287 Works

Construction of lncRNA-related ceRNA regulatory network in diabetic subdermal endothelial cells

Jiangbo Wan & Bo Liu
Long non-coding RNAs (lncRNAs) were considered to be involved in vascular complications in diabetes mellitus, but still only limited knowledge in this regard has been obtained. Herein, we further explored the roles of lncRNAs and mRNAs in diabetic vasculopathy (DV) through conducting bioinformatics analysis using data set downloaded from GEO database. The differentially expressed lncRNAs and mRNAs were identified by edge package. GO enrichment analysis and KEGG pathway analysis were performed based on clusterprofiler package....

Identification of fibronectin 1 (FN1) and complement component 3 (C3) as immune infiltration-related biomarkers for diabetic nephropathy using integrated bioinformatic analysis

Yuejun Wang, Mingming Zhao & Yu Zhang
Immune cell infiltration (ICI) plays a pivotal role in the development of diabetic nephropathy (DN). Evidence suggests that immune-related genes play an important role in the initiation of inflammation and the recruitment of immune cells. However, the underlying mechanisms and immune-related biomarkers in DN have not been elucidated. Therefore, this study aimed to explore immune-related biomarkers in DN and the underlying mechanisms using bioinformatic approaches. In this study, four DN glomerular datasets were downloaded, merged,...

Circular RNA Circ_0005564 promotes osteogenic differentiation of bone marrow mesenchymal cells in osteoporosis

Zitao Liu, Qiyu Liu, Shanchuang Chen, Haitao Su & Tao Jiang
Circular RNA (CircRNA) plays a potential role in bone formation. We aimed to study the circRNAs expression profiles and their functions in osteogenic differentiation of human bone marrow stromal cells (BMSCs). Firstly, we established osteogenic differentiation of BMSCs displaying increased mRNA expression of osteogenic differentiation marker (RUNX2, OPN, and OCN), increased ALP activity and protein expression, and increased mineralized nodules formation, as well as morphological alteration. Then, we employed high-throughput sequencing to analyze circRNA expression...

Genome-wide screening for the G-protein-coupled receptor (GPCR) pathway-related therapeutic gene RGS19 (regulator of G protein signaling 19) in bladder cancer

Yue Liu, Weiming Lou, Guang Chen, Bing Ding, Jin Kuang, Yize Zhang, Cong Wang, Sainan Duan, Ying Deng & Xiongbing Lu
Bladder cancer is one of the most severe genitourinary cancers, causing high morbidity worldwide. However, the underlying molecular mechanism is not clear, and it is urgent to find target genes for treatment. G-protein-coupled receptors are currently a target of high interest for drug design. Thus, we aimed to identify a target gene-related to G-protein-coupled receptors for therapy. We used The Cancer Genome Atlas (TCGA) and DepMap databases to obtain the expression and clinical data of...

Identification of microRNA hsa-miR-30c-5p as an inhibitory factor in the progression of hepatocellular carcinoma and investigation of its regulatory network via comprehensive analysis

Shangshang Hu, Jinyan Zhang, Xiaoyu Fang, Guoqing Guo, Jing Dai, Zhiyong Sheng, Dongdong Li, Jiasheng Chen, Li Zhang, Chuanmiao Liu & Yu Gao
Hepatocellular carcinoma (HCC) is a primary liver cancer with high morbidity and mortality. An increasing number of abnormal gene expressions were identified to be associated with the progression of HCC. Previous studies showed that the hsa-miR-30 c-5p (miR-30 c), one of the miR-30 family members, might play a role in suppressing tumor progression in a variety of tumors. The present study aims to examine miR-30 c effects in the development of HCC. The role of...

A seven-gene signature and the C–C motif chemokine receptor family genes are the sarcoma-related immune genes

Jiarui Chen, Tuo Liang, Jiemei Cen, Jie Jiang, Shixin Pan, Shengsheng Huang, Liyi Chen, Xuhua Sun, Hao Li, Tianyou Chen, Wei Liang, Shian Liao, Chaojie Yu, Yuanlin Yao, Zhen Ye, Wuhua Chen, Hao Guo, Xinli Zhan & Chong Liu
Cells of the tumor microenvironment exert a vital influence on sarcoma prognosis. This study aimed to analyze and identify differentially expressed genes (DEGs) related to immunity and their significance as immune biomarkers for the accurate prediction of overall survival of patients with sarcoma. The Cancer Genome Atlas was adopted for obtaining sarcoma gene microarray and corresponding clinical information. ESTIMATE algorithm was used to calculate tumor immune microenvironment indices. Immune-associated DEGs were identified using the limma...

MiRNA based tumor mutation burden diagnostic and prognostic prediction models for endometrial cancer

Nan Lu, Jinhui Liu, Chengjian Ji, Yichun Wang, Zhipeng Wu, Shuning Yuan, Yan Xing & Feiyang Diao
Uterus Corpus Endometrial cancer (UCEC) is the sixth most common malignant tumor worldwide. In this research, we identified diagnostic and prognostic biomarkers to reflect patients’ immune microenvironment and prognostic. Various data of UCEC patients from the TCGA database were obtained. Firstly, patients were divided into a high tumor mutation burden (TMB) level group and a low TMB level group according to the level of TMB. Then, differentially expressed miRNAs between the two groups were obtained....

Efficacy and safety of Chinese patent medicine (Kang-ai injection) as an adjuvant in the treatment of patients with hepatocellular carcinoma: a meta-analysis

Chuihua Sun, Fang Dong, Ting Xiao & Wenni Gao
Kang-ai injection (KAI) is an authorized herbal medicine used in cancer treatment. However, its clinical efficacy in hepatocellular carcinoma (HCC) has not been investigated thoroughly. To systematically evaluate the efficacy and safety of KAI in patients with HCC. The Web of Science, PubMed, Cochrane Library, EMBASE, CBM, CNKI, VIP and Wanfang databases were systematically searched (date range: inception to December 2020) using the key terms ‘Kang-ai injection’ and ‘hepatocellular carcinoma’. The current analysis included controlled...

Naoxintong accelerates diabetic wound healing by attenuating inflammatory response

Leyu Fang, Lu Chen, Min Song, Juan He, Lusha Zhang, Chunxiao Li, Qianyi Wang, Wenjie Yang, Wei Sun, Yuze Leng, Hong Shi, Shaoxia Wang, Xiumei Gao & Hong Wang
Naoxintong (NXT), a prescribed traditional Chinese medicine, widely used in cerebrovascular and cardiovascular diseases, could be effective in diabetic wounds. This study evaluates the wound healing activity of NXT by employing an excisional wound splinting model. NXT was dissolved in saline and given daily by gavage. Wounds were induced at the dorsum of non-diabetic (db/+) and diabetic (db/db) mice and treated with saline or 700 mg/kg/d NXT for 16 days. Wound closure was measured every...

Pegmatite magmatic evolution and rare metal mineralization of the Dahongliutan pegmatite field, Western Kunlun Orogen: Constraints from the B isotopic composition and mineral-chemistry

Rui Cao, Yongbao Gao, Bin Chen, Leon Bagas, Shengchao Yan, Chao Huang & Hui Zhao
The Dahongliutan rare-metal pegmatite deposit, associated with the pegmatite dikes hosted by Dahongliutan pluton and metasedimentary rocks, is a new discovered Li–Be deposit in the the West Kunlun orogen, Northwest China. The Dahongliutan pegmatite is a classic and typical example of a highly fractionated Li-Ce-Ta (LCT) type pegmatite, with distinct regional zonation composed of well-developed garnet-tourmaline-microcline (GTM), beryl-tourmaline-muscovite (BTM) and spodumene-albite (SA) pegmatites from the barren core inward to outer zone. Detailed field studies, together...

Triassic igneous activities in the east flank of the East Kunlun orogenic belt: the Daheba complex example

Nan Tian, Feng-Yue Sun, Zhong-Cui Pan, Liang Li, Yan Gu, Dong-Qian Wu, Jia-Fang Deng, Zhe-Dong Liu, Li Wang & Ya-Jing Zhang
The Triassic igneous complexes in the east flank of the East Kunlun orogenic belt (E-KOB) provide a window through which to investigate the Mesozoic magmatism in the E-KOB. Here, we report the precise timing of Triassic magmatism and magma petrogenesis of different rock types in the east flank of the E-KOB based on the petrology, mineral chemistry, geochemistry, zircon geochronology and Lu-Hf isotopes. Zircon U-Pb dating reveals that the Daheba complex was crystallized in 242–239...

Structural insights into dpCoA-RNA decapping by NudC

Wei Zhou, Zeyuan Guan, Fen Zhao, Yage Ye, Fang Yang, Ping Yin & Delin Zhang
Various kinds of cap structures, such as m7G, triphosphate groups, NAD and dpCoA, protect the 5′ terminus of RNA. The cap structures bond covalently to RNA and affect its stability, translation, and transport. The removal of the caps is mainly executed by Nudix hydrolase family proteins, including Dcp2, RppH and NudC. Numerous efforts have been made to elucidate the mechanism underlying the removal of m7G, triphosphate group, and NAD caps. In contrast, few studies related...

The lipoprotein NlpD in Cronobacter sakazakii responds to acid stress and regulates macrophage resistance and virulence by maintaining membrane integrity

Xuemeng Ji, Ping Lu, Juan Xue, Ning Zhao, Yan Zhang, Lu Dong, Xuejiao Zhang, Ping Li, Yaozhong Hu, Jin Wang, Bowei Zhang, Jingmin Liu, Huan lv & Shuo Wang
Cronobacter sakazakii, an emerging opportunistic pathogen, is implicated in severe foodborne outbreak infections in premature and full-term infants. Generally, acid tolerance is vital for the pathogenesis of foodborne pathogens; however, its role in C. sakazakii virulence remains largely unknown. To screen out acid-tolerance determinants from transposon mutants, anovel counterselection method using gentamicin and acid was developed. Using the counterselection method and growth assay, we screened several acid-sensitive mutants and found that nlpD encodes an acid-resistance...

Genome-wide identification and functional prediction of circular RNAs in response to heat stress in Chinese Holstein cows

Ying Qi, Lin Zhang, Yuemei Guo, Jing Wang, Mingxing Chu, Yiming Zhang, Junfei Guo & Qiuling Li
Heat stress (HS) leads to substantial economic loss of dairy industry each year. The negative effect of HS in dairy cows is becoming one of the more urgent issue due to accelerating side-effects of global warming. Various genes are involved in HS response but the information about the role of noncoding RNAs, especially circular RNAs (circRNAs) is largely unknown. In our study, we aimed to investigate the different expression profile of circRNAs between HS and...

RETRACTED ARTICLE: Long noncoding RNA H19 regulates HIF-1α/AXL signaling through inhibiting miR-20b-5p in endometrial cancer

He Zhu, Yue-Mei Jin, Xue-Man Lyu, Li-Mei Fan & Fei Wu
We, the Editors and Publisher of the journal Cell Cycle, have retracted the following article: He Zhu, Yue-Mei Jin, Xue-Man Lyu, Li-Mei Fan & Fei Wu (2019) Long noncoding RNA H19 regulates HIF-1α/AXL signaling through inhibiting miR-20b-5p in endometrial cancer, Cell Cycle, 18:19, 2454-2464, DOI: 10.1080/15384101.2019.1648958 Since publication, the authors have found significant errors in the statistical analysis of the research reported in this article. As this error directly impacts the accuracy of the results...

RR3DD: an RNA global structure-based RNA three-dimensional structural classification database

Xu Hong, Jinfang Zheng, Juan Xie, Xiaoxue Tong, Xudong Liu, Qi Song, Sen Liu & Shiyong Liu
The three-dimensional (3D) structure of RNA usually plays an important role in the recognition with RNA-binding protein. Along with the discovering of RNAs, several RNA databases are developed to study the functions of RNA based on sequence, secondary structure, local 3D structural motif and global structure. Based on RNA function and structure, different RNAs are classified and stored in SCOR and DARTS, respectively. The classification of RNA structures is useful in RNA structure prediction and...

Discovery of a subgenotype of human coronavirus NL63 associated with severe lower respiratory tract infection in China, 2018

Yanqun Wang, Xin Li, Wenkuan Liu, Mian Gan, Lu Zhang, Jin Wang, Zhaoyong Zhang, Airu Zhu, Fang Li, Jing Sun, Guoxian Zhang, Zhen Zhuang, Jiaying Luo, Dehui Chen, Shuyan Qiu, Li Zhang, Duo Xu, Chris Ka Pun Mok, Fuchun Zhang, Jingxian Zhao, Rong Zhou & Jincun Zhao
Human coronavirus NL63 (HCoV-NL63) is primarily associated with common cold in children, elderly and immunocompromised individuals. Outbreaks caused by HCoV-NL63 are rare. Here we report a cluster of HCoV-NL63 cases with severe lower respiratory tract infection that arose in Guangzhou, China, in 2018. Twenty-three hospitalized children were confirmed to be HCoV-NL63 positive, and most of whom were hospitalized with severe pneumonia or acute bronchitis. Whole genomes of HCoV-NL63 were obtained using next-generation sequencing. Phylogenetic and...

Additional file 3 of Temporal expression study of miRNAs in the crown tissues of winter wheat grown under natural growth conditions

Menglei Wang, Chenhui Yang, Kangning Wei, Miao Zhao, Liqiang Shen, Jie Ji, Li Wang, Daijing Zhang, Junqiang Guo, Yun Zheng, Juanjuan Yu, Mo Zhu, Haiying Liu & Yong-Fang Li
Additional file 3: Table S2. Expression of wheat new miRNAs in crown tissues.

Additional file 4 of Temporal expression study of miRNAs in the crown tissues of winter wheat grown under natural growth conditions

Menglei Wang, Chenhui Yang, Kangning Wei, Miao Zhao, Liqiang Shen, Jie Ji, Li Wang, Daijing Zhang, Junqiang Guo, Yun Zheng, Juanjuan Yu, Mo Zhu, Haiying Liu & Yong-Fang Li
Additional file 4: Table S3. Information of wheat_miRNA2693 and wheat_miR5099.

Inefficient integration during multiple facial processing in pre-morbid and early phases of psychosis

TianHong Zhang, YingYu Yang, LiHua Xu, XiaoChen Tang, YeGang Hu, Xin Xiong, YanYan Wei, HuiRu Cui, YingYing Tang, HaiChun Liu, Tao Chen, Zhi Liu, Li Hui, ChunBo Li, XiaoLi Guo & JiJun Wang
We used eye-tracking to evaluate multiple facial context processing and event-related potential (ERP) to evaluate multiple facial recognition in individuals at clinical high risk (CHR) for psychosis. In total, 173 subjects (83 CHRs and 90 healthy controls [HCs]) were included and their emotion perception performances were accessed. A total of 40 CHRs and 40 well-matched HCs completed an eye-tracking task where they viewed pictures depicting a person in the foreground, presented as context-free, context-compatible, and...

Cholesterol depletion sensitizes gallbladder cancer to cisplatin by impairing DNA damage response

Yonglong Zhang, Yanfeng Liu, Jinlin Duan, Hui Wang, Yuchen Zhang, Ke Qiao & Jian Wang
Gallbladder cancer (GBC) is the common malignancy of the bile tract system with extremely poor clinical outcomes, owing to its metastatic property and intrinsic resistance to the first-line drugs. Although it is well-established that cholesterol abnormity contributes to gallstone formation, a leading risk factor for GBC, the link of cholesterol homeostasis with GBC has not been investigated. The present study systematically examined the genes implicated in cholesterol homeostasis, and revealed altered gene expressions of de...

sRNA23, a novel small RNA, regulates to the pathogenesis of Streptococcus suis serotype 2

Quanming Xu, Hong Chen, Wen Sun, Yongyi Zhang, Dewen Zhu, Kul Raj, Ji-Long Chen & Ye Chen
Streptococcus suis serotype 2 (S. suis 2) is an important ubiquitous zoonotic pathogen. To date, regulatory factors and their implication in S. suis pathogenesis are not fully understood. Small non-coding RNAs (sRNAs) have been proven to function as important regulatory factors in bacterial pathogenesis and stress adaptation. Here, we identified a differentially downregulated S. suis 05ZYH33 sRNA after iron starvation by RNA-seq, which we named sRNA23. The presence of sRNA23 was further confirmed by RACE...

Additional file 8 of Temporal expression study of miRNAs in the crown tissues of winter wheat grown under natural growth conditions

Menglei Wang, Chenhui Yang, Kangning Wei, Miao Zhao, Liqiang Shen, Jie Ji, Li Wang, Daijing Zhang, Junqiang Guo, Yun Zheng, Juanjuan Yu, Mo Zhu, Haiying Liu & Yong-Fang Li
Additional file 8: Table S5. Sequence of primers used in this study.

Suppressed inflammation in obese children induced by a high-fiber diet is associated with the attenuation of gut microbial virulence factor genes

Hui Li, Guojun Wu, Liping Zhao & Menghui Zhang
In our previous study, a gut microbiota-targeted dietary intervention with a high-fiber diet improved the immune status of both genetically obese (Prader-Willi Syndrome, PWS) and simple obese (SO) children. However, PWS children had higher inflammation levels than SO children throughout the trial, the gut microbiota of the two cohorts was similar. As some virulence factors (VFs) produced by the gut microbiota play a role in triggering host inflammation, this study compared the characteristics and changes...

SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation

Patricia Richard, Shuang Feng, Yueh-Lin Tsai, Wencheng Li, Paola Rinchetti, Ubayed Muhith, Juan Irizarry-Cole, Katharine Stolz, Lionel A. Sanz, Stella Hartono, Mainul Hoque, Saba Tadesse, Hervé Seitz, Francesco Lotti, Michio Hirano, Frédéric Chédin, Bin Tian & James L. Manley
SETX (senataxin) is an RNA/DNA helicase that has been implicated in transcriptional regulation and the DNA damage response through resolution of R-loop structures. Mutations in SETX result in either of two distinct neurodegenerative disorders. SETX dominant mutations result in a juvenile form of amyotrophic lateral sclerosis (ALS) called ALS4, whereas recessive mutations are responsible for ataxia called ataxia with oculomotor apraxia type 2 (AOA2). How mutations in the same protein can lead to different phenotypes...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Huazhong University of Science and Technology
  • Chinese Academy of Medical Sciences & Peking Union Medical College
  • Shanghai Jiao Tong University
  • Fudan University
  • Sun Yat-sen University
  • Sichuan University
  • Zhejiang University
  • Chinese Academy of Sciences
  • Capital Medical University
  • Peking University