173 Works

Myotubularin related protein 7 is essential for the spermatogonial stem cell homeostasis via PI3K/AKT signaling

Dan Zhao, Cong Shen, Tingting Gao, Hong Li, Yueshuai Guo, Feng Li, Chenchen Liu, Yuanyuan Liu, Xia Chen, Xi Zhang, Yangyang Wu, Yi Yu, Meng Lin, Yan Yuan, Xiaofang Chen, Xiaoyan Huang, Shenmin Yang, Jun Yu, Jun Zhang & Bo Zheng
Myotubularin related protein 7 (MTMR7), a key member of the MTMR family, depicts phosphatase activity and is involved in myogenesis and tumor growth. We have previously identified MTMR7 in the proteomic profile of mouse spermatogonial stem cell (SSC) maturation and differentiation, implying that MTMR7 is associated with neonatal testicular development. In this study, to further explore the distribution and function of MTMR7 in mouse testis, we studied the effect of Mtmr7 knockdown on neonatal testicular...

Biological characteristics associated with virulence in Clostridioides difficile ribotype 002 in Hong Kong

Ka Yi Kong, Thomas N. Y. Kwong, Hung Chan, Kristine Wong, Samuel S. Y. Wong, Anu P. Chaparala, Raphael C. Y. Chan, Lin Zhang, Joseph J. Y. Sung, Jun Yu, Peter M. Hawkey, Margaret Ip, William K. K. Wu & Sunny H. Wong
Clostridioides difficile infection (CDI) is a common cause of nosocomial diarrhea and can sometimes lead to pseudo-membranous colitis and toxic megacolon. We previously reported that the PCR ribotype 002 was a common C. difficile ribotype in Hong Kong that was associated with increased mortality. In this study, we assessed in vitro bacteriological characteristics and in vivo virulence of ribotype 002 compared to other common ribotypes, including ribotypes 012, 014 and 046. We observed significantly higher...

RETRACTED ARTICLE: KIAA1429 promotes osteosarcoma progression by promoting stem cell properties and is regulated by miR-143-3p

Qicai Han, Jie Yang, Hao Yang, Chao Li, Juan Li & Yuan Cao
We, the Editors and Publisher of the journal Cell Cycle, have retracted the following article: Qicai Han, Jie Yang, Hao Yang, Chao Li, Juan Li & Yuan Cao (2020) KIAA1429 promotes osteosarcoma progression by promoting stem cell properties and is regulated by miR-143-3p, Cell Cycle, 19:10, 1172-1185, DOI: 10.1080/15384101.2020.1749465 Since publication, concerns have been raised about similarity of the data in another published article: Yang J, Han Q, Li C, Yang H, Chen X, Wang...

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...

Construction of a novel risk model based on the random forest algorithm to distinguish pancreatic cancers with different prognoses and immune microenvironment features

Yalan Lei, Rong Tang, Jin Xu, Bo Zhang, Jiang Liu, Chen Liang, Qingcai Meng, Jie Hua, Xianjun Yu, Wei Wang & Si Shi
Immune-related long noncoding RNAs (irlncRNAs) are actively involved in regulating the immune status. This study aimed to establish a risk model of irlncRNAs and further investigate the roles of irlncRNAs in predicting prognosis and the immune landscape in pancreatic cancer. The transcriptome profiles and clinical information of 176 pancreatic cancer patients were retrieved from The Cancer Genome Atlas (TCGA). Immune-related genes (irgenes) downloaded from ImmPort were used to screen 1903 immune-related lncRNAs (irlncRNAs) using Pearson’s...

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...

A defective lysophosphatidic acid-autophagy axis increases miscarriage risk by restricting decidual macrophage residence

Hui-Li Yang, Zhen-Zhen Lai, Jia-Wei Shi, Wen-Jie Zhou, Jie Mei, Jiang-Feng Ye, Tao Zhang, Jian Wang, Jian-Yuan Zhao, Da-Jin Li & Ming-Qing Li
Massive infiltrated and enriched decidual macrophages (dMφ) have been widely regarded as important regulators of maternal-fetal immune tolerance and trophoblast invasion, contributing to normal pregnancy. However, the characteristics of metabolic profile and the underlying mechanism of dMφ residence remain largely unknown. Here, we observe that dMφ display an active glycerophospholipid metabolism. The activation of ENPP2-lysophosphatidic acid (LPA) facilitates the adhesion and retention, and M2 differentiation of dMφ during normal pregnancy. Mechanistically, this process is mediated...

A defective lysophosphatidic acid-autophagy axis increases miscarriage risk by restricting decidual macrophage residence

Hui-Li Yang, Zhen-Zhen Lai, Jia-Wei Shi, Wen-Jie Zhou, Jie Mei, Jiang-Feng Ye, Tao Zhang, Jian Wang, Jian-Yuan Zhao, Da-Jin Li & Ming-Qing Li
Massive infiltrated and enriched decidual macrophages (dMφ) have been widely regarded as important regulators of maternal-fetal immune tolerance and trophoblast invasion, contributing to normal pregnancy. However, the characteristics of metabolic profile and the underlying mechanism of dMφ residence remain largely unknown. Here, we observe that dMφ display an active glycerophospholipid metabolism. The activation of ENPP2-lysophosphatidic acid (LPA) facilitates the adhesion and retention, and M2 differentiation of dMφ during normal pregnancy. Mechanistically, this process is mediated...

ATG7-mediated autophagy facilitates embryonic stem cell exit from naive pluripotency and marks commitment to differentiation

Jilong Zhou, Hainan He, Jing-Jing Zhang, Xin Liu, Wang Yao, Chengyu Li, Tian Xu, Shu-Yuan Yin, Dan-Ya Wu, Cheng-Li Dou, Qiao Li, Jiani Xiang, Wen-Jing Xiong, Li-Yan Wang, Jun-ming Tang, Zhouyiyuan Xue, Xia Zhang & Yi-Liang Miao
Macroautophagy/autophagy is a conserved cellular mechanism to degrade unneeded cytoplasmic proteins and organelles to recycle their components, and it is critical for embryonic stem cell (ESC) self-renewal and somatic cell reprogramming. Whereas autophagy is essential for early development of embryos, no information exists regarding its functions during the transition from naive-to-primed pluripotency. Here, by using an in vitro transition model of ESCs to epiblast-like cells (EpiLCs), we find that dynamic changes in ATG7-dependent autophagy are...

CircRIMKLB promotes myoblast proliferation and inhibits differentiation by sponging miR-29c to release KCNJ12

Jian Wang, Yifan Wen, Jiawei Xu, Binglin Yue, Jialin Zhong, Li Zheng, Chuzhao Lei, Hong Chen & Yongzhen Huang
Muscle development is a complex process that was regulated by many factors, among which non-coding RNAs (ncRNAs) play a vital role in regulating multiple life activities of muscle cells. Circular RNA (circRNA), a type of non-coding RNA with closed-loop structure, has been reported to affect multiple life processes. However, the roles of circRNAs on muscle development have not been fully elucidated. The present study aimed to determine whether and how circRIMKLB affects muscle development. Our...

ATG7-mediated autophagy facilitates embryonic stem cell exit from naive pluripotency and marks commitment to differentiation

Jilong Zhou, Hainan He, Jing-Jing Zhang, Xin Liu, Wang Yao, Chengyu Li, Tian Xu, Shu-Yuan Yin, Dan-Ya Wu, Cheng-Li Dou, Qiao Li, Jiani Xiang, Wen-Jing Xiong, Li-Yan Wang, Jun-Ming Tang, Zhouyiyuan Xue, Xia Zhang & Yi-Liang Miao
Macroautophagy/autophagy is a conserved cellular mechanism to degrade unneeded cytoplasmic proteins and organelles to recycle their components, and it is critical for embryonic stem cell (ESC) self-renewal and somatic cell reprogramming. Whereas autophagy is essential for early development of embryos, no information exists regarding its functions during the transition from naive-to-primed pluripotency. Here, by using an in vitro transition model of ESCs to epiblast-like cells (EpiLCs), we find that dynamic changes in ATG7-dependent autophagy are...

Selective autophagic degradation of ACLY (ATP citrate lyase) maintains citrate homeostasis and promotes oocyte maturation

Hainan He, Junling Wang, Xingmei Mou, Xin Liu, Qiao Li, Mingyue Zhong, Bingbing Luo, Zhisheng Yu, Jingjing Zhang, Tian Xu, Chengli Dou, Danya Wu, Wei Qing, Linhui Wu, Kai Zhou, Zhengang Fan, Tingting Wang, Taotao Hu, Xia Zhang, Jilong Zhou & Yi-Liang Miao
Macroautophagy/autophagy is a cellular and energy homeostatic mechanism that contributes to maintain the number of primordial follicles, germ cell survival, and anti-ovarian aging. However, it remains unknown whether autophagy in granulosa cells affects oocyte maturation. Here, we show a clear tendency of reduced autophagy level in human granulosa cells from women of advanced maternal age, implying a potential negative correlation between autophagy levels and oocyte quality. We therefore established a co-culture system and show that...

Protein disulfide isomerases (PDIs) negatively regulate ebolavirus structural glycoprotein expression in the endoplasmic reticulum (ER) via the autophagy-lysosomal pathway

Bin Wang, Jing Zhang, Xin Liu, Qingqing Chai, Xiaoran Lu, Xiaoyu Yao, Zhichang Yang, Liangliang Sun, Silas F. Johnson, Richard C Schwartz & Yong-Hui Zheng
Zaire ebolavirus (EBOV) causes a severe hemorrhagic fever in humans and non-human primates with high morbidity and mortality. EBOV infection is dependent on its structural glycoprotein (GP), but high levels of GP expression also trigger cell rounding, detachment, and downregulation of many surface molecules that is thought to contribute to its high pathogenicity. Thus, EBOV has evolved an RNA editing mechanism to reduce its GP expression and increase its fitness. We now report that the...

Comparative transcriptomic analysis of rabbit interscapular brown adipose tissue whitening under physiological conditions

Lei Li, Qian Wan, Qiaoyun Long, Tao Nie, Shiting Zhao, Liufeng Mao, Chuanli Cheng, Chao Zou, Kerry Loomes, Aimin Xu, Liangxue Lai, Xin Liu, Ziyuan Duan, Xiaoyan Hui & Donghai Wu
Interscapular brown adipose tissue (iBAT) of both rabbits and humans exhibits a similar whitening phenomenon under physiological conditions. However, a detailed characterization of iBAT whitening in them is still lacking. Here, we chose rabbits as a model to gain a better understanding of the molecular signature changes during the whitening process of iBAT by transcriptomic analysis of rabbit iBAT at day 1, day 14, 1 month and 4 months after birth. We applied non-invasive MRI...

Additional file 2 of SIRPα antibody combined with oncolytic virus OH2 protects against tumours by activating innate immunity and reprogramming the tumour immune microenvironment

Defeng Kong, Zhenrong Yang, Guoliang Li, Quanyou Wu, Zhaoru Gu, Duo Wan, Qi Zhang, Xiaoli Zhang, Shujun Cheng, Binlei Liu, Kaitai Zhang & Wen Zhang
Additional file 2: Table S2. GSVA gene list.

Additional file 2 of SIRPα antibody combined with oncolytic virus OH2 protects against tumours by activating innate immunity and reprogramming the tumour immune microenvironment

Defeng Kong, Zhenrong Yang, Guoliang Li, Quanyou Wu, Zhaoru Gu, Duo Wan, Qi Zhang, Xiaoli Zhang, Shujun Cheng, Binlei Liu, Kaitai Zhang & Wen Zhang
Additional file 2: Table S2. GSVA gene list.

Water chemistry dataset in eastern Siberian rivers

Ping Wang, Shiqi Liu, Qiwei Huang, Olga Gabysheva, Zehong Li, Jialing Zhang, Ekaterina Kazak, Yu Liu, Tcogto Bazarzhapov, Raisa Shpakova, Victor Gabyshev, Sergey Pozdniakov & Natalia Frolova
The dataset includes major ion (Ca, Mg, Na, K, HCO3, SO4, and Cl) data spanning 1940-2019, with 9487 groups of chemical results from 1434 water samples collected mainly in six large river basins in eastern Siberia.

Water chemistry dataset in eastern Siberian rivers

Ping Wang, Shiqi Liu, Qiwei Huang, Olga Gabysheva, Zehong Li, Jialing Zhang, Ekaterina Kazak, Yu Liu, Tcogto Bazarzhapov, Raisa Shpakova, Victor Gabyshev, Sergey Pozdniakov & Natalia Frolova
The dataset includes major ion (Ca, Mg, Na, K, HCO3, SO4, and Cl) data spanning 1940-2019, with 9487 groups of chemical results from 1434 water samples collected mainly in six large river basins in eastern Siberia.

Additional file 15 of Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

Bing Zhang, Zhuoting Chen, Qixue Sun & Jianxiu Liu
Additional file 15: Table S8: Conserved acetylated proteins and acetylated sites in three grasses.

Additional file 15 of Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

Bing Zhang, Zhuoting Chen, Qixue Sun & Jianxiu Liu
Additional file 15: Table S8: Conserved acetylated proteins and acetylated sites in three grasses.

Additional file 11 of Evolution of different rice ecotypes and genetic basis of flooding adaptability in Deepwater rice by GWAS

Xueqiang Wang, Yan Zhao, Conghui Jiang, Libing Wang, Lei Chen, Fengmei Li, Yanhong Zhang, Yinghua Pan & Tianzhen Zhang
Additional file 11 Table S10. Genome-wide detection and functional annotation of selective sweep regions in the upland XI rice.

Additional file 16 of Evolution of different rice ecotypes and genetic basis of flooding adaptability in Deepwater rice by GWAS

Xueqiang Wang, Yan Zhao, Conghui Jiang, Libing Wang, Lei Chen, Fengmei Li, Yanhong Zhang, Yinghua Pan & Tianzhen Zhang
Additional file 16 Table S15. Genome-wide detection and functional annotation of selective sweep regions in the irrigated XI rice.

Additional file 1 of Elevated NRAS expression during DCIS is a potential driver for progression to basal-like properties and local invasiveness

Ze-Yi Zheng, Hanan Elsarraj, Jonathan T. Lei, Yan Hong, Meenakshi Anurag, Long Feng, Hilda Kennedy, Yichao Shen, Flora Lo, Zifan Zhao, Bing Zhang, Xiang H.-F. Zhang, Ossama W. Tawfik, Fariba Behbod & Eric C. Chang
Additional file 1: Table S1. Pathological, Biomarker and Demographic Characteristics of the patients in the TMAs.

Additional file 3 of Elevated NRAS expression during DCIS is a potential driver for progression to basal-like properties and local invasiveness

Ze-Yi Zheng, Hanan Elsarraj, Jonathan T. Lei, Yan Hong, Meenakshi Anurag, Long Feng, Hilda Kennedy, Yichao Shen, Flora Lo, Zifan Zhao, Bing Zhang, Xiang H.-F. Zhang, Ossama W. Tawfik, Fariba Behbod & Eric C. Chang
Additional file 3: Table S2. NRAS-silencing induced a switch from basal to luminal gene expression pattern in SUM102PT cells as measured by RNA-seq.

Additional file 3 of Elevated NRAS expression during DCIS is a potential driver for progression to basal-like properties and local invasiveness

Ze-Yi Zheng, Hanan Elsarraj, Jonathan T. Lei, Yan Hong, Meenakshi Anurag, Long Feng, Hilda Kennedy, Yichao Shen, Flora Lo, Zifan Zhao, Bing Zhang, Xiang H.-F. Zhang, Ossama W. Tawfik, Fariba Behbod & Eric C. Chang
Additional file 3: Table S2. NRAS-silencing induced a switch from basal to luminal gene expression pattern in SUM102PT cells as measured by RNA-seq.

Registration Year

  • 2023
    15
  • 2022
    134
  • 2021
    14
  • 2020
    7
  • 2019
    3

Resource Types

  • Dataset
    173

Affiliations

  • Beijing Institute of Genomics
    173
  • University of Chinese Academy of Sciences
    138
  • Capital Medical University
    126
  • Sun Yat-sen University
    123
  • Shandong University
    121
  • Shanghai Jiao Tong University
    120
  • Huazhong University of Science and Technology
    119
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    118
  • Wuhan University
    114
  • Zhejiang University
    111