Tumor necrosis factor-alpha（TNF-α） has been found to be centrally involved in the development of ischemia-reperfusion injury（IRI）-induced inflammation and apoptosis. Knockdown of TNF-α gene using small interferi...Tumor necrosis factor-alpha（TNF-α） has been found to be centrally involved in the development of ischemia-reperfusion injury（IRI）-induced inflammation and apoptosis. Knockdown of TNF-α gene using small interfering RNA（si RNA） may protect renal IRI. Renal IRI was induced in mice by clamping the left renal pedicle for 25 or 35 min. TNF-α si RNA was administered intravenously to silence the expression of TNF-α. The therapeutic effects of si RNA were evaluated in terms of renal function, histological examination, and overall survival following lethal IRI. A single systemic injection of TNF-α si RNA resulted in significant knockdown of TNF-α expression in ischemia-reperfusion injured kidney. In comparison with control mice, levels of BUN and serum creatinine were significantly reduced in mice treated with si RNA. Pathological examination demonstrated that tissue damage caused by IRI was markedly reduced as a result of TNF-α si RNA treatment. Furthermore, survival experiments showed that nearly 90% of control mice died from lethal IRI, whereas more than 50% of si RNApretreated mice survived until the end of the eight-day observation period. We have demonstrated for the first time that silencing TNF-α by specific si RNA can significantly reduce renal IRI and protect mice against lethal kidney ischemia, highlighting the potential for si RNA-based clinical therapy.展开更多
MicroRNAs(miRNAs)and small interfering RNAs(siRNAs)regulate gene expression in eukaryotes.Plant miRNAs modulate their targets mainly via messenger RNA(mRNA)cleavage.Small RNA(sRNA)targets have been extensively investi...MicroRNAs(miRNAs)and small interfering RNAs(siRNAs)regulate gene expression in eukaryotes.Plant miRNAs modulate their targets mainly via messenger RNA(mRNA)cleavage.Small RNA(sRNA)targets have been extensively investigated in Arabidopsis using computational prediction,experimental validation,and degradome sequencing.However,small RNA targets are largely unknown in rice(Oryza sativa).Here,we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11(Oryza sativa L.ssp.indica).One hundred and seventy-seven transcripts targeted by a total of 87 unique miRNAs were identified.Of targets for the conserved miRNAs between Arabidopsis and rice,transcription factors comprise around 70%(58 in 82),indicating that these miRNAs act as masters of gene regulatory nodes in rice.In contrast,non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks.In addition,5 AUXIN RESPONSE FACTORs(ARFs)cleaved by the TAS3 derived ta-siRNAs were also detected.A total of 40 sRNA targets were further validated via RNA ligasemediated 5′rapid amplification of cDNA ends(RLM 5′-RACE).Our degradome results present a detailed sRNAtarget interaction atlas,which provides a guide for the study of the roles of sRNAs and their targets in rice.展开更多
Hepatocellular carcinoma(HCC) is the 5th most common malignancy which is responsible for more than half million annual mortalities; also, it is the third leading cause of cancer related death. Unfavorablesystemic side...Hepatocellular carcinoma(HCC) is the 5th most common malignancy which is responsible for more than half million annual mortalities; also, it is the third leading cause of cancer related death. Unfavorablesystemic side-effects of chemotherapeutic agents and susceptibility to the degradation of small interfering RNAs(si RNAs), which can knock down a specific gene involved in the disease, have hampered their clinical application. So, it could be beneficial to develop an efficient carrier for the stabilization and specific delivery of drugs and si RNA to cells. Targeted nanoparticles have gained considerable attention as an efficient drug and gene delivery system, which is due to their capability in achieving the highest accumulation of cytotoxic agents in tumor tissue, modifiable drug pharmacokinetic- and bio-distribution, improved effectiveness of treatment, and limited sideeffects. Recent studies have shed more light on the advantages of novel drug loaded carrier systems vs free drugs. Most of the animal studies have reported improvement in treatment efficacy and survival rate using novel carrier systems. Targeted delivery may be achieved passively or actively. In passive targeting, no ligand as homing device is used, while targeting is achieved by incorporating the therapeutic agent into a macromolecule or nanoparticle that passively reaches the target organ. However, in active targeting, the therapeutic agent or carrier system is conjugated to a tissue or cell-specific receptor which is overexpressed in a special malignancy using a ligand called a homing device. This review covers a broad spectrum of targeted nanoparticles as therapeutic and nonviral si RNA delivery systems, which are developed for enhanced cellular uptake and targeted gene silencing in vitro and in vivo and their characteristics and opportunities for the clinical applications of drugs and therapeutic si RNA are discussed in this article. Asialoglycoprotein receptors, low-density lipoprotein, ganglioside GM1 cell surface ligand, epidermal growth factor receptor receptors, monoclonal antibodies, retinoic acid receptors, integrin receptors targeted by Arg-Gly-Asp peptide, folate, and transferrin receptors are the most widely studied cell surface receptors which are used for the site specific delivery of drugs and si RNA-based therapeutics in HCC and discussed in detail in this article.展开更多
Inversions are DNA rearrangements that are essential for plant gene evolution and adaptation to environmental changes. We demonstrate the creation of targeted inversions and previously reported targeted deletion mutat...Inversions are DNA rearrangements that are essential for plant gene evolution and adaptation to environmental changes. We demonstrate the creation of targeted inversions and previously reported targeted deletion mutations via delivery of a pair of RNA-guided endonucleases(RGENs) of CRISPR/Cas9. The efficiencies of the targeted inversions were2.6% and 2.2% in the Arabidopsis FLOWERING TIME(At FT) and TERMINAL FLOWER 1(At TFL1)loci, respectively. Thus, we successfully established an approach that can potentially be used to introduce targeted DNA inversions of interest for functional studies and crop improvement.展开更多
目的:膀胱癌(bladder cancer,BLCA)是具有高发病率的泌尿系统肿瘤之一,临床常规诊疗方法可提高患者的生存率,但肿瘤的复发和转移致使患者的预后仍然较差。长链非编码RNA(long non-coding RNA,lncRNA)在调控肿瘤发生、发展及癌症免疫中...目的:膀胱癌(bladder cancer,BLCA)是具有高发病率的泌尿系统肿瘤之一,临床常规诊疗方法可提高患者的生存率,但肿瘤的复发和转移致使患者的预后仍然较差。长链非编码RNA(long non-coding RNA,lncRNA)在调控肿瘤发生、发展及癌症免疫中具有重要作用,可以作为一种新型的标志物预测患者预后及免疫应答。本研究基于生物信息学分析,构建BLCA预后模型,并筛选出BLCA的靶向分子药物。方法:从癌症基因组图谱(The Cancer Genome Atlas,TCGA)数据库下载RNA测序数据和临床数据,并将BLCA患者分为训练集和验证集。基于加权基因共表达网络分析(weighted gene co-expression network analysis,WGCNA)的方法提取免疫相关lncRNAs(immune related lncRNAs,IRlncRNAs),通过最小绝对收缩和选择算子(least absolute shrinkage and selection operator,LASSO)回归的方法构建预后模型,利用美国国家生物技术信息中心(National Center for Biotechnology Information,NCBI)数据库和泛癌数据进行预后基因集的肿瘤相关性分析,并依据Kaplan-Meier分析和受试者操作特征(receiver operating characteristic,ROC)曲线评价该模型的预后准确性。根据风险打分将样本分为高风险组与低风险组,并在此基础上通过风险差异基因筛选出高风险基因。最后,通过CMap数据库筛选抑制高风险基因表达的药物,从而降低BLCA患者的发病风险,提高患者的生存率。结果:基于TCGA数据库中的414例肿瘤样本和19例癌旁样本,预处理得到1342个免疫相关基因(immune related genes,IRGs)和409个临床数据,并通过WGCNA得到927个生存数据。根据Pearson相关分析和单因素Cox分析,得到74个与预后相关的IR-lncRNAs(|R|>0.4,P<0.05)。运用LASSO回归构建预后模型,得到12个IR-lncRNAs和21个IRGs。通过后续分析可知:该预后模型可预测高、低风险组患者的生存及预后情况,并验证了预后模型的独立预测能力及预测准确性,最后筛选了11种BLCA的潜在靶向药物。结论:本研究为BLCA患者构建了一个基于IRGs和IR-lncRNAs的预后模型,筛选了11种潜在的靶向分子药物,为BLCA患者的治疗提供了新思路。展开更多
文摘Tumor necrosis factor-alpha（TNF-α） has been found to be centrally involved in the development of ischemia-reperfusion injury（IRI）-induced inflammation and apoptosis. Knockdown of TNF-α gene using small interfering RNA（si RNA） may protect renal IRI. Renal IRI was induced in mice by clamping the left renal pedicle for 25 or 35 min. TNF-α si RNA was administered intravenously to silence the expression of TNF-α. The therapeutic effects of si RNA were evaluated in terms of renal function, histological examination, and overall survival following lethal IRI. A single systemic injection of TNF-α si RNA resulted in significant knockdown of TNF-α expression in ischemia-reperfusion injured kidney. In comparison with control mice, levels of BUN and serum creatinine were significantly reduced in mice treated with si RNA. Pathological examination demonstrated that tissue damage caused by IRI was markedly reduced as a result of TNF-α si RNA treatment. Furthermore, survival experiments showed that nearly 90% of control mice died from lethal IRI, whereas more than 50% of si RNApretreated mice survived until the end of the eight-day observation period. We have demonstrated for the first time that silencing TNF-α by specific si RNA can significantly reduce renal IRI and protect mice against lethal kidney ischemia, highlighting the potential for si RNA-based clinical therapy.
基金This work was supported by National Basic Research Program of China(Nos.2009CB941500 and 2005CB522400 to X.C.)by National Natural Science Foundation of China(Grant Nos.30870534 and 30621001 to X.C.).
文摘MicroRNAs(miRNAs)and small interfering RNAs(siRNAs)regulate gene expression in eukaryotes.Plant miRNAs modulate their targets mainly via messenger RNA(mRNA)cleavage.Small RNA(sRNA)targets have been extensively investigated in Arabidopsis using computational prediction,experimental validation,and degradome sequencing.However,small RNA targets are largely unknown in rice(Oryza sativa).Here,we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11(Oryza sativa L.ssp.indica).One hundred and seventy-seven transcripts targeted by a total of 87 unique miRNAs were identified.Of targets for the conserved miRNAs between Arabidopsis and rice,transcription factors comprise around 70%(58 in 82),indicating that these miRNAs act as masters of gene regulatory nodes in rice.In contrast,non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks.In addition,5 AUXIN RESPONSE FACTORs(ARFs)cleaved by the TAS3 derived ta-siRNAs were also detected.A total of 40 sRNA targets were further validated via RNA ligasemediated 5′rapid amplification of cDNA ends(RLM 5′-RACE).Our degradome results present a detailed sRNAtarget interaction atlas,which provides a guide for the study of the roles of sRNAs and their targets in rice.
文摘Hepatocellular carcinoma(HCC) is the 5th most common malignancy which is responsible for more than half million annual mortalities; also, it is the third leading cause of cancer related death. Unfavorablesystemic side-effects of chemotherapeutic agents and susceptibility to the degradation of small interfering RNAs(si RNAs), which can knock down a specific gene involved in the disease, have hampered their clinical application. So, it could be beneficial to develop an efficient carrier for the stabilization and specific delivery of drugs and si RNA to cells. Targeted nanoparticles have gained considerable attention as an efficient drug and gene delivery system, which is due to their capability in achieving the highest accumulation of cytotoxic agents in tumor tissue, modifiable drug pharmacokinetic- and bio-distribution, improved effectiveness of treatment, and limited sideeffects. Recent studies have shed more light on the advantages of novel drug loaded carrier systems vs free drugs. Most of the animal studies have reported improvement in treatment efficacy and survival rate using novel carrier systems. Targeted delivery may be achieved passively or actively. In passive targeting, no ligand as homing device is used, while targeting is achieved by incorporating the therapeutic agent into a macromolecule or nanoparticle that passively reaches the target organ. However, in active targeting, the therapeutic agent or carrier system is conjugated to a tissue or cell-specific receptor which is overexpressed in a special malignancy using a ligand called a homing device. This review covers a broad spectrum of targeted nanoparticles as therapeutic and nonviral si RNA delivery systems, which are developed for enhanced cellular uptake and targeted gene silencing in vitro and in vivo and their characteristics and opportunities for the clinical applications of drugs and therapeutic si RNA are discussed in this article. Asialoglycoprotein receptors, low-density lipoprotein, ganglioside GM1 cell surface ligand, epidermal growth factor receptor receptors, monoclonal antibodies, retinoic acid receptors, integrin receptors targeted by Arg-Gly-Asp peptide, folate, and transferrin receptors are the most widely studied cell surface receptors which are used for the site specific delivery of drugs and si RNA-based therapeutics in HCC and discussed in detail in this article.
基金financially supported by the National Natural Science Foundation of China(No.31361140364)the National Major Project for Developing New GM Crops(No.2016ZX080009-001)the Agricultural Science and Technology Innovation Program(ASTIP)of CAAS to Chuanxiao Xie
文摘Inversions are DNA rearrangements that are essential for plant gene evolution and adaptation to environmental changes. We demonstrate the creation of targeted inversions and previously reported targeted deletion mutations via delivery of a pair of RNA-guided endonucleases(RGENs) of CRISPR/Cas9. The efficiencies of the targeted inversions were2.6% and 2.2% in the Arabidopsis FLOWERING TIME(At FT) and TERMINAL FLOWER 1(At TFL1)loci, respectively. Thus, we successfully established an approach that can potentially be used to introduce targeted DNA inversions of interest for functional studies and crop improvement.
文摘目的:膀胱癌(bladder cancer,BLCA)是具有高发病率的泌尿系统肿瘤之一,临床常规诊疗方法可提高患者的生存率,但肿瘤的复发和转移致使患者的预后仍然较差。长链非编码RNA(long non-coding RNA,lncRNA)在调控肿瘤发生、发展及癌症免疫中具有重要作用,可以作为一种新型的标志物预测患者预后及免疫应答。本研究基于生物信息学分析,构建BLCA预后模型,并筛选出BLCA的靶向分子药物。方法:从癌症基因组图谱(The Cancer Genome Atlas,TCGA)数据库下载RNA测序数据和临床数据,并将BLCA患者分为训练集和验证集。基于加权基因共表达网络分析(weighted gene co-expression network analysis,WGCNA)的方法提取免疫相关lncRNAs(immune related lncRNAs,IRlncRNAs),通过最小绝对收缩和选择算子(least absolute shrinkage and selection operator,LASSO)回归的方法构建预后模型,利用美国国家生物技术信息中心(National Center for Biotechnology Information,NCBI)数据库和泛癌数据进行预后基因集的肿瘤相关性分析,并依据Kaplan-Meier分析和受试者操作特征(receiver operating characteristic,ROC)曲线评价该模型的预后准确性。根据风险打分将样本分为高风险组与低风险组,并在此基础上通过风险差异基因筛选出高风险基因。最后,通过CMap数据库筛选抑制高风险基因表达的药物,从而降低BLCA患者的发病风险,提高患者的生存率。结果:基于TCGA数据库中的414例肿瘤样本和19例癌旁样本,预处理得到1342个免疫相关基因(immune related genes,IRGs)和409个临床数据,并通过WGCNA得到927个生存数据。根据Pearson相关分析和单因素Cox分析,得到74个与预后相关的IR-lncRNAs(|R|>0.4,P<0.05)。运用LASSO回归构建预后模型,得到12个IR-lncRNAs和21个IRGs。通过后续分析可知:该预后模型可预测高、低风险组患者的生存及预后情况,并验证了预后模型的独立预测能力及预测准确性,最后筛选了11种BLCA的潜在靶向药物。结论:本研究为BLCA患者构建了一个基于IRGs和IR-lncRNAs的预后模型,筛选了11种潜在的靶向分子药物,为BLCA患者的治疗提供了新思路。
