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期刊论文 38

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大豆臭虫（SSB） 1

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immune escape and microenvironment between RG-like and pri-OPC-like glioma revealed by single-cell RNA-seq

《医学前沿（英文）》 doi: 10.1007/s11684-023-1017-7

摘要： The association of neurogenesis and gliogenesis with glioma remains unclear. By conducting single-cell RNA-seq analyses on 26 gliomas, we reported their classification into primitive oligodendrocyte precursor cell (pri-OPC)-like and radial glia (RG)-like tumors and validated it in a public cohort and TCGA glioma. The RG-like tumors exhibited wild-type isocitrate dehydrogenase and tended to carry EGFR mutations, and the pri-OPC-like ones were prone to carrying TP53 mutations. Tumor subclones only in pri-OPC-like tumors showed substantially down-regulated MHC-I genes, suggesting their distinct immune evasion programs. Furthermore, the two subgroups appeared to extensively modulate glioma-infiltrating lymphocytes in distinct manners. Some specific genes not expressed in normal immune cells were found in glioma-infiltrating lymphocytes. For example, glial/glioma stem cell markers OLIG1/PTPRZ1 and B cell-specific receptors IGLC2/IGKC were expressed in pri-OPC-like and RG-like glioma-infiltrating lymphocytes, respectively. Their expression was positively correlated with those of immune checkpoint genes (e.g., LGALS3) and poor survivals as validated by the increased expression of LGALS3 upon IGKC overexpression in Jurkat cells. This finding indicated a potential inhibitory role in tumor-infiltrating lymphocytes and could provide a new way of cancer immune evasion.

关键词： single-cell RNA-seq     glioma     radial glia     primitive oligodendrocyte precursor cell     immune escape    

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Effects of vitrification and cryostorage duration on single-cell RNA-Seq profiling of vitrified-thawed

Ying Huo, Peng Yuan, Qingyuan Qin, Zhiqiang Yan, Liying Yan, Ping Liu, Rong Li, Jie Yan, Jie Qiao

《医学前沿（英文）》 2021年 第15卷 第1期   页码 144-154 doi: 10.1007/s11684-020-0792-7

摘要： Oocyte cryopreservation is widely used for clinical and social reasons. Previous studies have demonstrated that conventional slow-freezing cryopreservation procedures, but not storage time, can alter the gene expression profiles of frozen oocytes. Whether vitrification procedures and the related frozen storage durations have any effects on the transcriptomes of human metaphase II oocytes remain unknown. Four women (30–32 years old) who had undergone IVF treatment were recruited for this study. RNA-Seq profiles of 3 fresh oocytes and 13 surviving vitrified-thawed oocytes (3, 3, 4, and 3 oocytes were cryostored for 1, 2, 3, and 12 months) were analyzed at a single-cell resolution. A total of 1987 genes were differentially expressed in the 13 vitrified-thawed oocytes. However, no differentially expressed genes were found between any two groups among the 1-, 2-, 3-, and 12-month storage groups. Further analysis revealed that the aberrant genes in the vitrified oocytes were closely related to oogenesis and development. Our findings indicated that the effects of vitrification on the transcriptomes of mature human oocytes are induced by the procedure itself, suggesting that long-term cryostorage of human oocytes is safe.

关键词： human metaphase II oocyte     vitrification     cryostorage duration     single-cell RNA-Seq     lncRNA    

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Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different

Xin Zou, Ke Chen, Jiawei Zou, Peiyi Han, Jie Hao, Zeguang Han

《医学前沿（英文）》   页码 185-192 doi: 10.1007/s11684-020-0754-0

摘要：

It has been known that, the novel coronavirus, 2019-nCoV, which is considered similar to SARS-CoV and originated from Wuhan (China), invades human cells via the receptor angiotensin converting enzyme II (ACE2). Moreover, lung cells that have ACE2 expression may be the main target cells during 2019-nCoV infection. However, some patients also exhibit non-respiratory symptoms, such as kidney failure, implying that 2019-nCoV could also invade other organs. To construct a risk map of different human organs, we analyzed the single-cell RNA sequencing (scRNA-seq) datasets derived from major human physiological systems, including the respiratory, cardiovascular, digestive, and urinary systems. Through scRNA-seq data analyses, we identified the organs at risk, such as lung, heart, esophagus, kidney, bladder, and ileum, and located specific cell types (i.e., type II alveolar cells (AT2), myocardial cells, proximal tubule cells of the kidney, ileum and esophagus epithelial cells, and bladder urothelial cells), which are vulnerable to 2019-nCoV infection. Based on the findings, we constructed a risk map indicating the vulnerability of different organs to 2019-nCoV infection. This study may provide potential clues for further investigation of the pathogenesis and route of 2019-nCoV infection.

关键词： 2019-nCoV     ACE2     single-cell RNA-seq    

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Identification of transporter proteins for PQQ-secretion pathways by transcriptomics and proteomics analysis in

Hui Wan,Yu Xia,Jianghua Li,Zhen Kang,Jingwen Zhou

《化学科学与工程前沿（英文）》 2017年 第11卷 第1期   页码 72-88 doi: 10.1007/s11705-016-1580-4

摘要： Pyrroloquinoline quinone (PQQ) plays a significant role as a redox cofactor in combination with dehydrogenases in bacteria. These dehydrogenases play key roles in the oxidation of important substrates for the biotechnology industry, such as vitamin C production. While biosynthesis of PQQ genes has been widely studied, PQQ-transport mechanisms remain unclear. Herein, we used both two-dimensional fluorescence-difference gel electrophoresis tandem mass spectrometry and RNA sequencing to investigate the effects of overexpression in an industrial strain of WSH-003. We have identified 73 differentially expressed proteins and 99 differentially expressed genes, a majority of which are related to oxidation-reduction and transport processes by gene ontology analysis. We also described several putative candidate effectors that responded to increased PQQ levels resulting from overexpression. Furthermore, quantitative PCR was used to verify five putative PQQ-transport genes among different PQQ producing strains, and the results showed that , and were upregulated in all conditions. Then the three genes were over-expressed in WSH-003 and PQQ production were detected. The results showed that extracellular PQQ of B932_1930 (a transporter) and B932_2186 (an ABC transporter permease) overexpression strains were enhanced by 1.77-fold and 1.67-fold, respectively. The results suggest that the proteins encoded by PqqB, B932_1930 and B932_2186 might enhance the PQQ secretion process.

关键词： 2D-DIGE     pqqB     pyrroloquinoline quinone     RNA-Seq     Vitamin C    

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BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN

《农业科学与工程前沿（英文）》 2021年 第8卷 第2期

摘要：

Weeping species are used both as ornamental plants and for breeding dwarf plant types. However, exploration of casual genes controlling weeping traits is rather limited. Here, we identified individuals with contrasting phenotypes from an F1 bi-parental mapping population of Prunus mume which was developed from a cross between the upright cultivar ‘Liuban’ and the weeping cultivar ‘Fentai Chuizhi’. Bulked segregant RNA sequencing was used and five QTLs on Chromosome 7 were identified. The Pm024074(PmUGT72B3) allele, belonging to the UDP-glycosyltransferase superfamily containing the coniferyl-alcohol glucosyltransferase domain, was identified in a genomic region overlapping with a previously identified QTL, and had a synonymous transition of T66(upright) to C (weeping) in the coding sequence and a 470-bp deletion in the promoter region. Pm024074 had exceptionally high expression in buds and stems of weeping P. mume. Weighted correlation network analysis indicates that genes neighboring Pm024074 were significantly associated with plant architecture. In addition, a reliable single nucleotide polymorphism marker was developed based on the variation in the Pm024074 gene, providing precise marker-assisted breeding for weeping traits. This study provides insights into the genetic mechanism governing the weeping trait in P. mume, and indicates potential applications for the manipulation of tree architecture.

关键词： BSR-seq / PmUGT72B3 / Prunus mume / UDP-glycosyltransferase / weeping shoots / WGCNA    

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Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation

null

《医学前沿（英文）》 2016年 第10卷 第3期   页码 297-310 doi: 10.1007/s11684-016-0452-0

摘要：

Studies on coding genes, miRNAs, and lncRNAs during erythroid development have been performed in recent years. However, analysis focusing on the integration of the three RNA types has yet to be done. In the present study, we compared the dynamics of coding genes, miRNA, and lncRNA expression profiles. To explore dynamic changes in erythropoiesis and potential mechanisms that control these changes in the transcriptome level, we took advantage of high throughput sequencing technologies to obtain transcriptome data from cord blood hematopoietic stem cells and the following four erythroid differentiation stages, as well as from mature red blood cells. Results indicated that lncRNAs were promising cell marker candidates for erythroid differentiation. Clustering analysis classified the differentially expressed genes into four subtypes that corresponded to dynamic changes during stemness maintenance, mid-differentiation, and maturation. Integrated analysis revealed that noncoding RNAs potentially participated in controlling blood cell maturation, and especially associated with heme metabolism and responses to oxygen species and DNA damage. These regulatory interactions were displayed in a comprehensive network, thereby inferring correlations between RNAs and their associated functions. These data provided a substantial resource for the study of normal erythropoiesis, which will permit further investigation and understanding of erythroid development and acquired erythroid disorders.

关键词： erythroid differentiation     hematopoietic stem cell     RNA-seq     miRNA     lncRNA    

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BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN

Xiaokang ZHUO, Tangchun ZHENG, Zhiyong ZHANG, Suzhen LI, Yichi ZHANG, Lidan SUN, Weiru YANG, Jia WANG, Tangren CHENG, Qixiang ZHANG

《农业科学与工程前沿（英文）》   页码 196-214 doi: 10.15302/J-FASE-2020379

摘要： Weeping species are used both as ornamental plants and for breeding dwarf plant types. However, exploration of casual genes controlling weeping traits is rather limited. Here, we identified individuals with contrasting phenotypes from an F bi-parental mapping population of which was developed from a cross between the upright cultivar ‘Liuban’ and the weeping cultivar ‘Fentai Chuizhi’. Bulked segregant RNA sequencing was used and five QTLs on Chromosome 7 were identified. The ( ) allele, belonging to the UDP-glycosyltransferase superfamily containing the coniferyl-alcohol glucosyltransferase domain, was identified in a genomic region overlapping with a previously identified QTL, and had a synonymous transition of T (upright) to C (weeping) in the coding sequence and a 470-bp deletion in the promoter region. had exceptionally high expression in buds and stems of weeping . Weighted correlation network analysis indicates that genes neighboring were significantly associated with plant architecture. In addition, a reliable single nucleotide polymorphism marker was developed based on the variation in the gene, providing precise marker-assisted breeding for weeping traits. This study provides insights into the genetic mechanism governing the weeping trait in , and indicates potential applications for the manipulation of tree architecture.

关键词： BSR-seq     PmUGT72B3     Prunus mume     UDP-glycosyltransferase     weeping shoots     WGCNA    

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PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing

《医学前沿（英文）》 2022年 第16卷 第2期   页码 251-262 doi: 10.1007/s11684-021-0915-9

摘要： Pathogenic microbes can induce cellular dysfunction, immune response, and cause infectious disease and other diseases including cancers. However, the cellular distributions of pathogens and their impact on host cells remain rarely explored due to the limited methods. Taking advantage of single-cell RNA-sequencing (scRNA-seq) analysis, we can assess the transcriptomic features at the single-cell level. Still, the tools used to interpret pathogens (such as viruses, bacteria, and fungi) at the single-cell level remain to be explored. Here, we introduced PathogenTrack, a python-based computational pipeline that uses unmapped scRNA-seq data to identify intracellular pathogens at the single-cell level. In addition, we established an R package named Yeskit to import, integrate, analyze, and interpret pathogen abundance and transcriptomic features in host cells. Robustness of these tools has been tested on various real and simulated scRNA-seq datasets. PathogenTrack is competitive to the state-of-the-art tools such as Viral-Track, and the first tools for identifying bacteria at the single-cell level. Using the raw data of bronchoalveolar lavage fluid samples (BALF) from COVID-19 patients in the SRA database, we found the SARS-CoV-2 virus exists in multiple cell types including epithelial cells and macrophages. SARS-CoV-2-positive neutrophils showed increased expression of genes related to type I interferon pathway and antigen presenting module. Additionally, we observed the Haemophilus parahaemolyticus in some macrophage and epithelial cells, indicating a co-infection of the bacterium in some severe cases of COVID-19. The PathogenTrack pipeline and the Yeskit package are publicly available at GitHub.

关键词： scRNA-seq     intracellular pathogen     microbe     COVID-19     SARS-CoV-2    

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Ribozyme and the mechanisms that underlie RNA catalysis

Timothy J. Wilson,Yijin Liu,David M. J. Lilley

《化学科学与工程前沿（英文）》 2016年 第10卷 第2期   页码 178-185 doi: 10.1007/s11705-016-1558-2

摘要： Ribozymes are widespread, and catalyze some extremely important reactions in the cell. Mechanistically most fall into one of two classes, using either metal ions or general acid-base catalysis. The nucleolytic ribozymes fall into the latter class, mostly using nucleobases. A sub-set of these use a combination of guanine base plus adenine acid to catalyze the cleavage reaction. New ribozymes are still being discovered at regular intervals and we can speculate on the potential existence of ribozymes that catalyze chemistry beyond phosphoryl transfer reactions, perhaps using small-molecule coenzymes.

关键词： RNA catalysis     RNA structure     catalytic mechanism    

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Characterization of chromatin accessibility in psoriasis

《医学前沿（英文）》 2022年 第16卷 第3期   页码 483-495 doi: 10.1007/s11684-021-0872-3

摘要： The pathological hallmarks of psoriasis involve alterations in T cell genes associated with transcriptional levels, which are determined by chromatin accessibility. However, to what extent these alterations in T cell transcriptional levels recapitulate the epigenetic features of psoriasis remains unknown. Here, we systematically profiled chromatin accessibility on Th1, Th2, Th1-17, Th17, and Treg cells and found that chromatin remodeling contributes significantly to the pathogenesis of the disease. The chromatin remodeling tendency of different subtypes of Th cells were relatively consistent. Next, we profiled chromatin accessibility and transcriptional dynamics on memory Th/Treg cells. In the memory Th cells, 803 increased and 545 decreased chromatin-accessible regions were identified. In the memory Treg cells, 713 increased and 1206 decreased chromatin-accessible regions were identified. A total of 54 and 53 genes were differentially expressed in the peaks associated with the memory Th and Treg cells. FOSL1, SPI1, ATF3, NFKB1, RUNX, ETV4, ERG, FLI1, and ETC1 were identified as regulators in the development of psoriasis. The transcriptional regulatory network showed that NFKB1 and RELA were highly connected and central to the network. NFKB1 regulated the genes of CCL3, CXCL2, and IL1RN. Our results provided candidate transcription factors and a foundational framework of the regulomes of the disease.

关键词： psoriasis     ATAC-seq     epigenetics     transcription factor    

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抗RNA病毒相关生物材料

姚康德,尹玉姬,张宝连,赵立国

《中国工程科学》 2003年 第5卷 第7期   页码 17-23

摘要：

在介绍RNA病毒结构、生殖、复制和转录的基础上，综述了抗病毒策略，其中包括抗SARS药物设计，RNA干扰，DNA疫苗释放系统，调控蛋白与糖胺聚糖衍生物或类似物相互作用，天然药物及肺泡组织工程等。这些实例涵盖了RNA病毒与蛋白质、DNA及多糖等生物材料的相互作用。生物材料作为基质或载体正在向细胞或/和基因活化的第三代生物材料发展，可望在抗病毒中发挥作用。

关键词： 抗RNA病毒     蛋白质     DNA     多糖     生物材料    

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基于RNA的生物防治——一种作物保护新模式 Review

Matthew Bramlett, Geert Plaetinck, Peter Maienfisch

《工程（英文）》 2020年 第6卷 第5期   页码 522-527 doi: 10.1016/j.eng.2019.09.008

摘要： 在过去的几年中，RNA干扰（RNAi）过程被认为是一种非常有前景的新方法，可作为化学和生物害虫防治剂、植物保护剂等叶面喷施、土壤或种子处理的补充。基于RNA的活性成分（AI）具有独特的作用方式，可以通过基因修饰（GM）和生物防治两种途径来实现。由于基于RNA的AI可利用自然过程来发挥控制作用，同时它们具有高度选择性，降低了非目标生物（NTO）的风险，因此基于RNA的AI有望提供未来作物保护剂所需要的选择性和可持续性。本文讨论了基于RNA的生物防治的替代方案在作物保护中的优势和局限性，以及RNA生物防治科罗拉多马铃薯甲虫（CPB）、玉米根虫（CRW）和大豆臭虫（SSB）的最新研究进展。在实现各种基于RNA的产品及其广泛使用和应用的道路上，仍然存在许多挑战。尽管如此，我们仍可预期到，基于RNA的AI将成为有价值的新工具，以补充当前的农作物保护解决方案。

关键词： 基于RNA的生物防治     RNA干扰（RNAi）     科罗拉多马铃薯甲虫（CPB）     玉米根虫（CRW）     大豆臭虫（SSB）    

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敲低特异性环状非编码RNA显著抑制骨肉瘤的进展 Article

王世东, 张红亮, 李博, 陈成龙, 任婷婷, 黄怡, 刘凯, 李敬敬, 郭卫

《工程（英文）》 2023年 第21卷 第2期   页码 187-193 doi: 10.1016/j.eng.2021.12.007

摘要： 异常表达的非编码环状RNA（circRNA）对骨肉瘤的发生和发展至关重要。本研究的目的是探索一种新的circRNA circ_000203 在骨肉瘤中的表达和作用，阐明其潜在机制。

关键词： 非编码RNA     骨肉瘤     circRNA     分子机制     敲低    

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Blockage of receptor-interacting protein 2 expression by small interfering RNA in murine macrophages

LIU Hongchun, CAO Zhongwei, JIN Jianjun, WANG Jiyao

《医学前沿（英文）》 2008年 第2卷 第2期   页码 166-170 doi: 10.1007/s11684-008-0030-1

摘要： This study aims to demonstrate that blocking the receptor-interacting protein2 (Rip2) expression can decrease inflammatory cytokine production by macrophage and protect mice from endotoxin lethality. Murine Rip2 small interfering RNA (siRNA) plasmids were constructed and transfected into macrophage and Rip2 expression was detected with reverse transcription-polymerase chain reaction (RT-PCR) and western blot. Cell proliferation was assayed with MTT. TNF-? concentration was assayed with ELISA and high-mobility group box 1 protein (HMGB1) level with semi-quantitative western blot after lipopolysaccharide (LPS) stimulation. LPS challenge was given after the plasmids were injected into mice and the survival rate was calculated. Rip2 siRNA plasmid could block the mRNA and protein expression of Rip2 and promote cell proliferation. Blocking Rip2 could attenuate LPS-induced TNF-? and HMGB1 production. The HMGB1 expression in the liver decreased to (40.21 ± 11.03) pg/g, and serum TNF-? level decreased to (300.43 ± 59.26) ng/L ( < 0.05). The survival rate of mice from endotoxemia was also improved ( < 0.05). The results demonstrate that Rip2 siRNA plasmid can block the expression of Rip2, decrease the production of TNF-? and HMGB1 and protect mice from fatal endotoxemia.
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Overexpressed long noncoding RNA CRNDE with distinct alternatively spliced isoforms in multiple cancers

Xuefei Ma, Wei Zhang, Rong Zhang, Jingming Li, Shufen Li, Yunlin Ma, Wen Jin, Kankan Wang

《医学前沿（英文）》 2019年 第13卷 第3期   页码 330-343 doi: 10.1007/s11684-017-0557-0

摘要： Alternative splicing is a tightly regulated process that contributes to cancer development. CRNDE is a long noncoding RNA with alternative splicing and is implicated in the pathogenesis of several cancers. However, whether deregulated expression of CRNDE is common and which isoforms are mainly involved in cancers remain unclear. In this study, we report that CRNDE is aberrantly expressed in the majority of solid and hematopoietic malignancies. The investigation of CRNDE expression in normal samples revealed that CRNDE was expressed in a tissue- and cell-specific manner. Further comparison of CRNDE expression in 2938 patient samples from 15 solid and hematopoietic tumors showed that CRNDE was significantly overexpressed in 11 malignancies, including 3 reported and 8 unreported, and also implicated that the overexpressed isoforms differed in various cancer types. Furthermore, anti-cancer drugs could efficiently repress CRNDE overexpression in cancer cell lines and primary samples, and even had different impacts on the expression of CRNDE isoforms. Finally, experimental profiles of 12 alternatively spliced isoforms demonstrated that the spliced variant CRNDE-g was the most highly expressed isoform in multiple cancer types. Collectively, our results emphasize the cancer-associated feature of CRNDE and its spliced isoforms, and may provide promising targets for cancer diagnosis and therapy.

关键词： long noncoding RNA     CRNDE     alternative splicing    

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标题 作者 时间 类型 操作

immune escape and microenvironment between RG-like and pri-OPC-like glioma revealed by single-cell RNA-seq

期刊论文

Effects of vitrification and cryostorage duration on single-cell RNA-Seq profiling of vitrified-thawed

Ying Huo, Peng Yuan, Qingyuan Qin, Zhiqiang Yan, Liying Yan, Ping Liu, Rong Li, Jie Yan, Jie Qiao

期刊论文

Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different

Xin Zou, Ke Chen, Jiawei Zou, Peiyi Han, Jie Hao, Zeguang Han

期刊论文

Identification of transporter proteins for PQQ-secretion pathways by transcriptomics and proteomics analysis in

Hui Wan,Yu Xia,Jianghua Li,Zhen Kang,Jingwen Zhou

期刊论文

BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN

期刊论文

Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation

null

期刊论文

BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN

Xiaokang ZHUO, Tangchun ZHENG, Zhiyong ZHANG, Suzhen LI, Yichi ZHANG, Lidan SUN, Weiru YANG, Jia WANG, Tangren CHENG, Qixiang ZHANG

期刊论文

PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing

期刊论文

Ribozyme and the mechanisms that underlie RNA catalysis

Timothy J. Wilson,Yijin Liu,David M. J. Lilley

期刊论文

Characterization of chromatin accessibility in psoriasis

期刊论文

抗RNA病毒相关生物材料

姚康德,尹玉姬,张宝连,赵立国

期刊论文

基于RNA的生物防治——一种作物保护新模式

Matthew Bramlett, Geert Plaetinck, Peter Maienfisch

期刊论文

敲低特异性环状非编码RNA显著抑制骨肉瘤的进展

王世东, 张红亮, 李博, 陈成龙, 任婷婷, 黄怡, 刘凯, 李敬敬, 郭卫

期刊论文

Blockage of receptor-interacting protein 2 expression by small interfering RNA in murine macrophages

LIU Hongchun, CAO Zhongwei, JIN Jianjun, WANG Jiyao

期刊论文

Overexpressed long noncoding RNA CRNDE with distinct alternatively spliced isoforms in multiple cancers

Xuefei Ma, Wei Zhang, Rong Zhang, Jingming Li, Shufen Li, Yunlin Ma, Wen Jin, Kankan Wang

期刊论文