ANALYTICAL CHEMISTRY
·
2024
·
IF 6.7
Jingyu Cui,Jiafang Piao,Houyu Han,Weipan Peng,Mengyao Lin,Dianming Zhou,Cheng Zhu,Xiaoqun Gong
Circulating microRNAs (miRNAs) have recently emerged as noninvasive disease biomarkers. Quantitative detection of circulating miRNAs could offer significant information for clinical diagnosis due to its significance in the development of biological processes. In response to the current challenges of circulating miRNA detection, we introduce a sensitive, selective, and versatile circulating miRNA detection strategy using terminal deoxynucleotidyl transferase (TdT)-catalyzed RNA-primed DNA polymerization (TCRDP) coupled with semiarbitrary qPCR (SAPCR). Semiarbitrary qPCR was first developed here to detect long fragment targets with only a short-known sequence or to detect a short fragment target after extension with terminal transferase. Besides, the subsequent results show that TdT has a preference for RNA, particularly for extending RNAs with purine-rich and unstructured ends. Consequently, utilizing this assay, we have successfully applied it to the quantitative analysis of circulating miR-122 in animal models, a sensitive and informative biomarker for drug-induced liver injury, and as low as 200 zmol of the target is detected with desirable specificity and sensitivity, indicating that the TCRDP-SAPCR can offer a promising platform for nucleic acids analysis.
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PubMed
高影响因子
Biomolecules and Biomedicine
·
2024
·
IF 0
Huaxian Chen,Xingyang Wan,Qiulan He,Guozhong Xiao,Yihui Zheng,Minyi Luo,Chaoxin Yang,Donglin Ren,Li Lu,Hui Peng,Hongcheng Lin
The cellular characteristics of intestinal cells involved in the therapeutic effects of astragaloside IV (AS-IV) for treating slow transit constipation (STC) remain unclear. This study aimed to determine the dynamics of colon tissue cells in the STC model and investigate the effects of AS-IV treatment by single-cell RNA sequencing (scRNA-seq). STC mouse models were developed using loperamide, with subsequent treatment using AS-IV. Colon tissues and feces were collected for scRNA-seq and targeted short-chain fatty acid quantification. We integrated scRNA-seq data with network pharmacology to analyze the effect of AS-IV on constipation. AS-IV showed improvement in defecation for STC mice induced by loperamide. Notably, in STC mice, epithelial cells, T cells, B cells, and fibroblasts demonstrated alterations in cell proportions and aberrant functions, which AS-IV partially rectified. AS-IV has the potential to modulate the metabolic pathway of epithelial cells through its interaction with peroxisome proliferator-activated receptor gamma (PPARγ). AS-IV reinstated fecal butyrate levels and improved energy metabolism in epithelial cells. The proportion of naïve CD4+T cells is elevated in STC, and the differentiation of these cells into regulatory T cells (Treg) is regulated by B cells and fibroblasts through the interaction of ligand-receptor pairs. AS-IV treatment can partially alleviate this trend. The status of fibroblasts in STC undergoes alterations, and the FB_C4_Adamdec1 subset, associated with angiogenesis and the Wingless-related integration (Wnt) pathway, emerges. Our comprehensive analysis identifies perturbations of epithelial cells and tissue microenvironment cells in STC and elucidates mechanisms underlying the therapeutic efficacy of AS-IV.
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PubMed
iScience
·
2024
·
IF 4.6
Jia-Qi Ma,Lu Wang,Yue Zhang,Yong-Qian Bian,Xiao-Peng Qu,Li-Jia Song,Chao Wang,Li Gao,Qi-Xing Fang,De-Chang Zhao,Liang-Liang Shen,Bei Liu
The hippocampus plays a critical role in learning and memory, and mice with epileptic cognitive impairment exhibit hippocampal atrophy. However, there is still a lack of research on the hippocampal cell atlas related to these disorders. Here, we utilized snRNA-seq to characterize the transcriptomic changes in hippocampal neurons of drug-resistant epilepsy (DRE) cognitive-impaired mice. The intercellular heterogeneity of 20 subpopulations of neurons was analyzed, focusing on aspects such as cell communication, gene expressions, GO and KEGG enrichment analysis, and module gene set analysis. Based on the degree of relevance to synaptic biological functions, the subpopulations associated with cognitive impairment (ExN1, 3, 8 and InN1, 6) were preliminarily identified. We also identified some key biomarkers in DRE cognitive-impaired mice, such as Ptprz1 and Calb1. Finally, we integrate and validate our dataset using identified well-annotated marker genes in the hippocampal region, further supporting the functional annotation of neuronal subpopulations.
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高影响因子
SENSORS AND ACTUATORS B-CHEMICAL
·
2022
·
IF 9.221
Ting Chen,Pengfei Liu,Huanxiang Wang,Yue Su,Sheng Li,Shimeng Ma,Xuan Xu,Jie Wen,Zhen Zou
Accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is of great importance to control the COVID-19 pandemic. The gold standard assays for COVID-19 diagnostics are mainly based on separately detecting open reading frame 1ab (ORF1ab) and nucleoprotein (N) genes by RT-PCR. However, the current approaches often obtain false positive-misdiagnose caused by cross-contamination or undesired amplification. To address this issue, herein, we proposed a dumbbell-type triplex molecular switch (DTMS)-based, logic-gated strategy for high-fidelity SARS-CoV-2 RNA detection. The DTMS consists of a triple-helical stem region and two-loop regions for recognizing the ORF1ab and N genes of SARS-CoV-2. Only when the ORF1ab and N gene are concurrent, DTMS experiences a structural rearrangement, thus, bringing the two pyrenes into spacer proximity and leading to a new signal readout. This strategy allows detecting SARS-CoV-2 RNA with a detection limit of 1.3 nM, independent of nucleic acid amplification, holding great potential as an indicator probe for screening of COVID-19 and other population-wide epidemics.
研究领域:
分子生物学
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病毒学
·
诊断学
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DOI
PubMed
高影响因子
Molecular Genetics & Genomic Medicine
·
2020
·Vol. 8
·期 5
·e1195
·
IF 1.995
Fei Cui,Zhe-xue Hao,Jin Li,Ya-lei Zhang,Xu-kai Li,Jian-xing He
Background This study is aimed to unravel the genetic factors associated with microRNA (miRNA) expression in regulating sex-determining region Y-box 2 ( SOX2 )-mediated cisplatin resistance in small-cell lung cancer (SCLC). Methods The relevance of SOX2 expression in SCLC was analyzed in a panel of SCLC cells by quantitative real-time PCR (qPCR) and western blot (WB). We selected DMS114 cell line, in which SOX2 was amplified via lentiviral vector-mediated transfection of the SOX2 genes and tested for the half-maximal inhibitory concentration (IC 50 ) by MTS assay. High-throughput sequencing and screening of differentially expressed miRNAs between SOX2 -overexpressing and normal control cells were performed. Finally, miRanda software was used to verify the miRNAs bound with SOX2 and qPCR was used to identify the expression of miRNAs which were binding with SOX2 . Results Cisplatin-resistant SOX2 -overexpressing DMS114 cell lines were successfully developed, showing a statistically significant increase in SOX2 expression by qPCR and WB. Our results showed a typically higher IC 50 value in SOX2 -overexpressing cells compared with the negative controls. The high-throughput sequencing analysis revealed that 68 miRNAs were upregulated and 24 miRNAs were downregulated in the SOX2 -overexpressing cells. The 24 downregulated miRNAs were further verified. Of them, a cancer-related miRNA, hsa-miR-340-5p, showed a higher binding affinity with SOX2 in network regulation mapping, which was also found to be markedly downregulated under qPCR analysis. Conclusion We demonstrated that downregulated expression of hsa-miR-340-5p may affect cisplatin resistance by mediating SOX2 expression in SCLC cells, which may provide a potential target for the therapy of chemoresistant SCLCs.
研究领域:
肿瘤学
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分子生物学
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医学遗传学
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DOI
PubMed
高影响因子
Chinese Medicine
·
2025
·Vol. 20
·期 1
·1-14
·
IF 5.7
Jiang Feng,Tang Jiayang,Wei Xiaoqi,Pan Hai,Fan Xinyi,Zhang Peng,Guo Shuzhen
Background Dilated cardiomyopathy (DCM) stands as one of the most prevalent and severe causes of heart failure. Inflammation plays a pivotal role throughout the progression of DCM to heart failure, while age acts as a natural predisposing factor for all cardiovascular diseases. These two factors often interact, contributing to cardiac fibrosis, which is both a common manifestation and a pathogenic driver of adverse remodeling in DCM-induced heart failure.MethodBulk RNA-seq, single-cell RNA-seq, Mendelian randomization analysis, animal model construction, and BMP6 knockdown were utilized to identify and validate potential specific markers and targets for intervention in DCM heart failure.Results We found that DCM hearts exhibit pronounced inflammatory cell infiltration and fibrosis. Both bulk RNA-seq and single-cell RNA-seq analyses revealed aberrant BMP6 expression specifically in fibroblasts. The ROC curve underscores the high specificity of BMP6 in relation to DCM, while Mendelian randomization analysis further confirms BMP6 as a protective factor against DCM. Notably, BMP6 knockdown led to a decrease in SMAD6 expression and a marked elevation in COL1A1 expression levels, indicating its antifibrotic role.Conclusion BMP6 emerges as a promising biomarker for DCM, and its functional role in exerting an antifibrotic effect underscores its potential as a therapeutic target.
研究领域:
心脏病学
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分子生物学
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基因组学
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医学遗传学
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PubMed
高影响因子
ANALYTICAL CHEMISTRY
·
2018
·
IF 6.042
Ting Hou,Ningning Xu,Wenxiao Wang,Lei Ge,Feng Li
In conventional photoelectrochemical (PEC) analysis, photoactive materials are usually immobilized on electrode surfaces, and such immobilization procedures are tedious and time-consuming, and it is also difficult to prepare electrodes with good reproducibility. To circumvent such limitations, we propose here a truly immobilization-free diffusivity-mediated PEC bionsensing strategy for microRNA assay, using methylene blue (MB) in solution as the photoactive probe, and nonmodified indium tin oxide (ITO) glass as the working electrode. The hybridization between the target microRNA and the MB-labeled single-stranded DNA probe (MB-DNA) triggers the digestion of MB-DNA by T7 exonuclease (T7 Exo), thus to generate MB-labeled mononucleotide, and then the released target microRNA initiates the subsequent cycling processes and generates a large amount of MB-labeled mononucleotides. Due to the diffusivity difference between MB-DNAs and MB-labeled mononucleotides, significantly increased photocurrent signal is observed for MB-labeled mononucleotides as compared to that of MB-DNAs. Therefore, via this “signal-on” mode and the T7 Exo facilitated signal amplification, a facile and highly sensitive immobilization-free PEC microRNA assay is readily realized, with a detection limit down to 27 aM. Moreover, this strategy exhibits excellent specificity and is successfully applied in detecting microRNA spiked in serum samples. Since all the reactions take place in homogeneous solutions and no electrode modification is needed, this PEC biosensing strategy exhibits the advantages of simplicity, rapidness, and good reproducibility. More significantly, it provides a novel concept to design truly immobilization-free PEC biosensing systems, and shows potential to be applied in bioanalysis and biochemical research.
研究领域:
生物分析
·
分子生物学
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DOI
高影响因子
PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY
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2024
·
IF 4.2
Tao Li,Lisha Yuan,Dun Jiang,Shanchun Yan
Strong multi-host adaptability significantly contributes to the rapid dissemination of Hyphantria cunea. The present study explores the involvement of cytochrome P450 monooxygenase (P450) in the multi-host adaptation of H. cunea and aims to develop RNA pesticides targeting essential P450 genes to disrupt this adaptability. The results showed that inhibiting P450 activity notably reduced larval weight and food-intake across seven plants groups. The P450 gene HcCYP6AE178 was highly upregulated in H. cunea larvae from medium- and low-preference host plant groups. Silencing HcCYP6AE178 significantly decreased H. cunea larval body weight, increased larval mortality, inhibited energy metabolism genes expression and interfered with growth regulatory genes expression. Overexpression of HcCYP6AE178 enhanced the tolerance of Drosophila and Sf9 cells to the plant defensive substances cytisine and coumarin. The RNA pesticide CS-ds HcCYP6AE178 constructed using chitosan (CS) exhibited remarkable stability. Treatment with CS-ds HcCYP6AE178 effectively reduced H. cunea larval body weight, heightened larval mortality, and disrupted growth regulatory genes expression in low-preference host plant groups. Combined treatment of CS-ds HcCYP6AE178 and coumarin significantly elevated H. cunea larval mortality compared to coumarin alone, accompanied by the inhibition of growth regulatory genes expression and an abnormal increase in energy metabolism genes expression. Taken together, HcCYP6AE178 is essential for the adaptation of H. cunea to multiple host plants, and RNA pesticides targeting HcCYP6AE178 can effectively impair the performance of H. cunea in different host plants.
研究领域:
昆虫学
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分子生物学
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植物保护
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DOI
高影响因子
JOURNAL OF NANOBIOTECHNOLOGY
·
2021
·Vol. 19
·期 1
·1-16
·
IF 10.435
Li Xiang,Zhang Li,Guo Xiamei,Xie Fei,Shen Cheng,Jun Yali,Luo Chao,Liu Longfei,Yu Xiaojuan,Zhang Zhengwei,Wang Qilong,Gao Yong,Xu Keping
Background Esophageal cancer is the fifth most common cancer affecting men in China. The primary treatment options are surgery and traditional radio-chemotherapy; no effective targeted therapy exists yet. Self-assembled RNA nanocarriers are highly stable, easily functionally modified, and have weak off-tumor targeting effects. Thus, they are among the most preferred carriers for mediating the targeted delivery of anti-tumor drugs. miR-375 was found to be significantly down-regulated in esophageal squamous cell carcinoma (ESCC) tissues and its overexpression effectively inhibits the proliferation, migration, and invasion of ESCC cells. Moreover, epidermal growth factor receptor (EGFR) was overexpressed in ESCC cells, and accumulation of RNA nanoparticles in ESCC tumors was enhanced by EGFR-specific aptamer (EGFRapt) modification.Results Herein, a novel four-way junction RNA nanocarrier, 4WJ-EGFRapt-miR-375-PTX simultaneously loaded with miR-375, PTX and decorated with EGFRapt, was developed. In vitro analysis demonstrated that 4WJ-EGFRapt-miR-375-PTX possesses strong thermal and pH stabilities. EGFRapt decoration facilitated tumor cell endocytosis and promoted deep penetration into 3D-ESCC spheroids. Xenograft mouse model for ESCC confirmed that 4WJ-EGFRapt-miR-375-PTX was selectively distributed in tumor sites via EGFRapt-mediating active targeting and targeted co-delivery of miR-375 and PTX exhibited more effective therapeutic efficacy with low systemic toxicity.Conclusion This strategy may provide a practical approach for targeted therapy of ESCC.Graphical Abstract
研究领域:
肿瘤学
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纳米技术
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分子生物学
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药学
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DOI
PubMed
高影响因子
Communications Biology
·
2026
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IF 5.8
Shen Jing,Zhu Lirong,Yang Ronghui,Liao Aijun
Multiple myeloma (MM) is a systemic malignancy characterized by the induction of osteolytic lesions. Cold-inducible RNA binding protein (CIRBP) has garnered attention in cancer research due to its dual role as either an oncogene or a tumor suppressor. In this study, publicly available single-cell RNA sequencing data, MM cell lines, and an in vivo xenograft model are utilized to assess the biological significance of CIRBP in MM. Analysis reveals frequent communication between MM cells and macrophages, alongside decreased CIRBP expression in patients. Functionally, CIRBP overexpression in MM cells inhibits short- and long-term viability, suppresses proliferation, and reduces tumor burden in vitro and in vivo. Furthermore, co-culture experiments confirm that CIRBP -expressing MM cells suppress macrophage chemotaxis and macrophage alternative activation, while CIRBP knockdown has opposite effects. Mechanistically, CIRBP binds to intron1 of pyruvate kinase M2 ( PKM2 ) precursor messenger RNA (pre-mRNA), inhibiting its splicing and promoting its nonsense-mediated decay, ultimately leading to downregulation of PKM2 . Elevated levels of PKM2 rescue the CIRBP-mediated suppression of macrophage chemotaxis and macrophage alternative activation. Our findings support the notion of CIRBP as a candidate tumor suppressor in MM and unveil a post-transcriptional regulatory mechanism governing PKM2-mediated macrophage plasticity.
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高影响因子
Nature Communications
·
2026
·
IF 18.1
Guo Junfan,Song Ziguo,Wang Wuke,Huang Shisheng,Zhang Yu,Li Guanglei,Huang Xingxu,Wang Xiaolong,Liu Jianghuai,Wu Lina
Therapeutic integration of large DNA fragments into precise genomic loci of human cells remains challenging. The IS621 recombinase, derived from the IS110 family, utilizes a bridge RNA (bRNA) containing an independently programmable target-binding loop (TBL) and donor-binding loop (DBL) to mediate sequence-specific recombination between target and donor DNA in prokaryotes. To expand its application to human cells, we rationally engineer the IS621 protein and its cognate bRNA. This ultimately leads to the development of enIS621-tebRNA, which is capable of driving site-specific, scarless insertion of large DNA fragments in human cells. We systematically evaluate the insertion efficiency of this system across multiple cell types, achieving integration rates up to 27.75% for kilobase-scale DNA cargos. Furthermore, we successfully achieve functional insertion of a CD19 chimeric antigen receptor (CAR) at relevant loci for T cell therapy, and establish site-specific integration of the gene encoding human Factor IX with implications for hemophilia B gene therapy. These results highlight the potential of the engineered enIS621-tebRNA system as a versatile platform for precise insertion of large DNA fragments in human cells.
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PubMed
高影响因子
MOLECULAR & CELLULAR PROTEOMICS
·
2025
·
IF 5.5
Yanyan Yi,Xiahe Huang,Wan Wang,Yingchun Wang,Jianru Zuo,Hongyan Guo
Nitric oxide (NO) is a crucial signaling molecule involved in various developmental processes and stress responses through post-translational protein modification and modulation of gene expression. Despite significant advances in understanding the mechanism of NO-mediated protein modifications, how NO regulates gene expression remains largely unclear. Here, we show that the energy sensor KIN10, a catalytic α-subunit of sucrose non-fermenting 1-related kinase 1 (SnRK1), plays a vital role in NO-mediated regulation of gene expression in Arabidopsis . NO-mediated S -nitrosylation at Cys-177 of KIN10 inhibits its degradation, leading to protein stabilization. A non-nitrosylatable mutation of Cys-177 to serine results in NO insensitivity and functional deficiencies. Quantitative phosphoproteomic analysis reveals that S -nitrosylation at Cys-177 of KIN10 modulates the phosphorylation of splicing factors within the spliceosome. We propose that NO regulates RNA splicing through the enhancement of KIN10 activity via S -nitrosylation, thereby establishing a molecular link between NO signaling and gene expression.
研究领域:
植物生物学
·
分子生物学
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信号转导
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遗传学
·
生物化学
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PubMed
高影响因子
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