SENSORS AND ACTUATORS B-CHEMICAL
·
2020
·
IF 7.1
Kaiwu Zhang,Xuan Wang,Caicheng Long,Jin Xu,Zixin Jiang,Bo Feng,Peng Zhang,Junjie Fei,Taiping Qing
DNA templated fluorescent copper nanoclusters (DNA-CuNCs) have demonstrated enormous potential for biochemical analysis. However, most of them are focused on DNA-related sensing. Here, we designed a hairpin DNA/RNA chimeric chain for the formation of fluorescent CuNCs and further applied it to detect reverse transcription-associated ribonuclease H (RNase H). The DNA/RNA chimera templated copper nanoclusters (DNA/RNA-CuNCs) exhibited similar spectral properties with DNA-CuNCs. In the presence of RNase H, the RNA segment in chimera is hydrolyzed and release short oligonucleotides, which fail to synthsize fluorescent CuNCs. The capabilities for RNase H detection from complex samples and screening of inhibitors were verified. This strategy exhibited high sensitivity for RNase H with a detectable minimum concentration of 5.5 × 10 −4 U mL -1 , which is lower than the developed fluorescent methods. This work will open up new thoughts to design new template for metal nanoclusters and broaden their application in RNA-related sensing.
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DOI
高影响因子
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
·
2019
·
IF 3.571
Zengpeng Lv,Chenhui Hu,Jingle Jiang,Song Jin,Quanwei Wei,Xihui Wei,Debing Yu,Fangxiong Shi
Genistein is abundant in animal feed. In this study, the side effects of high-dose genistein on intestinal health and hypothalamic RNA profile were evaluated. Chicks exposed to high-dose genistein by intraperitoneal injection (416 ± 21, 34.5 ± 2.5) and feed supplementation (308 ± 19, 27.2 ± 2.1) both showed a reduced body weight gain and feed intake in comparison with the control group (261 ± 16, 22.7 ± 1.6, P < 0.01). In comparison with the control (22.4 ± 0.5, 33.3 ± 2.4), serum levels of albumin and total protein were decreased after high-dose genistein injection (21.6 ± 0.5, 31.8 ± 1.6) and diet supplementation (20.6 ± 0.9, 29.9 ± 2.5, P < 0.001). Interestingly, the genistein diet presented the chick hypothalamus with downregulated expression of bitter receptors (TAS1R3, P < 0.05). Meanwhile, it upregulated the expressions of TAS2R1 (P < 0.05) and downstream genes (PLCB2 and IP3R3) in the ileum (P < 0.05). Accordingly, high-dose dietary genistein reduced villus height and the abundance of Lactobacillus, along with the increased abundance of pathogenic bacteria in the ileum (P < 0.05). Furthermore, transcriptomic analysis identified 348 differently expressed genes (168 upregulated and 224 downregulated) in the high-dose dietary genistein treated group in comparison with the control (P < 0.05, |log2FoldChange| > 0.585). Therefore, high-dose dietary genistein altered the hypothalamic RNA profile and signal processing. Cluster analysis further revealed that high-dose dietary genistein significantly influenced apoptosis, the immune process, and the whole synthesis of steroid hormones in the hypothalamus (P < 0.05). In conclusion, high-dose dietary genistein altered the hypothalamic RNA profile and intestinal health of female chicks.
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DOI
PubMed
高影响因子
Acta Pharmaceutica Sinica B
·
2024
·
IF 14.7
Li Qiao,Zhiyao Li,Bowen Li,Fu Zhang,Zhuo Yao,Chongzhi Wu,Honglin Tang,Qi Pan,Peihua Shi,Yuan Ping
Osteoarthritis (OA) is a type of highly prevalent heterogeneous degenerative disease that leads to joint pain, deformity, the destruction of articular cartilage, and eventual disability. The current treatment strategies for OA often suffer from systemic side effects, poor anti-inflammatory efficacy, and persistent pain. To address these issues, we develop light-inducible nanomedicine that enables the co-delivery of anti-inflammatory drug (diacerein, DIA) and small interfering RNA (siRNA) targeting nerve growth factor (NGF) for pain relief to enhance the therapeutic efficacy of OA. The nanomedicine is based on poly( β -amino-ester)-coated gold nanocages (AuNCs), which is further incorporated with the phase-change material (lauric acid/stearic acid, LA/SA). Following intra-articular (IA) injection in vivo , the nanomedicine displays high degree of drug accumulation and retention in the joint lesion of OA mouse models. The photothermal effect, induced by AuNCs, not only promotes DIA and siRNA release, but also upregulates the expression of heat shock protein 70 (HSP-70) to resist the apoptosis of chondrocytes in the inflammatory condition. The internalization of both DIA and siRNA results in strong anti-inflammatory and pain-relieving effects, which greatly contribute to the joint repair of OA mice. This study offers a promising combination strategy for OA treatment.
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DOI
PubMed
高影响因子
ACS Applied Materials & Interfaces
·
2025
·
IF 8.2
Mingyuan Li,Xianglong Wang,Mengsi Yin,Faxin Zhang,Wenlin Ma,Linze Che,Jinhao Yu,Yan Cheng,Mengju Xu,Xiaofu Liang,Wen Su,Hongmeng Ren,Weixue Si,Jingsi Ma,Shaodan Peng,Xiaolong Zhao,Jiaping Zhou,Ziqi Wu,Jiang Deng,Hua Sun
Lung cancer is the most prevalent and deadly tumor globally, marked by drug resistance and a poor prognosis. Specialized formulations with strong lung targeting are currently lacking. Docetaxel (DTX) and TUBB3-siRNA represent chemotherapy and RNA interference (RNAi), two strategies for lung cancer treatment. Lipid nanoparticles (LNPs) are nanocarriers suitable for nucleic acid delivery. In this study, spray freeze-drying (SFD) converted LNP colloidal solutions into inhalable dry powders. Fresh and rehydrated LNP (SFD) showed sizes below 200 nm, ζ potentials near 0 mV, and uniform roundness by transmission electron microscopy. The geometric particle size distribution (D50) of TUBB3-LNPs, DTX-LNPs, and TUBB3/DTX-LNPs inhalable powders did not differ significantly (1.99–5.90 μm). The median mass aerodynamic diameter (MMAD) was 2.61 ± 0.32 μm, suitable for pulmonary deposition. Experiments with BEAS-2B and H460 cells showed that TUBB3/DTX-LNPs had low cytotoxicity and good biocompatibility with BEAS-2B but strongly inhibited H460 cells. Differences in apoptosis induced by fresh LNPs and rehydrated LNP (SFD) indicate that the SFD process preserves normal cell viability while maintaining tumor inhibition. Because dry powder inhalers combine the drug formulation with the delivery device, a specialized single-dose prefilled device was developed that featured four symmetrically configured orifices (vents) located in the middle of the tube body; it achieved a high dry powder emptying rate of 95–100%. Furthermore, this study demonstrated the lung-targeting efficacy and sustained-release properties of the formulation.
研究领域:
药剂学
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纳米技术
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肿瘤学
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药物递送
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呼吸医学
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生物化学
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产品关联
DOI
PubMed
高影响因子
TECHNOLOGY IN CANCER RESEARCH & TREATMENT
·
2020
·
IF 2.074
AiJun Huang,LiPing Chen,YiMing Wang,ShuQiang Ma,Song Jin,Hanzhou Cai,Xingzhong Huang,Hongbo Zhang,ZengRong Wang,Kun Lin,Fangsiyu Lin
Background:5-fluorouracil (5-FU) is a widely used drug for cancer treatment, but its effect and underlying mechanisms on osteosarcoma (OS) cells remain unclear.Methods:U2OS and MG63 cells were treated with 0, 50, 100, and 500 μM 5-FU. MTS and flow cytometry were used to examine the effect of 5-FU on cell viability and apoptosis, respectively. Circular RNA (circRNA) expression was detected using RNA sequencing and quantitative real-time PCR (qPCR). Differentially expressed circRNAs were further subjected to the Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) analysis to predict their functions. A circRNA–miRNA–mRNA interaction network was generated to analyze the regulatory networks of 5-FU–induced differentially expressed circRNAs. Western blotting (WB) was used to verify the protein in the downstream of circRNAs.Results:5-FU inhibited the cell viability of the MG63 cells in a concentration-dependent manner. The most significant effect was observed in the cells treated with 500 μM 5-FU. Apoptosis was also increased in the MG63 cells after 500 μM 5-FU treatment for 3 days. RNA sequencing results showed that 183 differentially expressed circRNAs (172 upregulated and 11 downregulated) in 5-FU–treated cells. KEGG and GO analysis showed that the differentially expressed circRNAs were primarily enriched in proliferation-, apoptosis-, and metabolism-related functions. qPCR was used to verify the most upregulated and downregulated circRNAs. The circRNA–miRNA–mRNA interaction network showed that these 8 circRNAs had a sizable regulatory network that links a series of genes involved in tumor suppression.Conclusion:5-FU treatment resulted in the differentially expressed circRNAs that were proliferation- and apoptosis-associated and were involved in the 5-FU–induced inhibition of tumor proliferation in OS cells.
研究领域:
肿瘤学
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分子生物学
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基因组学
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癌症治疗
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DOI
PubMed
高影响因子
International Journal of Nanomedicine
·
2025
·
IF 6.5
Wenqiang Xue,Jinglei Du,Yingying Wei,Shizhao Zhou,Shicai Wang,Yongzhen Yang,Lin Chen,Shiping Yu
Background Small interfering RNA (siRNA) provides a new method for anti-tumor therapy by targeting Survivin gene in liver cancer. However, free Survivin siRNA is easily degraded and cleared by endonucleases or macrophages in the blood circulation. Therefore, it is urgent to construct a safe and efficient delivery system to achieve effective transfection of Survivin siRNA.Methods In this study, cationic carbon dots (CCDs) with active targeting ability (FA-PEI-CDs) were designed and prepared using carbon dots (CDs), polyethyleneimine (PEI), and folic acid (FA). Then, Survivin siRNA was loaded by electrostatic adsorption to design a gene-loaded complex with gene silencing effect (FA-PEI-CDs@Survivin siRNA).Results As FA-PEI-CDs had good dispersibility, an average diameter of about 21.71 nm and a zeta potential of 5.11 mV. They had good proton buffering capacity and excellent biocompatibility and could not cause erythrocyte hemolysis and thrombosis. When FA-PEI-CDs were mixed with Survivin siRNA at a mass ratio of 2:1, they can completely load siRNA without being interfered by polyanion in vivo and avoid the degradation of siRNA by serum or intracellular nuclease, which significantly increased the circulation time of siRNA in blood. Meantime, when the mass ratio of FA-PEI-CDs to Survivin siRNA was 3:1, the maximum transfection efficiency was 22.8% and 28.5% in HL-7702 cells and HepG2 cells, respectively. In vitro cell experiments confirmed that the gene complex can specifically kill tumor cells without damaging normal liver cells. In vivo tumor inhibition experiments further confirmed that FA-PEI-CDs@Survivin siRNA can cause tumor cell necrosis and reduce the expression of Survivin protein.Conclusion In summary, FA-PEI-CDs can carry Survivin siRNA to achieve tumor gene silencing therapy, which will expand the treatment of liver cancer and provide a new idea for carbon nanomaterials in biological genetic engineering.
研究领域:
医学
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遗传学
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纳米材料科学
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DOI
PubMed
高影响因子
STAR Protocols
·
2023
·
IF 0
Ran Li,Peng Zou
Summary Knowledge about the spatial organization of RNAs in eukaryotic cells is crucial for understanding their functions. Here, we present a detailed MERR APEX-seq protocol to achieve spatiotemporally resolved mapping of the subcellular transcriptome in cultured mammalian cells. This protocol provides detailed description of constructing cell lines stably expressing APEX2, immunofluorescence characterization, MERR APEX labeling, enrichment of biotinylated RNA, library construction and high-throughput sequencing, and MERR APEX-seq data analysis. For complete details on the use and execution of this protocol, please refer to Li et al. (2022). 1
研究领域:
分子生物学
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细胞生物学
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转录组学
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基因组学
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DOI
PubMed
Viruses-Basel
·
2025
·Vol. 17
·期 11
·1452
·
IF 3.5
Nuo Wang,Ping He,Bohan Xu,Hongping Wei,Junping Yu
Diagnosis of dengue virus infections typically relies on RT-PCR-based methods, for which reliable positive controls are essential. Viral RNA is an ideal positive control, but its inherent instability poses a major challenge. Herein, we report a simple and effective method for stabilizing dengue virus RNA by immobilizing it onto silk fibroin films (RNA-SFFs). We evaluated various substrate surfaces for RNA-SFFs preparation and found that the inner surface of sealable bags is optimal for uniform film formation and easy harvesting. Screening different silk fibroin concentrations revealed that even low concentrations (2.8%) effectively preserved RNA well and kept Ct constant for up to 16 days at 25 °C, 37 °C, and even 45 °C (extreme weather for transportations). Due to its rapid film formation and ease of peeling, 7% silk fibroin was selected. Notably, the RNA-SFFs demonstrated robust resistance to UV irradiation, with no significant Ct value changes after 4 h of exposure. Long-term stability testing at −20 °C, 25 °C, and 37 °C showed that dengue serotype 1–4 RNA-SFFs remained stable for the entire duration of the study—up to 56 weeks (approximately 14 months)—at all tested temperatures. These results demonstrate that RNA-SFFs are highly stable, portable, and practical as positive controls for dengue diagnostics, with strong potential for use in on-site and resource-limited settings.
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DOI
PubMed
高影响因子
ACS Synthetic Biology
·
2025
·
IF 3.9
Jing Wu,Ziqian Xiao,Yuhui Du,Minglan Luo,Jiacheng Zhang,Pei Guo,Zhipeng Chen,Binyuan Yang,Tingjian Chen
Aptamer-based sensors (aptasensors) have been extensively employed in biosensing and diagnostics. However, the broader application of aptasensors fabricated with DNA and RNA aptamers has been limited due to the intolerance of DNA and RNA to nucleases in biological fluids. A majority of sugar-modified nucleic acids, in particular 2’-F and 2’-OMe-modified nucleic acids, demonstrate a remarkable resistance to nuclease degradation and thus hold great potential in the development of more stable aptamers and aptasensors. In this work, employing enzymes including a laboratory-evolved polymerase for 2’-modified nucleic acids, we carried out systematic evolution of ligands by exponential enrichment (SELEX) experiments to obtain 2’-F/OMe-RNA aptamers for Bacillus cereus 5/B/6 metallo-β-lactamase (B. cereus 5/B/6 MBL), a crucial marker of many penicillin-resistant strains. Three aptamers composed of 2’-OMe-A, 2’-F-U, 2’-F-C, and 2’-OMe-G nucleotides (Apt-FUC1, Apt-FUC2, and Apt-FUC3) have been obtained and systematically characterized. All of them exhibited excellent target binding affinities, with equilibrium dissociation constant (Kd ) values of 95.9, 70.0, and 81.3 nM, and outstanding biological stability. Combining FAM-labeled Apt-FUC1, Apt-FUC2, and Apt-FUC3 with graphene oxide (GO), which could quench the fluorescence of FAM, we successfully constructed three sensitive and biologically stable 2’-F/OMe-RNA aptasensors for B. cereus 5/B/6 MBL, with the limit of detection (LOD) values of 0.38, 0.27, and 0.29 nM. Moreover, these three aptasensors all demonstrated good specificity for target detection in biological samples. This work has established a streamlined strategy for generating stable 2’-F/OMe-RNA aptamers and aptasensors, which should broaden the application of sugar-modified nucleic acids in biosensing and diagnostics.
研究领域:
分子诊断
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核酸工程
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生物传感器
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酶检测
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抗生素耐药性
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合成生物学
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DOI
PubMed
高影响因子
Data
·
2025
·Vol. 11
·期 1
·4
·
IF 2
Nataliya G. Luzgina,Svetlana N. Tarbeeva,Daniil D. Romashin,Konstantin G. Ptitsyn,Svetlana A. Khmeleva,Leonid K. Kurbatov,Sergey P. Radko,Anna S. Kozlova,Polina A. Veselova,Ekaterina V. Ilgisonis,Alexander L. Rusanov
The aryl hydrocarbon receptor (AhR) plays a crucial role in mediating xenobiotic responses, as well as regulating broader metabolic, differentiation, and stress response programs. In this study, we present a comprehensive long-read RNA sequencing dataset that examines transcriptional changes in the HepaRG human cell line during differentiation induced by dimethyl sulfoxide (DMSO) and acute activation of the AhR with 3-methylcholanthrene (3-MC). We identified 946 genes that were differentially expressed between the NonDiff and Diff conditions (303 genes upregulated and 643 genes downregulated), and 1786 genes that showed differential expression between Diff and Ind conditions (961 genes upregulated and 825 genes downregulated). The acute induction of 3-MC produced a robust AhR signature, characterized by the robust induction ofCYP1A1andCYP1B1, along with a coordinated downregulation of several constitutive hepatic genes involved in drug metabolism (e.g.,CYP3A4andCYP2C8). To facilitate further analysis and reuse of our data, we have provided processed gene-level count matrices, transcript per million (TPM) tables, and detailed differential expression results, as well as analysis scripts. This resource supports research into AhR biology, pharmacogene regulation, and the development of methods for long-read transcriptomics in liver models.Dataset:https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1366635Dataset License:CC-BY 4.0
研究领域:
分子生物学
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毒理学
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药物基因组学
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转录组学
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细胞生物学
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环境健康
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产品关联
DOI
高影响因子
ACS Sensors
·
2022
·
IF 9.618
Haiyang Yu,Huibin Zhang,Jinhua Li,Zheng Zhao,Minhua Deng,Zhanpeng Ren,Ziqin Li,Chenglong Xue,Mitch Guijun Li,Zhaowei Chen
The disease caused by severe acute respiratory syndrome coronavirus, SARS-CoV-2, is termed COVID-19. Even though COVID-19 has been out for more than two years, it is still causing a global pandemic. Due to the limitations of sample collection, transportation, and kit performance, the traditional reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method has a long detection period and high testing costs. An increased risk of infection is inevitable, since many patients may not be diagnosed in time. The CRISPR-Cas13a system can be designed for RNA identification and knockdown, as a promising platform for nucleic acid detection. Here, we designed a solution-gated graphene transistor (SGGT) biosensor based on the CRISPR-Cas13a system. Using the gene-targeting capacity of CRISPR-Cas13a and gate functionalization via multilayer modification, SARS-CoV-2 nucleic acid sequences can be quickly and precisely identified without the need for amplification or fluorescence tagging. The limit of detection (LOD) in both buffer and serum reached the aM level, and the reaction time was about 10 min. The results of the detection of COVID-19 clinical samples from throat swabs agree with RT-PCR. In addition, the interchangeable gates significantly minimize the cost and time of device fabrication. In a nutshell, our biosensor technology is broadly applicable and will be suitable for point-of-care (POC) testing.
研究领域:
生物技术
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纳米技术
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分子生物学
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医学诊断
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DOI
PubMed
高影响因子
Human Cell
·
2022
·Vol. 35
·期 5
·1577-1590
·
IF 4.374
Hu Yixiang,Zhang Wenyou,Liu Zheng,Xing Qichang,Liu Renzhu,Yan Qingzi,Li Wencan,Liu Xiang
Cervical cancer is one of the most frequent types of cancer in women, which is characterized by high invasion and metastatic tendency in its advanced stage. Emerging evidence indicated that long non-coding RNAs (LncRNAs) are involved in the pathogenesis of cervical cancer. LINC01287 has been reported to play crucial regulatory roles in the pathogenesis and progression of multiple cancers. However, up until now, whether LINC01287 is associated with the initiation and development of cervical cancer remains largely unknown. In the present study, expression levels of LINC01287, miR-513a-5p and stress-associated endoplasmic reticulum protein 1 (SERP1) mRNA were quantified utilizing qRT-PCR. A series of functional experiments including CCK-8 assay, colony formation assay, transwell assay, flow cytometry, and tumor xenograft growth of cervical cancer cells were performed for studying the effects of LINC01287. The luciferase reporter assay, pull-down assay, and western blot were used to confirm the downstream targets of LINC01287 and miR-513a-5p. The results demonstrate that LINC01287 was highly expressed in cervical cancer tissue samples and cell lines. High LINC01287 predicts a poor prognosis for cervical cancer patients. Additional gain- and loss-of-function experiments demonstrated that silencing LINC01287 inhibited cervical cancer cells proliferation, colony formation, migration, apoptosis in vitro and retarded tumor growth and metastasis in vivo. Furthermore, the dual-luciferase reporter gene system and RNA pulldown assay validated that LINC01287 positively regulated SERP1 expressions by sponging miR-513a-5p, and LINC01287 inhibited cervical cancer progression by regulating miR-513a-5p/SERP1 axis. In conclusion, the current study first identified that LINC01287/miR-513a-5p/SERP1 axis played an important role in cervical cancer progression. LINC01287 might be a prognostic biomarker and a target for new therapies in patients with cervical cancer.
研究领域:
肿瘤学
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分子生物学
·
遗传学
✓ 已验证
DOI
PubMed
高影响因子
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