Frontiers in bioscience (Landmark edition)最新文献

Background: Mucopolysaccharidosis (MPS) is a class of hereditary metabolic diseases that demonstrate itself by accumulating incompletely degraded glycosaminoglycans (GAGs). MPS are classified according to the kind(s) of stored GAG(s) and specific genetic/enzymatic defects. Despite the accumulation of the same type of GAG, two MPS diseases, Sanfilippo (MPS III) and Morquio (MPS IV), are further distinguished into subclasses based on different enzymes that are deficient. Although genetic defects in MPS are known, molecular mechanisms of particular MPS types are still incomplete. This work aimed to investigate gene expression patterns in MPS III and MPS IV subtypes to identify dysregulated genes that could indicate unidentified molecular mechanisms of the diseases.

Methods: Transcriptomic analyses were conducted to assess gene expression patterns in MPS and control cells. Western blotting and immunohistochemistry determined selected protein levels (products of the most significantly dysregulated genes). Effects of decreased levels of gene expression were investigated using small interferring RNA (siRNA)-mediated gene silencing.

Results: Transcriptomic analyses indicated 45 commonly dysregulated genes among all MPS III subtypes and as many as 150 commonly dysregulated genes among both MPS IV subtypes. A few genes revealed particularly high levels of dysregulation, including PFN1, MFAP5, and MMP12. Intriguingly, elevated levels of profilin-1 (product of the PFN1 gene) could be reduced by decreasing GAG levels in genistein-treated MPS III and MPS IV cells, while silencing of PFN1 caused a significant decrease in GAG accumulation in these cells, indicating an interdependent correlation between profilin-1 and GAG levels.

Conclusions: A plethora of commonly dysregulated genes were identified in MPS subtypes III and IV. Some of these genes, like PFN1, MFAP5, and MMP12, revealed highly pronounced changes in expression relative to control cells. An interdependent correlation between GAG levels and the expression of the PFN1 gene was identified. Thus, PFN1 could be suggested as a potential new therapeutic target for MPS III and IV.

Background: Epidermal growth factor receptor 4 (ERBB4) and neuregulin 4 (NRG4) have been shown to reduce steatosis and prevent the development of non-alcoholic steatohepatitis in mouse models, but little to nothing is known about their role in non-alcoholic fatty liver disease (NAFLD) in humans. This study is the first to investigate the expression of ERBB4 and NRG4 mRNAs and their role in lipid metabolism in the livers of individuals with obesity, type 2 diabetes and biopsy-proven NAFLD.

Methods: Liver biospecimens were obtained intraoperatively from 80 individuals. Quantitative reverse transcription polymerase chain reaction was used to measure the expression levels of mRNAs ERBB4 and NRG4, as well as key lipogenesis genes in the liver tissue of the donors. Histological analysis was conducted on liver biopsies from 36 subjects, and the levels of the examined transcripts were compared with the stage of NAFLD.

Results: In individuals with elevated body mass index (BMI), ERBB4 and NRG4 levels decreased, while ACACA levels increased. A strong negative correlation was observed between NRG4 and ACACA levels. No deregulation of the analyzed transcripts was detected in NAFLD.

Conclusions: The study demonstrates a decrease in ERBB4 and NRG4 mRNA expression in the livers of subjects with high BMI but not in those with NAFLD. The correlation of the studied transcripts with major lipogenesis genes was assessed, and on this basis a putative scheme for NRG4-mediated suppression of hepatic de novo lipogenesis was hypothesised, offering new research vectors in this field.

Background: Fusion genes are important biomarkers in cancer research because their expression can produce abnormal proteins with oncogenic properties. Long-read RNA sequencing (long-read RNA-seq), which can sequence full-length mRNA transcripts, facilitates the detection of such fusion genes. Several tools have been proposed for detecting fusion genes in long-read RNA-seq datasets derived from cancer cells. However, the high sequencing error rate in long-read RNA-seq makes fusion gene detection challenging.

Methods: To address this issue, additional steps were incorporated into the fusion detection tool to improve detection accuracy. These steps include anchoring breakpoints to exon boundaries, realigning unaligned regions, and clustering breakpoints. To evaluate the accuracy of our tool in detecting fusion genes, we compared its detection accuracy with two representative existing tools, JAFFAL and FusionSeeker.

Results: Our tool outperformed the two existing tools in detecting fusion genes, as demonstrated in long-read RNA-seq datasets. We also identified potentially novel fusion genes consistently detected across multiple tools or datasets.

Conclusions: The application of our tool to the detection of fusion genes in long-read RNA-seq datasets from two different cancer cell lines demonstrated the detection effectiveness of this tool.

Acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) is a common critical illness. Supportive therapy is still the main strategy for ALI/ARDS. Macrophages are the predominant immune cells in the lungs and play a pivotal role in maintaining homeostasis, regulating metabolism, and facilitating tissue repair. During ALI/ARDS, these versatile cells undergo polarization into distinct subtypes with significant variations in transcriptional profiles, developmental trajectory, phenotype, and functionality. This review discusses developments in the analysis of alveolar macrophage subtypes in the study of ALI/ARDS, and the potential value of targeting new macrophage subtypes in the diagnosis, prognostic evaluation, and treatment of ALI/ARDS.

Background: Psoriasis is a chronic and incurable skin inflammation driven by an abnormal immune response. Our study aims to investigate the potential of interferon-γ (IFN-γ) primed mesenchymal stem cells (IMSCs) in targeting T cells to attenuate psoriasis-like inflammation, and to elucidate the underlying molecular mechanism involved.

Methods: Mesenchymal stem cells (MSCs) were isolated from the umbilical cord and identified based on their surface markers. Psoriasis models were established and then treated with IMSCs. Flow cytometry analysis was used to examine cell surface markers and T cell percentages. Indoleamine-2,3-dioxygenase (IDO) was knocked down by small interfering RNA (siRNA) and examined with western blot assay. The proliferative capacity of T cells was assessed using water-soluble tetrazolium salt-1(WST-1). Additionally, an immunohistochemical assay was used to determine epidermal thickness. The psoriasis area and severity index (PASI) scores were also assessed.

Results: We observed significant therapeutic efficacy of IMSCs against psoriasis-like inflammation in mice. Treatment with IMSCs resulted in a notable reduction in T cell infiltration within psoriatic lesions. Furthermore, we demonstrated that the therapeutic efficacy was mediated by the upregulation of IDO through IFN-γ stimulation. In vitro, IDO inhibited T cell proliferation, and in vivo, the therapeutic efficacy was eliminated when MSCs were transfected with IDO siRNA.

Conclusion: IMSCs can treat psoriasis by suppressing T cell infiltration and the suppression is mediated by IDO.

This review explores the intricate relationship between glaucoma and circadian rhythm disturbances. As a principal organ for photic signal reception and transduction, the eye plays a pivotal role in coordinating the body's circadian rhythms through specialized retinal ganglion cells (RGCs), particularly intrinsically photosensitive RGCs (ipRGCs). These cells are critical in transmitting light signals to the suprachiasmatic nucleus (SCN), the central circadian clock that synchronizes physiological processes to the 24-hour light-dark cycle. The review delves into the central circadian body clock, highlighting the importance of the retino-hypothalamic tract in conveying light information from the eyes to the SCN. It underscores the role of melanopsin in ipRGCs in absorbing light and initiating biochemical reactions that culminate in the synchronization of the SCN's firing patterns with the external environment. Furthermore, the review discusses local circadian rhythms within the eye, such as those affecting photoreceptor sensitivity, corneal thickness, and intraocular fluid outflow. It emphasizes the potential of optical coherence tomography (OCT) in studying structural losses of RGCs in glaucoma and the associated circadian rhythm disruption. Glaucomatous retinal damage is identified as a cause of circadian disruption, with mechanisms including oxidative stress, neuroinflammation, and direct damage to RGCs. The consequences of such disruption are complex, affecting systemic and local circadian rhythms, sleep patterns, mood, and metabolism. Countermeasures, with implications for glaucoma management, are proposed that focus on strategies to improve circadian health through balanced melatonin timing, daylight exposure, and potential chronotherapeutic approaches. The review calls for further research to elucidate the mechanisms linking glaucoma and circadian disruption and to develop effective interventions to address this critical aspect of the disease.

Background: Acute lung injury (ALI) significantly impacts the survival rates in intensive care units (ICU). Releasing a lot of pro-inflammatory mediators during the progression of the disease is a core feature of ALI, which may lead to uncontrolled inflammation and further damages the tissues and organs of patients. This study explores the potential therapeutic mechanisms of Dexmedetomidine (Dex) in ALI.

Methods: In present study, cecal ligation puncture (CLP)-established ALI model mice and lipopolysaccharide (LPS)-stimulated RAW264.7 cell line were established to discover the influence of Dex. The evaluation of lung injury in vivo using histopathology, TUNEL assay, and analysis of inflammatory factors in bronchoalveolar lavage fluid (BALF) and serum. The receptor for advanced glycation end products (RAGE)/Caspase-11-dependent pyroptosis-related proteins and macrophage polarization markers were analyzed using western blot, immunofluorescence, and flow cytometry. Finally, the mechanism of Dex in macrophages was further verified in vitro.

Results: In vivo, Dex alleviated lung injury and decreased TUNEL-positive cell expression in CLP group. Dex decreased tumor necrosis factor-alpha (TNF-α), interleukin (IL)-6 and IL-17A levels in BALF and serum, while increasing IL-10 expression. Dex treatment decreased the protein levels of RAGE, caspase-11, IL-1β and Gasdermin-D (GSDMD) in both in cells and in mice. Dex also down-regulated the synthesis of inducible nitric oxide synthase (iNOS) of classical activation phenotype (M1) markers, and up-regulated the synthesis of CD206 and Arg-1 of alternate activation phenotype (M2) markers.

Conclusions: Dex treatment can inhibit inflammation and reduce lung injury caused by CLP. It could be associated with mediating M1 and M2 polarization and suppressing RAGE/Caspase-11-depended pyroptosis.

Background: There is a growing interest in exploring the biological characteristics of nanoparticles and exploring their potential applications. However, there is still a lack of research into the potential genotoxicity of fullerene derivatives and their impact on gene expression in human cells. In this study, we investigated the effects of a water-soluble fullerene derivative, C60[C6H4SCH2COOK]5H (F1), on human embryonic lung fibroblasts (HELF).

Methods: 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) test was used to study the cytotoxicity of F1; reactive oxygen species (ROS) level was determined with 2,7-DCFH-DA; gene expression level was evaluated by reverse transcription polymerase chain reaction (RT-PCR); protein expression level was determined by flow cytofluorometry; fluorescence microscopy was used for visualization; Mann-Whitney statistical U-test was used for data processing. The differences were considered significant at p < 0.01.

Results: F1 at a concentration of 0.3 mg/mL causes a short-term (up to 1 hour) increase in the number of double-strand breaks and oxidative DNA damage in HELF. Within 1 to 24 hours, F1 penetrates through the cell and nuclear membrane of HELF and localizes in the nucleus. In this case, the response of cells to DNA damage is activated: the functional activity of DNA repair genes, antioxidant and anti-apoptotic genes is increased within 24 hours. Due to the processes of activation of cell division and inhibition of apoptosis, an increase in the population of HELF cells in the presence of the fullerene derivative F1 is observed. F1 has a stabilizing effect on cell nuclei under the action of 1 Gy radiation.

Conclusions: An increase in antioxidant protection, activation of repair genes, anti-apoptotic genes, progression of the cell cycle, and a decrease in the level of oxidative damage, and DNA breaks in cells indicates the cytoprotective properties of F1.

Background: Aneuploidy is crucial yet under-explored in cancer pathogenesis. Specifically, the involvement of brain expressed X-linked gene 4 (BEX4) in microtubule formation has been identified as a potential aneuploidy mechanism. Nevertheless, BEX4's comprehensive impact on aneuploidy incidence across different cancer types remains unexplored.

Methods: Patients from The Cancer Genome Atlas (TCGA) were stratified into high-score (training) and low-score (control) groups based on the aneuploidy score. Mfuzz expression pattern clustering and functional enrichment were applied to genes with BEX4 as the core to explore their regulatory mechanisms. Various machine learning techniques were employed to screen aneuploidy-associated genes, after which aneuploidy characteristic subtypes were established in cancers. Moreover, the aneuploidy characteristics across multiple cancer types were investigated by integrating the extent of tumor cell stemness acquisition and a series of immune traits. Immunohistochemistry and proliferation assay mainly verified the anti-tumor effect of different BEX4 level.

Results: Functional clustering results showed that aneuploidy and stemness were significantly associated in kidney chromophobe (KICH) and thyroid carcinoma (THCA). And cell metabolism and cell cycle had key effects. Residual analysis indicates superior screening performance by random forest (RF). An aneuploid feature gene set with BEX4 as the core was screened to construct a Nomogram model. BEX4, calmodulin regulated spectrin associated protein 2 (CAMSAP2), and myristoylated alanine rich protein kinase C substrate (MARCKS) were identified as aneuploidy characteristic hub genes. Molecular subtypes in thymoma (THYM), thyroid carcinoma (THCA), and kidney chromophobe (KICH) showed significant differences in tumor cell stemness among different subtypes. The competitive endogenous RNA (ceRNA)-Genes network revealed that hub genes, co-regulated by hsa-miR-425-5p, hsa-miR-200c-3p, and others, regulate microtubules, centrosomes, and microtubule cytoskeleton. Furthermore, elevated BEX4 emerged as a significant protective factor in Pancreatic adenocarcinoma (PAAD), KICH, kidney renal papillary cell carcinoma (KIRP), and kidney renal clear cell carcinoma (KIRC).

Conclusions: BEX4, CAMSAP2, and MARCKS specifically express in microtubules, centrioles, and cytoskeletons, influencing tumor chromosome division and inducing aneuploidy. Additionally, the relationship between the acquisition of tumor cell stemness and the severity of aneuploidy varies significantly across tumor types, displaying positive and negative correlations.

Objective: The current study aimed to develop an experimental approach for the direct co-culture of three-dimensional breast cancer cells using single-cell RNA sequencing (scRNA-seq).

Methods: The following four cell culture groups were established in the Matrigel matrix: the untreated Michigan Cancer Foundation (MCF)-7 cell culture group, the MCF-7 cell culture plus cisplatin group, the untreated co-culture group, and the cell co-culture plus cisplatin group. For cell co-culture, MCF-7 cells, human mammary fibroblasts, and human umbilical vein endothelial cells were mixed at a ratio of 1:1:1. Cisplatin was applied at a concentration of 1.25 μg/mL, and the cells were harvested after 2 days and subjected to scRNA-seq. Data were analyzed using a single-cell RNA sequencing data analysis pipeline with R language.

Results: The response of MCF-7 cells to cisplatin differed among the four groups. The transcriptomic response of MCF-7 cells to cisplatin in the co-culture model was not as significant as that in the mono-culture model. Moreover, the pathways related to apoptosis, DNA damage, hypoxia, and metastasis in the co-culture groups were enriched in the genes that were differentially expressed based on cisplatin treatment.

Conclusion: scRNA-seq analysis revealed that the response of MCF-7 cells to cisplatin in the co-culture model was lower than that in the mono-culture model. Therefore, the three-dimensional cell co-culture model can be applied to tumor research to better mimic the pathophysiological environment in vivo and can be a well-modified research method.