feed efficiency ratio (29.58 ± 1.45%), and protein efficiency ratio (475.95 ± 15.32%). Hematological analysis revealed neutrophilia (52%, p < 0.05), a moderated neutrophil-to-lymphocyte ratio, and stable erythron parameters, indicating primed innate immunity without systemic stress. Plasma alanine aminotransferase and aspartate aminotransferase levels decreased by 30-40% relative to other groups (p < 0.05), evidencing improved hepatic integrity and lipid metabolism. Intestinal histology showed moderate mucosal fold hypertrophy at 10 mg/kg, whereas the highest dose (100 mg/kg) caused epithelial sloughing and inflammation. These results demonstrate that a precision microdose (10 mg/kg) of host-adapted B. subtilis can outperform multicomponent commercial supplements by significantly enhancing growth, immunity, and organ health. This probiotic strategy provides a sustainable, eco-friendly alternative for warm-water carp aquaculture, supporting circular economy principles and reducing reliance on antibiotics.

Gastric cancer (GC) is the fifth most common malignancy and one of the leading causes of cancer-related death worldwide. Its histological and molecular heterogeneity make it particularly challenging to manage. The Cancer Genome Atlas classifies GC into four molecular subtypes: Epstein-Barr virus-associated GC (EBVaGC), microsatellite instability-high (MSI-H), chromosomal instability (CIN), and genomic stability (GS), each of which has distinct genetic and epigenetic characteristics. Among this biomarker diversity, non-coding RNAs (ncRNAs) such as microRNAs (miRNAs) and long non-coding RNAs play a key role in diagnosis, prognosis, and targeted therapy. For instance, the EBVaGC subtype features PIK3CA mutations and hypermethylation of tumor suppressor genes such as CDKN2A, alongside ncRNAs such as EBV-encoded RNAs and H19 that enhance immunogenicity and response to programmed death-1/programmed death-ligand 1 inhibitors. MSI-H-GC is characterized by high mutational load and DNA mismatch repair defects, and ncRNAs such as MIR99AHG serve as prognostic and immunomodulatory markers. CIN-GC, the most common subtype, is associated with amplification of genes such as ERBB2/HER2 (human epidermal growth factor receptor 2) and ncRNAs such as miR-22 and TERRA, which exacerbate CIN and are linked to a poor prognosis may be amenable to HER2-targeted therapies. GS-GC is characterized by RHOA and CDH1 mutations and epithelial-to-mesenchymal transition (EMT) features, where ncRNAs such as HOX antisense intergenic RNA, ZFAS1, and Linc00152 affect invasion and metastasis by regulating EMT. Through interactions with miRNAs and signaling pathways, these ncRNAs not only influence prognosis but also represent novel therapeutic targets. Integrating multiomics approaches and developing ncRNA-based biomarker panels are essential for advancing precision medicine in GC.

Glucose homeostasis is an essential physiological process to ensure a stable energy supply to all tissues while preventing the harmful consequences of hypo- or hyperglycemia. The endocrine pancreas plays a central role in maintaining this process, where β-cells and α-cells secrete insulin and glucagon to coordinate systemic glucose metabolism, storage, and production. In this context, β-cells act as the main glucose sensors, closely linking extracellular glucose fluctuations to insulin release. This sensing is dependent on glucose transporters (GLUTs), which regulate cellular glucose uptake through their dynamic trafficking to the plasma membrane. The resultant increase in ATP links metabolism to electrical activity and exocytosis of insulin granules. β-cells maintain plasma glucose within the physiological range of 4-5.5 mM by integrating glucose uptake with metabolic signaling, thereby lowering elevated postprandial concentrations to ∼7.8 mM. In type 2 diabetes, defects in GLUT regulation reduce β-cell responsiveness, impair insulin secretion, and destabilize glucose homeostasis, highlighting GLUT dynamics as a target to maintain normoglycemia.

IL-18 is a member of the IL-1 family of cytokines, which is highly expressed in intestinal epithelial cells (IECs). Upon barrier breach, IL-18 is matured to its bioactive form as a result of inflammasome activation, released from the cell via Gasdermin D pores, and sensed by IL-18 receptor 1-positive (IL18R1⁺) immune cells to initiate an inflammatory response. In addition to this epithelial-out signaling network, we recently uncovered an epithelial-intrinsic IL-18 signaling pathway in the murine small intestine and identified enterochromaffin cells and revival stem cells (revSC) as IL18R1⁺ bearing IEC populations in the recovering crypt. Here, we discuss the mechanism, and physiological relevance, as well as some of the open questions presented by this discovery in relation to intestinal health and disease.

Mitochondria, originating from symbiotic ancestors, are acknowledged as the powerhouses of the cell. Their relevance to various cancer types is underscored by altered glucose metabolism (Warburg effect). Mitochondrial DNA (mtDNA) plays a crucial role in oxidative damage and is a significant contributor to cancer onset and progression. Tobacco and alcohol consumption increases reactive oxygen species generation, inducing oxidative stress that disrupts respiratory activity and mtDNA, thereby promoting carcinogenesis. This review emphasizes the link between mitochondrial dysfunction and cancer, particularly in oral squamous cell carcinoma (OSCC), highlighting the role of mtDNA mutations. This review discusses environmental factors, such as tobacco use and human papillomavirus infection, that impact mitochondrial function, stresses the importance of mitochondrial-targeted therapies, and explores the influence of microRNAs (miRNAs) on mitochondrial metabolism in cancer cells. Mitocans and miRNAs have emerged as promising therapeutic agents for OSCC. The subsequent sections delve into recent pivotal research on mitochondria, identifying mtDNA alterations as potential cancer biomarkers. These insights promise new perspectives on noninvasive cancer detection, heralding advancements in cancer therapeutics.

Cuproptosis is a regulated cell death mechanism that has recently been identified and is distinct from other known cell death mechanisms (e.g., apoptosis, Ferroptosis, necrotic apoptosis, etc.). Cuproptosis causes oligomer formation through the abnormal accumulation of intracellular copper ions that target binding to lipocytosed proteins, especially those involved in the tricarboxylic acid cycle. At the same time, it can destabilize iron-containing sulfur proteins, thereby inducing proteotoxic stress, leading to triggered cell death. It has also been shown that cuproptosis is also associated with oxidative stress activation and inhibition of the ubiquitin-proteasome system. Genes linked to cuproptosis were screened, and knocking out seven genes reversed cuproptosis: reductase-ferredoxin 1; the three genes of the lipoic acid pathway-lipoyltransferase 1, lipoyl synthase, and dihydrolipoamide dehydrogenase; and the acylated protein targets-dihydrolipoyl transacetylase (DLAT), pyruvate dehydrogenase complex component A1 (PDHA1), and pyruvate dehydrogenase complex component B (PDHB). Among them, the β subunit of pyruvate dehydrogenase, encoded by the PDHB gene, can form a tetramer with the α subunit and irreversibly catalyze the physiological function of converting pyruvate to acetyl-CoA since DLAT provides structural support and also exhibits enzymatic activity within the pyruvate dehydrogenase complex (PDC). Furthermore, within the PDC, the primary target of cuproptosis is DLAT rather than PDHB or PDHA1. Consequently, the involvement of PDHB in the inactivation of PDC caused by cuproptosis is more likely a secondary consequence. In this review, the characteristics of the cuproptosis-associated gene PDHB and its role in the biological function and pathogenesis of the disease are discussed.