ANALYTICA CHIMICA ACTA
·
2025
·
IF 6
Mimi Li,Lina Wang,Yue Hu,Yi Liu,Shuang Xu,Kexing Peng,Chenghong Li,Hui Huang,Lichao Fang,Lulu Li,Huamin Liu,Xiaolong Wang,Junsong Zheng
Sensitive and efficient detection of RNA methylation sites is considered an integral part of epigenetic assessment. Contrary to previous studies on the detection of RNA m5C or m6A methylation alone, this study innovatively designed a biosensor capable of detecting RNA m5C or m6A methylation at the same time. Substances with specific electrochemical reactions such as ferrocene (FC) or methylene blue (MB) were modified onto the hairpin probe. When the hairpin probe was activated under specific conditions, it triggered a dendritic nonlinear hybridization chain reaction (HCR), which resulted in signal amplification. Gold (Au) and iron tetraoxide (Fe 3 O 4 ) composite nanomaterials were employed as the linking materials: the carboxylated ends of Fe 3 O 4 were connected to an antibody that specifically recognizes the m5C and m6A methylation sites, while Au nanoparticle ends adhering to the carboxylated Fe 3 O 4 surface are connected to the HCR enhanced signal amplifier. The m5C antibody was linked to Fc-containing HCR amplification products by this material, and similarly, the m6A antibody was linked to MB-containing amplifiers. Thus, the dandelion complex, a multifunctional body with methyl recognition and signal amplification, was formed. The capture probe immobilized on the surface of the gold electrode by Au–S recognized the target RNA sequence by base complementary pairing. Upon addition of the dandelion complex, due to its multi-functionality, the amplified signals were carried to the electrode by the antigen-antibody recognition mechanism, generating a current signal. The positions and heights of the current signal peaks enabled rapid determination of target RNA methyl modification sites and their abundance. The detection limits of this biosensor for RNA m5C and m6A were 4.68 × 10 −16 M and 1.10 × 10 −15 M, respectively, and the linear range was from 10 −15 mol/L to 10 −8 mol/L. The sensor developed in this study has the advantages of cost-effectiveness, ease of fabrication, and fast response time, and has the potential to be promoted for RNA methylation detection.
研究领域:
分子生物学
·
生物传感技术
·
表观遗传学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
Frontiers in Cell and Developmental Biology
·
2022
·
IF 6.081
Zhou Tong,Chen Guobin,Chen Meng,Wang Yubin,Zou Guiwei,Liang Hongwei
Sex dimorphism is a key feature of Chinese soft-shelled turtle (Pelodiscus sinensis). The males (M) have higher econosmic value than females (F) due to wider calipash and faster growth. Exogenous hormones like estradiol and methyltestosterone can induce sexual reversal to form new phenotypes (pseudo-female, PF; pseudo-male, PM) without changing the genotype. The possibility of inducing sexual reversal is particularly important in aquaculture breeding, but the underlying biological mechanisms remain unclear. Here we applied a direct RNA sequencing method with ultralong reads using Oxford Nanopore Technologies to study the transcriptome complexity in P. sinensis. Nanopore sequencing of the four gender types (M, F, PF, and PM) showed that the distribution of read length and gene expression was more similar between same-sex phenotypes than same-sex genotypes. Compared to turtles with an M phenotype, alternative splicing was more pronounced in F turtles, especially at alternative 3′ splice sites, alternative 5′ splice sites, and alternative first exons. Furthermore, the two RNA methylation modifications m5C and m6A were differentially distributed across gender phenotypes, with the M type having more modification sites in coding sequence regions, but fewer modification sites in 3′UTR regions. Quantitative analysis of enriched m6A RNAs revealed that the N6-methylated levels of Odf2, Pacs2, and Ak1 were significantly higher in M phenotype individuals, while the N6-methylated levels of Ube2o were reduced after sexual reversal from both M and F phenotypes. Taken together, these findings reveal an important role of epigenetics during sexual reversal in Chinese soft-shelled turtles.
研究领域:
发育生物学
·
分子生物学
·
水产养殖学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
·
2024
·
IF 3.1
Chen Hua,Han Cailing,Ha Chunfang
Uterine corpus endometrial carcinoma (UCEC) is one of the most common gynecologic tumors. Due to the high recurrence and metastasis of UCEC, it is crucial for patients to find new biomarkers for diagnosis and therapy. In this study, R software and the TCGA database were used to screen candidate UCEC predictive markers. Western blot and RT-qPCR were performed to detect protein and mRNA expression of EXT1 in UCEC cell lines. In addition, MTT assay, flow cytometry, transwell assay, and wound healing assay were conducted to assess the cell viability, apoptosis, invasion, and migration in UCEC cells. Overlap-extension PCR technique was employed to construct the vector targeting the deletion of the methylated segment of EXT1. The results showed that a total of 11 candidate genes were obtained and EXT1 was identified as a potential target. The expression and methylation levels of EXT1 were both increased in UCEC tissues and cell lines, as well as elevated EXT1 was closely related to the poor prognosis of patients. Besides, the knockdown of EXT1 significantly inhibited the malignant biological behaviors in UCEC cells. Additionally, the current study also found that the deletion of 1559–2146 bp CpG island segment upregulated EXT1 expression and promoted malignant biological behaviors in UCEC cells. Furthermore, the presence of m7G RNA methylation in UCEC cells also was found. In conclusion, the methylation of EXT1 influenced the gene expression, thereby affecting the malignant biological behaviors in UCEC cells and regulating the pathological progression of UCEC. Graphical
研究领域:
肿瘤学
·
分子生物学
·
基因组学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
·
2024
·
IF 6.2
Cuiyuan Jin,Caiyun Wang,Chen Zhang,Qi Ye,Yuanxiang Jin,Liyun Shi
As a fungicide with the characteristics of high effectiveness, internal absorption and broad spectrum, imazalil is widely used to prevent and treat in fruits and vegetables. Here, pregnant C57BL/6 mice were exposed to imazalil at dietary levels of 0, 0.025‰, and 0.25‰ through drinking water during pregnancy and lactation. We then analyzed the phenotype, metabolome, and expression of related genes and proteins in the livers of mice. There was a marked decrease in the body and liver weights of male offspring mice after maternal imazalil exposure, while this effect on the dam and female offspring was slight. Metabolomics analyses revealed that imazalil significantly altered the metabolite composition of liver samples from both dams and offspring. The preliminary results of the analysis indicated that glucolipid metabolism was the pathway most significantly affected by imazalil. We performed a coabundance association analysis of metabolites with significant changes in the pathway of glycolipid metabolism, and IMZ altered the networks of both dams and offspring compared with the network in control mice, especially in male offspring. The hepatic triglyceride, non-esterified fatty acid and glucose levels were increased significantly in the dams but decreased significantly in male offspring after maternal imazalil exposure. Furthermore, the expression levels of genes associated with glycolipid metabolism and m 6 A RNA methylation were significantly affected by maternal intake of imazalil. Imazalil-induced glucolipid metabolism disturbance was highly correlated with m 6 A RNA methylation. In conclusion, maternal imazalil exposure resulted in glucolipid metabolism disturbance and abnormal m 6 A RNA methylation in the livers of dams and offspring mice. We expected that the information acquired in this study will provide novel evidence for understanding the effect of maternal imazalil exposure on potential health risks.
研究领域:
毒理学
·
代谢组学
·
分子生物学
·
发育生物学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
International Journal of Oral Science
·
2024
·Vol. 16
·期 1
·1-13
·
IF 10.8
Li Shujin,Feng Tian,Liu Yuantong,Yang Qichao,Song An,Wang Shuo,Xie Jun,Zhang Junjie,Yuan Bifeng,Sun Zhijun
N 1 -methyladenosine (m 1 A) RNA methylation is critical for regulating mRNA translation; however, its role in the development, progression, and immunotherapy response of head and neck squamous cell carcinoma (HNSCC) remains largely unknown. Using Tgfbr1 and Pten conditional knockout (2cKO) mice, we found the neoplastic transformation of oral mucosa was accompanied by increased m 1 A modification levels. Analysis of m 1 A-associated genes identified TRMT61A as a key m 1 A writer linked to cancer progression and poor prognosis. Mechanistically, TRMT61A-mediated tRNA-m 1 A modification promotes MYC protein synthesis, upregulating programmed death-ligand 1 (PD-L1) expression. Moreover, m 1 A modification levels were also elevated in tumors treated with oncolytic herpes simplex virus (oHSV), contributing to reactive PD-L1 upregulation. Therapeutic m 1 A inhibition sustained oHSV-induced antitumor immunity and reduced tumor growth, representing a promising strategy to alleviate resistance. These findings indicate that m 1 A inhibition can prevent immune escape after oHSV therapy by reducing PD-L1 expression, providing a mutually reinforcing combination immunotherapy approach.
研究领域:
肿瘤学
·
免疫学
·
分子生物学
·
癌症治疗
✓ 已验证
产品关联
DOI
PubMed
高影响因子
CHEMOSPHERE
·
2024
·
IF 8.1
Qiuhui Qian,Qian Pu,Xin Li,XingCheng Liu,Anyu Ni,Xiaowen Han,Zejun Wang,Xuedong Wang,Jin Yan,Huili Wang
Triclosan (TCS), a prevalent contaminant in aquatic ecosystems, has been identified as a potential threat to both aquatic biota and human health. Despite its widespread presence, research into the immunotoxic effects of TCS on aquatic organisms is limited, and the underlying mechanisms driving these effects remain largely unexplored. Herein, we investigated the developmental and immune toxicities of environmentally relevant concentrations of TCS in zebrafish, characterized by morphological anomalies, histopathological impairments, and fluctuations in cytological differentiation and biomarkers following both acute (from 6 to 72/120 hpf) and chronic exposure periods (from 30 to 100 dpf). Specifically, acute exposure to TCS resulted in a significant increase in innate immune cells, contrasted by a marked decrease in T cells. Furthermore, we observed that TCS exposure elicited oxidative stress and a reduction in global m 6 A levels, alongside abnormal expressions within the m 6 A modification enzyme system in zebrafish larvae. Molecular docking studies suggested that mettl3 might be a target molecule for TCS interaction. Intriguingly, the knock-down of mettl3 mirrored the effects of TCS exposure, adversely impacting the growth and development of zebrafish, as well as the differentiation of innate immune cells. These results provide insights into the molecular basis of TCS-induced immunotoxicity through m 6 A-RNA epigenetic modification and aid in assessing its ecological risks, informing strategies for disease prevention linked to environmental contaminants.
研究领域:
水生毒理学
·
分子生物学
·
环境科学
·
免疫学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
AQUATIC TOXICOLOGY
·
2024
·
IF 4.1
Jinyun Li,Lu Fang,Miaocui Xi,Anyu Ni,Qiuhui Qian,Zejun Wang,Huili Wang,Jin Yan
Triclosan (TCS), recognized as an endocrine disruptor, has raised significant concerns due to its widespread use and potential health risks. To explore the impact of TCS on lipid metabolism, both larval and adult zebrafish were subjected to acute and chronic exposure to TCS. Through analyzes of biochemical and physiological markers, as well as Oil Red O (ORO) and hematoxylin and eosin (H&E) staining, our investigation revealed that TCS exposure induced hepatic and intestinal lipid accumulation in larval and adult zebrafish, leading to structural damage and inflammatory responses in these tissues. The strong affinity of TCS with PPARγ and subsequent pathway activation indicate that PPARγ pathway plays a crucial role in TCS-induced lipid buildup. Furthermore, we observed a decrease in m6A-RNA methylation levels in the TCS-treated group, which attributed to the increased activity of the demethylase FTO and concurrent suppression of the methyltransferase METTL3 gene expression by TCS. The alteration in methylation dynamics is identified as a potential underlying mechanism behind TCS-induced lipid accumulation. To address this concern, we explored the impact of folic acid—a methyl donor for m6A-RNA methylation—on lipid accumulation in zebrafish. Remarkably, folic acid administration partially alleviated lipid accumulation by restoring m6A-RNA methylation. This restoration, in turn, contributed to a reduction in inflammatory damage observed in both the liver and intestines. Additionally, folic acid partially mitigates the up-regulation of PPARγ and related genes induced by TCS. These findings carry substantial implications for understanding the adverse effects of environmental pollutants such as TCS. They also emphasize the promising potential of folic acid as a therapeutic intervention to alleviate disturbances in lipid metabolism induced by environmental pollutants.
研究领域:
环境毒理学
·
分子生物学
·
脂质代谢
·
斑马鱼研究
·
表观遗传学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
ADVANCED FUNCTIONAL MATERIALS
·
2025
·
IF 19
Yangcenzi Xie,Wenqian Tian,Chao Zheng,Ming Li
RNA N 6 -methyladenosine (m 6 A) modification plays critical roles in diverse biological processes and human diseases, but its functional studies are greatly impeded by the inability to quantify the m 6 A methylation in whole-transcriptomes. Here, An integrated label-free surface-enhanced Raman spectroscopy (SERS) profiling strategy, named m 6 A-SERS-profiler, is developed for quantitative transcriptome-wide m 6 A detection of cellular and serum RNA. The m 6 A-SERS-profiler is rationally designed through coupling the plasmonic liquid microparticle-based label-free SERS biosensing with the custom deep learning-assisted spectral analysis of m 6 A methylation signatures. With this m 6 A-SERS-profiler, direct identification of SERS spectral signatures of canonical nucleoside monophosphates and N 6 -methyladenosine 5′-monophosphate is achieved. The applicability of the m 6 A-SERS-profiler is verified by quantifying the m 6 A methylation status of microRNA and natural RNA in total RNA isolated from cancer cells and clinical serums. The results reveal a significant difference in the m 6 A RNA methylation among breast cancer cells of different subtypes and between clinical serums from healthy individuals and breast cancer patients. Moreover, the method can quantitatively track the m 6 A dynamics in cancer cells caused by pharmacological inhibition of the m 6 A methyltransferase. Thus, this m 6 A-SERS-profiler holds great promise for transcriptome-wide quantitative detection of m 6 A RNA methylation to investigate biological functions and dynamics of m 6 A methylation in human diseases.
研究领域:
生物化学
·
分子生物学
·
生物物理学
·
癌症研究
·
分析化学
✓ 已验证
产品关联
DOI
高影响因子
Applied Biological Chemistry
·
2025
·Vol. 68
·期 1
·1-11
·
IF 2.7
Dou Yufeng,Yang Jiao,Huang Na,Lu Xiaoxiao,Yan Liping
Background Pneumonia is a serious respiratory disease that significantly impacts human health. Quercetin (QUE), a plant extract, has been shown to exert protective effects against lung injury, but its precise mechanisms remain unclear. Methods Lipopolysaccharide (LPS) was used to induce injury in embryonic lung fibroblasts. Cell viability, proliferation, and apoptosis were assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay, 5-ethynyl-2’-deoxyuridine (EdU) staining, and flow cytometry assay, respectively. Reactive oxygen species (ROS), malondialdehyde (MDA), and Fe 2+ levels were evaluated using corresponding assay kits. The levels of inflammatory factors were determined by enzyme-linked immunosorbent assay (ELISA). Quantitative real-time PCR (qRT-PCR) and western blot were employed to analyze the expression and correlation of related genes. Methylated RNA immunoprecipitation (MeRIP) was employed to verify the regulatory mechanism between genes. Results QUE inhibited embryonic lung fibroblast injury. Both transducin β-like 1 X-linked receptor 1 (TBL1XR1) and methyltransferase 3 (METTL3) were highly expressed in lung injury tissues and cells, which were decreased by QUE treatment. TBL1XR1 deficiency weakened LPS-induced embryonic lung fibroblast injury. Mechanistically, METTL3 mediated the N 6 -methyladenosine (m6A) methylation and stabilized the TBL1XR1 mRNA. TBL1XR1 up-regulation alleviated the retardation of METTL3 absence on embryonic lung fibroblast injury. Furthermore, METTL3 overexpression reversed the inhibition of QUE on embryonic lung fibroblast injury. Conclusion QUE inhibited embryonic lung fibroblast injury by regulating the METTL3-mediated m6A methylation of TBL1XR1 mRNA.
研究领域:
分子生物学
·
药理学
·
呼吸医学
·
表观遗传学
·
细胞生物学
✓ 已验证
产品关联
DOI
高影响因子
INTERNATIONAL IMMUNOPHARMACOLOGY
·
2024
·
IF 4.8
Zhongkai Zhao,Zeyu Miao,Yuyang Hou,Yifan Zhong,Xiaorong Zhang,Xuedong Fang
Background A newly identified type of cell death due to intracellular copper accumulation is known as cuproptosis and RNA methylation is a post-transcriptional modification mechanism, both of which perform vital roles in the immune microenvironment of colorectal cancer (CRC), but the link between the two needs more research. Methods TCGA database provided RNA-seq data and details clinically of CRC samples. Cuproptosis-related RNA methylation regulators (CRRMRs) were identified by correlation analysis. We screened 6 CRRMRs for prognostic model construction by employing LASSO-Cox regression analysis and calculated risk scores by CRRMRs (CuMS). GSE39582 and GSE38832 cohort were used as external validation sets. This research concentrated on the connection between the prognostic model and somatic mutation, anti-cancer drug sensitivity, immune infiltration, immune checkpoint expression. In addition, we investigated the differential expression of YTHDC2 in epithelial cell subpopulations by single-cell analysis with GSE166555, calculated cuproptosis scores and performed pathway enrichment. In vitro experiments were performed to explore the consequences of knockdown of YTHDC2 on CRC cell proliferation and migration, as well as changes in CRC cell viability in response to elesclomol after knockdown of YTHDC2. In vivo experiments, we constructed the cell line-derived xenograft model to further validate the results of the in vitro experiments. Results The prognosis of CRC can be predicted by CuMS, which GSE39582 and GSE38832 confirmed. Two CuMS groups showed different tumor mutation burden (TMB) and immune infiltration. CuMS was connected to emerging immune checkpoints CD47 and PVR, therefore, it can be clinically complementary to TMB and microsatellite instability (MSI) status. In single-cell analysis, a subpopulation of epithelial cells with high YTHDC2 expression had a high cuproptosis score. In vitro experiments, knocking down YTHDC2 promoted cell proliferation and migration in CRC, and weaken the inhibitory effect of elesclomol and elesclomol-Cu on cell viability, which in vivo experiments validated. Conclusion We developed a prognostic model constructed by 6 CRRMRs to assess overall survival and immune microenvironment of CRC patients. YTHDC2 might regulate cuproptosis in multiple ways.
研究领域:
肿瘤学
·
分子生物学
·
免疫学
·
基因组学
·
生物信息学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
·
2021
·
IF 3.935
Ji-shuo Chang,Zhong-xiao Lin,Ya-juan Liu,Si-ming Yang,Yu Zhang,Xi-yong Yu
Previous studies have reported that nucleic acid methylation is a critical element in cardiovascular disease, and most studies mainly focused on sequencing and biochemical research. Here we developed an Ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/ MS) method for the quantification analysis of the dissociative epigenetic modified nucleosides (5mdC, 5mrC, m 6 A) in Myocardial Infarction (MI) SD rats from different periods (1 week, 4 weeks, 8 weeks) after the surgery. The samples for analysis were obtained from heart tissue and blood of the rats. All the quantification results are compared with the sham-operated group. Total RNA and DNA were isolated by enzymatic hydrolytic methods before the UPLC-MS/MS analysis. The statistical analysis demonstrates the dynamic changes of modified nucleosides in MI rats, and it showed good specificity, accuracy, stability and less samples were needed in the method. In this paper, we discovered that the concentration of 5mdC, 5mrC, m 6 A from heart tissue significantly increased at 8 weeks after the surgery. Furthermore, UPLC-MS/MS helps us observe the similar change of the concentration of those 3 methylated biomarkers in peripheral blood after 8 weeks. The result shows that the dynamic process of those 3 methylated biomarkers in peripheral blood is related to the content of methylated biomarkers from the heart tissue. Based on the scientific evidence available, we proved that the methylation of genetic materials in peripheral blood is similar to myocardial infarction tissue. The relation between them indicates that peripheral blood could be a promising alternative to the heart tissue which monitor the level of methylation and MI diagnosis-aided.
研究领域:
心血管疾病
·
表观遗传学
·
分析化学
·
分子生物学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）