38 Works

Genome-wide comparison of the GRAS protein family in eight Rosaceae species and GRAS gene expression analysis in Chinese white pear (Pyrus bretschneideri Rehder)

Wenjing Chang, Manyi Sun, Mingyue Zhang, Zikai Tang, Jiawen Sheng, Yueyuan Liu, Bobo Song, Jiaming Li, Kejiao Zhao & Jun Wu
The GRAS protein family encodes a family of plant-specific transcription factors that have diverse and significant functions in regulating plant development and anthocyanin biosynthesis. Our study represents the comprehensive identification and comparison of GRAS protein family genes in the Rosaceae. Here, 535 GRAS genes were screened from eight Rosaceae species. Phylogenetic analysis revealed that whole-genome duplication (WGD) events and dispersed duplication events were the major mechanisms promoting the expansion of the GRAS protein family in...

Dominant factors of the phosphorus regulatory network differ under various dietary phosphate loads in healthy individuals

Guoxin Ye, Jiaying Zhang, Zhaori Bi, Weichen Zhang, Minmin Zhang, Qian Zhang, Mengjing Wang & Jing Chen
The purpose of this study was to explore the contribution of each factor of the phosphorus metabolism network following phosphorus diet intervention via Granger causality analysis. In this study, a total of six healthy male volunteers were enrolled. All participants sequentially received regular, low-, and high-phosphorus diets. Consumption of each diet lasted for five days, with a 5-day washout period between different diets. Blood and urinary samples were collected on the fifth day of consumption...

Effects of intensive blood pressure control on mortality and cardiorenal function in chronic kidney disease patients

Yong Zhang, Jing-Jing Li, An-Jun Wang, Bo Wang, Shou-Liang Hu, Heng Zhang, Tian Li & Yan-Hong Tuo
Blood pressure (BP) variability is highly correlated with cardiovascular and kidney outcomes in patients with chronic kidney disease (CKD). However, appropriate BP targets in patients with CKD remain uncertain. We searched PubMed, Embase, and the Cochrane Library for randomized controlled trials (RCTs) of CKD patients who underwent intensive BP management. Kappa score was used to assess inter-rater agreement. A good agreement between the authors was observed to inter-rater reliability of RCTs selection (kappa = 0.77;...

Nucleo-cytoplasmic RNA distribution responsible for maintaining neuroinflammatory microenvironment

Yuyan Liao, Chenghao Kuang, Zheng Bao, Yijing He, Long Gu, Qianke Tao, Xiancheng Qiu, Ghosh Dipritu, Xi Kong, Lifang Zhang, Jianhua Peng, Yong Jiang & Shigang Yin
Subcellular localization of transcripts is highly associated with regulation of gene expression, synthesis of protein, and also the development of the human brain cortex. Although many mechanisms are prevalent in the occurrence of neuroinflammation, the mechanisms based on differences in subcellular localization of transcripts have not been explored. To characterize the dynamic profile of nuclear and cytoplasmic transcripts during the progress of haemorrhage-induced neuroinflammation, we isolated nucleo-cytoplasmic RNA fractions of oxyhaemoglobin (oxy-Hb) treated microglia cells...

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...

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...

Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients

Yong Xiong, Yuan Liu, Liu Cao, Dehe Wang, Ming Guo, Ao Jiang, Dong Guo, Wenjia Hu, Jiayi Yang, Zhidong Tang, Honglong Wu, Yongquan Lin, Meiyuan Zhang, Qi Zhang, Mang Shi, Yingle Liu, Yu Zhou, Ke Lan & Yu Chen
Circulating in China and 158 other countries and areas, the ongoing COVID-19 outbreak has caused devastating mortality and posed a great threat to public health. However, efforts to identify effectively supportive therapeutic drugs and treatments has been hampered by our limited understanding of host immune response for this fatal disease. To characterize the transcriptional signatures of host inflammatory response to SARS-CoV-2 (HCoV-19) infection, we carried out transcriptome sequencing of the RNAs isolated from the bronchoalveolar...

SRSF5 regulates alternative splicing of DMTF1 pre-mRNA through modulating SF1 binding

Jialiang Li, Guangyue Li, Yige Qi, Yao Lu, Hao Wang, Ke Shi, Dangdang Li, Jinming Shi, Daniel B. Stovall & Guangchao Sui
Among the three DMTF1 splicing isoforms, DMTF1α acts as a tumour suppressor through promoting p14ARF expression, while DMTF1β exhibits an oncogenic role likely through antagonizing DMTF1α. However, the molecular mechanism underlying alternative splicing of DMTF1 pre-mRNA has not been delineated. In the current study, we discovered SRSF5 as a regulatory protein binding to a region located between DMTF1β and α acceptor splice sites to promote DMTF1β and γ splicing. We demonstrated that SRSF5 expression positively...

SRSF5 regulates alternative splicing of DMTF1 pre-mRNA through modulating SF1 binding

Jialiang Li, Guangyue Li, Yige Qi, Yao Lu, Hao Wang, Ke Shi, Dangdang Li, Jinming Shi, Daniel B. Stovall & Guangchao Sui
Among the three DMTF1 splicing isoforms, DMTF1α acts as a tumour suppressor through promoting p14ARF expression, while DMTF1β exhibits an oncogenic role likely through antagonizing DMTF1α. However, the molecular mechanism underlying alternative splicing of DMTF1 pre-mRNA has not been delineated. In the current study, we discovered SRSF5 as a regulatory protein binding to a region located between DMTF1β and α acceptor splice sites to promote DMTF1β and γ splicing. We demonstrated that SRSF5 expression positively...

Inference on moderation effect with third-variable effect analysis – application to explore the trend of racial disparity in oncotype dx test for breast cancer treatment

Qingzhao Yu, Lu Zhang, Xiaocheng Wu & Bin Li
Third variable effect refers to the effect from a third variable that explains an observed relationship between an exposure and an outcome. Depending on whether there is causal relationship, typically, a third variable takes the format of a mediator or a confounder. A moderation effect is a special case of the third-variable effect, where the moderator and other variables have an interactive effect on the outcome. In this paper, we extend the R package ‘mma’...

Whole-transcriptome analysis of rat cavernosum and identification of circRNA-miRNA-mRNA networks to investigate nerve injury erectile dysfunction pathogenesis

Jie Huang, Jianxiong Ma, Jie Wang, Ke Ma, Kang Zhou, Wenjie Huang, Fan Zhao, Bodong Lv & Qing Hu
There is growing evidence that circular RNAs (circRNAs) play a vital role in many kinds of diseases, including erectile dysfunction (ED). Nevertheless, the role of circRNAs in cavernous nerve-damaging ED (CNI-ED) is unknown. Here, we aimed to discover novel circRNAs, probed their potential role in the CNI-ED, and construct a ceRNA network of circRNAs. Twelve male Sprague Dawley rats were randomly divided into 2 groups by us: bilateral cavernous nerve crush (BCNC) and control groups....

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...

MicroRNA-146a-5p enhances T helper 17 cell differentiation via decreasing a disintegrin and metalloprotease 17 level in primary sjögren’s syndrome

Xiaoyan Wang, Shaojun Xin, Youqing Wang, Duo Ju, Quan Wu, Ye Qiu, Xuemin Niu, Wei Liu, Jianyou Li & Pengtian Ji
In clinical practice, we found that microRNA (miR)-146a-5p is significantly up-regulated in peripheral blood mononuclear cells (PBMCs) of primary sjögren’s syndrome (pSS) patients. In vitro experiments confirmed that miR-146a-5p promotes T helper 17 (Th17) cell differentiation, but the specific mechanism is still unknown. To solve this problem, 20 pSS patients and 20 healthy subjects were enrolled in this study and PBMCs were isolated from their blood. The expression of the membrane IL-23 R (mIL-23 R)...

A novel transcription factor UvCGBP1 regulates development and virulence of rice false smut fungus Ustilaginoidea virens

Xiaoyang Chen, Pingping Li, Hao Liu, Xiaolin Chen, Junbin Huang, Chaoxi Luo, Guotian Li, Tom Hsiang, David B. Collinge & Lu Zheng
Ustilaginoidea virens, causing rice false smut (RFS) is an economically important ascomycetous fungal pathogen distributed in rice-growing regions worldwide. Here, we identified a novel transcription factor UvCGBP1 (Cutinase G-box binding protein) from this fungus, which is unique to ascomycetes. Deletion of UvCGBP1 affected development and virulence of U. virens. A total of 865 downstream target genes of UvCGBP1 was identified using ChIP-seq and the most significant KEGG enriched functional pathway was the MAPK signaling pathway....

Network pharmacology-based analysis in determining the mechanisms of Huoxin pill in protecting against myocardial infarction

Jia He, Da Wo, En Ma, Qing Wang, Jinxiao Chen, Jun Peng, Weidong Zhu & Dan-ni Ren
Huoxin pill (HXP) is a commonly used TCM prescription for treatment of cardiovascular diseases. However, its mechanism in protecting against myocardial infarction (MI) remains unknown. We performed a network pharmacology analysis to explore the bioactive ingredients, therapeutic effects, and mechanisms of HXP in protecting against MI. HPLC was used to identify major bioactive compounds, and overlap with MI target genes were visualised. 10-Week old C57BL/6 mice were randomly assigned as: Sham-operated control, MI + Phosphate...

Network pharmacology-based analysis in determining the mechanisms of Huoxin pill in protecting against myocardial infarction

Jia He, Da Wo, En Ma, Qing Wang, Jinxiao Chen, Jun Peng, Weidong Zhu & Dan-ni Ren
Huoxin pill (HXP) is a commonly used TCM prescription for treatment of cardiovascular diseases. However, its mechanism in protecting against myocardial infarction (MI) remains unknown. We performed a network pharmacology analysis to explore the bioactive ingredients, therapeutic effects, and mechanisms of HXP in protecting against MI. HPLC was used to identify major bioactive compounds, and overlap with MI target genes were visualised. 10-Week old C57BL/6 mice were randomly assigned as: Sham-operated control, MI + Phosphate...

Whole-transcriptome analysis of rat cavernosum and identification of circRNA-miRNA-mRNA networks to investigate nerve injury erectile dysfunction pathogenesis

Jie Huang, Jianxiong Ma, Jie Wang, Ke Ma, Kang Zhou, Wenjie Huang, Fan Zhao, Bodong Lv & Qing Hu
There is growing evidence that circular RNAs (circRNAs) play a vital role in many kinds of diseases, including erectile dysfunction (ED). Nevertheless, the role of circRNAs in cavernous nerve-damaging ED (CNI-ED) is unknown. Here, we aimed to discover novel circRNAs, probed their potential role in the CNI-ED, and construct a ceRNA network of circRNAs. Twelve male Sprague Dawley rats were randomly divided into 2 groups by us: bilateral cavernous nerve crush (BCNC) and control groups....

Efficacy of statins on renal function in patients with chronic kidney disease: a systematic review and meta-analysis

Lin Zhao, Shu Li & Ying Gao
Studies have shown that the use of statins could significantly improve lipid profiles; however, it remains controversial whether the use of statins could improve renal function in patients with chronic kidney disease (CKD). Therefore, we conducted a meta-analysis of randomized controlled trials (RCTs) to evaluate the effects of statins on renal function in patients with CKD. We systematically searched PubMed, EMBASE, and the Cochrane Library databases for eligible RCTs from inception to October 2020. Pooled...

Effects of intensive blood pressure control on mortality and cardiorenal function in chronic kidney disease patients

Yong Zhang, Jing-Jing Li, An-Jun Wang, Bo Wang, Shou-Liang Hu, Heng Zhang, Tian Li & Yan-Hong Tuo
Blood pressure (BP) variability is highly correlated with cardiovascular and kidney outcomes in patients with chronic kidney disease (CKD). However, appropriate BP targets in patients with CKD remain uncertain. We searched PubMed, Embase, and the Cochrane Library for randomized controlled trials (RCTs) of CKD patients who underwent intensive BP management. Kappa score was used to assess inter-rater agreement. A good agreement between the authors was observed to inter-rater reliability of RCTs selection (kappa = 0.77;...

Dominant factors of the phosphorus regulatory network differ under various dietary phosphate loads in healthy individuals

Guoxin Ye, Jiaying Zhang, Zhaori Bi, Weichen Zhang, Minmin Zhang, Qian Zhang, Mengjing Wang & Jing Chen
The purpose of this study was to explore the contribution of each factor of the phosphorus metabolism network following phosphorus diet intervention via Granger causality analysis. In this study, a total of six healthy male volunteers were enrolled. All participants sequentially received regular, low-, and high-phosphorus diets. Consumption of each diet lasted for five days, with a 5-day washout period between different diets. Blood and urinary samples were collected on the fifth day of consumption...

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...

Functional identification of a rare vascular endothelial growth factor a (VEGFA) variant associating with the nonsyndromic cleft lip with/without cleft palate

Bohui Sun, Yangjia Liu, Wenbin Huang, Qian Zhang, Jiuxiang Lin, Weiran Li, Jieni Zhang & Feng Chen
Vascular endothelial growth factor A (VEGFA) is a crucial growth factor, which participates in multiple processes of human growth and development, such as angiogenesis and osteogenesis and is also necessary for development of palate. The purpose of this study was to investigate the effect of a rare VEGFA mutation (NM_001025366.2 773 T > C p.Val258Ala) on the cell functions and osteogenesis. Here, we found that the VEGFA mutation has adverse effects on the function of...

Functional identification of a rare vascular endothelial growth factor a (VEGFA) variant associating with the nonsyndromic cleft lip with/without cleft palate

Bohui Sun, Yangjia Liu, Wenbin Huang, Qian Zhang, Jiuxiang Lin, Weiran Li, Jieni Zhang & Feng Chen
Vascular endothelial growth factor A (VEGFA) is a crucial growth factor, which participates in multiple processes of human growth and development, such as angiogenesis and osteogenesis and is also necessary for development of palate. The purpose of this study was to investigate the effect of a rare VEGFA mutation (NM_001025366.2 773 T > C p.Val258Ala) on the cell functions and osteogenesis. Here, we found that the VEGFA mutation has adverse effects on the function of...

MicroRNA-146b-3p regulates the dysfunction of vascular smooth muscle cells via repressing phosphoinositide-3 kinase catalytic subunit gamma

Xijing Zhuang, Feng Gao, Lei Shi, Wei Liu, Wenjun Wang, Xuezhi He & Yang Gao
MicroRNAs are crucial regulators in the phenotype switch of vascular smooth muscle cells (VSMCs). Nonetheless, the role of miR-146b-3p in VSMCs remains unclear. In the present study, platelet-derived growth factor-BB (PDGF-BB) at different concentrations was employed to stimulate VSMCs for different times, to establish the model of VSMC dysfunction. The relative expression of miR-146b-3p was quantified by quantitative real-time polymerase chain reaction (qRT-PCR). The proliferation of VSMCs was measured by BrdU assay. Flow cytometry analysis...

Prediction of intrahepatic cholestasis of pregnancy in the first 20 weeks of pregnancy

Xinyuan Zhang, Yu Chen, Stephen Salerno, Yi Li, Libin Zhou, Xiaoxi Zeng & Huafeng Li
Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disease associated with a significant risk of fetal complications including pre-term delivery and fetal death. Typically, it was diagnosed in the third trimester of pregnancy. This study utilized characteristics from routine maternal examinations in the first 20 weeks’ gestation to predict ICP in pregnant women. This is a retrospective case-control study. 13,329 medical records were collected on pregnant women presenting to the West China Second University...

Registration Year

  • 2021
    38

Resource Types

  • Dataset
    38

Affiliations

  • Beijing Tian Tan Hospital
    38
  • Capital Medical University
    31
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    28
  • Chinese Academy of Sciences
    26
  • Shanghai Jiao Tong University
    24
  • Sun Yat-sen University
    22
  • Huazhong University of Science and Technology
    22
  • Fudan University
    21
  • Sichuan University
    20
  • Peking University
    18