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Yao M, Zhang L, Teng X, Lei Y, Xing X, Ren T, Pan Y, Zhang L, Li Z, Lin J, Zheng Y, Xing L, Zhou J, Wu C. Transcriptomic profiling of Dip2a in the neural differentiation of mouse embryonic stem cells. Comput Struct Biotechnol J 2024; 23:700-710. [PMID: 38292475 PMCID: PMC10825174 DOI: 10.1016/j.csbj.2023.12.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 02/01/2024] Open
Abstract
Introduction The disconnected-interacting protein 2 homolog A (DIP2A), a member of disconnected-interacting 2 protein family, has been shown to be involved in human nervous system-related mental illness. This protein is highly expressed in the nervous system of mouse. Mutation of mouse DIP2A causes defects in spine morphology and synaptic transmission, autism-like behaviors, and defective social novelty [5], [27], indicating that DIP2A is critical to the maintenance of neural development. However, the role of DIP2A in neural differentiation has yet to be investigated. Objective To determine the role of DIP2A in neural differentiation, a neural differentiation model was established using mouse embryonic stem cells (mESCs) and studied by using gene-knockout technology and RNA-sequencing-based transcriptome analysis. Results We found that DIP2A is not required for mESCs pluripotency maintenance, but loss of DIP2A causes the neural differentiation abnormalities in both N2B27 and KSR medium. Functional knockout of Dip2a gene also decreased proliferation of mESCs by perturbation of the cell cycle and profoundly inhibited the expression of a large number of neural development-associated genes which mainly enriched in spinal cord development and postsynapse assembly. Conclusions The results of this report demonstrate that DIP2A plays an essential role in regulating differentiation of mESCs towards the neural fate.
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Affiliation(s)
- Mingze Yao
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Lei Zhang
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
- Center of Reproductive Medicine, Children's Hospital of Shanxi and Women Health Center of Shanxi, Taiyuan 030006, China
| | - Xiaojuan Teng
- Dermatology Hospital, Southern Medical University, Guangzhou 510000, China
| | - Yu Lei
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Xiaoyu Xing
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Tinglin Ren
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Yuanqing Pan
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Liwen Zhang
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Zhengfeng Li
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510000, China
| | - Jingxia Lin
- Dermatology Hospital, Southern Medical University, Guangzhou 510000, China
| | - Yaowu Zheng
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Li Xing
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou 510000, China
| | - Changxin Wu
- Institutes of Biomedical Sciences, Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
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Lin Y, Zhang Y, Sun H, Jiang H, Zhao X, Teng X, Lin J, Shu B, Sun H, Liao Y, Zhou J. NanoDeep: a deep learning framework for nanopore adaptive sampling on microbial sequencing. Brief Bioinform 2023; 25:bbad499. [PMID: 38189540 PMCID: PMC10772945 DOI: 10.1093/bib/bbad499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 11/21/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024] Open
Abstract
Nanopore sequencers can enrich or deplete the targeted DNA molecules in a library by reversing the voltage across individual nanopores. However, it requires substantial computational resources to achieve rapid operations in parallel at read-time sequencing. We present a deep learning framework, NanoDeep, to overcome these limitations by incorporating convolutional neural network and squeeze and excitation. We first showed that the raw squiggle derived from native DNA sequences determines the origin of microbial and human genomes. Then, we demonstrated that NanoDeep successfully classified bacterial reads from the pooled library with human sequence and showed enrichment for bacterial sequence compared with routine nanopore sequencing setting. Further, we showed that NanoDeep improves the sequencing efficiency and preserves the fidelity of bacterial genomes in the mock sample. In addition, NanoDeep performs well in the enrichment of metagenome sequences of gut samples, showing its potential applications in the enrichment of unknown microbiota. Our toolkit is available at https://github.com/lysovosyl/NanoDeep.
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Affiliation(s)
- Yusen Lin
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Yongjun Zhang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Hang Sun
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Hang Jiang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Xing Zhao
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Xiaojuan Teng
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Jingxia Lin
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Bowen Shu
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Hao Sun
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Yuhui Liao
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou, China
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Zhao Y, Ma R, Wang C, Hu R, Wu W, Sun X, Chen B, Zhang W, Chen Y, Zhou J, Yuan P. CAPG interference induces apoptosis and ferroptosis in colorectal cancer cells through the P53 pathway. Mol Cell Probes 2023; 71:101919. [PMID: 37468079 DOI: 10.1016/j.mcp.2023.101919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/21/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023]
Abstract
PURPOSE Given the high incidence and mortality rates of colorectal cancer (CRC) and the inadequacy of existing treatments for many patients, this study aimed to explore the potential of Capping Actin Protein (CAPG), a protein involved in actin-related movements, as a novel therapeutic target for CRC. METHODS Bioinformatic analysis of gene expression was conducted using the UALCAN website. Cell proliferation was measured using the CCK-8 kit. Cell cycle, apoptosis, and ferroptosis were analyzed using flow cytometry. Tumorigenesis was evaluated by the subcutaneous inoculation of CRC cells into BALB/c nude female mice. Differentially expressed genes and signaling pathways were identified using RNA sequencing. RESULTS CAPG was significantly overexpressed in human CRC tissues and its upregulation was correlated with poor overall survival. CAPG knockdown led to notable inhibition of CRC cells in vitro and in vivo. Interference with CAPG blocked the cell cycle at the G1 phase and triggered apoptosis and ferroptosis by upregulating the P53 pathway in CRC cells. CONCLUSION CRC patients with higher CAPG levels have a poorer prognosis. CAPG inhibits apoptosis and ferroptosis, while promoting CRC cell proliferation by repressing the P53 pathway. Our study suggests that CAPG may be a potential therapeutic target for CRC prognosis and treatment.
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Affiliation(s)
- Yingying Zhao
- Guangdong Institute of Gastroenterology, Guangzhou, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Rui Ma
- Guangdong Institute of Gastroenterology, Guangzhou, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chuyue Wang
- Guangdong Institute of Gastroenterology, Guangzhou, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Rong Hu
- Guangdong Institute of Gastroenterology, Guangzhou, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Weili Wu
- Guangdong Institute of Gastroenterology, Guangzhou, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiang Sun
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Baotao Chen
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | | | - You Chen
- Guangdong Institute of Gastroenterology, Guangzhou, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Ping Yuan
- Guangdong Institute of Gastroenterology, Guangzhou, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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Zhou JJ, Wang W, Fu YY, Zhang Q, Li RQ, Zhao S, Sun QN, Wang DR. [Feasibility study of R method of gastrojejunostomy applied to Billroth II digestive tract reconstruction after laparoscopic radical distal gastrectomy]. Zhonghua Wei Chang Wai Ke Za Zhi 2023; 26:790-793. [PMID: 37574297 DOI: 10.3760/cma.j.cn441530-20221205-00507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
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Huang J, Jiang Y, Lin W, Chen R, Zhou J, Guo S, Zhao M, Xie Q, Chen X, Zhao M, Zhao Z, Yang B, Zheng J, Liao Y. Virulence and Adhesion of the Treponema pallidum Nichols Strain Simultaneously Decrease in a Continuous-Infection New Zealand White Rabbit Model. ACS Infect Dis 2023; 9:1221-1231. [PMID: 37192527 DOI: 10.1021/acsinfecdis.2c00601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Syphilis is a sexually transmitted disease caused by T. pallidum, and the T. pallidum Nichols strain is widely used with the New Zealand white rabbit model for evaluating drug and vaccine protection. However, changes in the virulence of T. pallidum during transmission are still unknown. Herein, we explored the virulence of T. pallidum in the rabbit model of continuous infection through phenotype observation and further investigated the relationship between virulence and adhesion. During the construction of the syphilis rabbit model, the optimal dose of 104/site of T. pallidum was determined to effectively observe the depiction of syphilis lesions and immune responses for further virulence evaluation. Its virulence was gradually weakened during the interaction with host cells or the testicular passage, which was also proven using the pathological phenotype of the syphilis rabbit model. In addition, the adhesive ability of T. pallidum was reduced with increasing generation, which was verified via the co-incubation of the pathogen with Sf1Ep cells. This study provides insight into the relationship by which the virulence and adhesion of T. pallidum were decreased in a New Zealand white rabbit model of continuous infection and contributes to our knowledge regarding the development of syphilis.
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Affiliation(s)
- Jialin Huang
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital, Southern Medical University, Guangzhou 510091, P. R. China
| | - Yinbo Jiang
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital, Southern Medical University, Guangzhou 510091, P. R. China
| | - Weiqiang Lin
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital, Southern Medical University, Guangzhou 510091, P. R. China
| | - Rongyi Chen
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital, Southern Medical University, Guangzhou 510091, P. R. China
| | - Jiajian Zhou
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital, Southern Medical University, Guangzhou 510091, P. R. China
| | - Shuang Guo
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital, Southern Medical University, Guangzhou 510091, P. R. China
| | - Minghai Zhao
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital, Southern Medical University, Guangzhou 510091, P. R. China
| | - Qiulin Xie
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital, Southern Medical University, Guangzhou 510091, P. R. China
| | - Xu Chen
- Department of Infectious Disease, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, P. R. China
| | - Meijiao Zhao
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital, Southern Medical University, Guangzhou 510091, P. R. China
| | - Zhen Zhao
- Materials Interfaces Center, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, P. R. China
| | - Bin Yang
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital, Southern Medical University, Guangzhou 510091, P. R. China
| | - Judun Zheng
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital, Southern Medical University, Guangzhou 510091, P. R. China
| | - Yuhui Liao
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital, Southern Medical University, Guangzhou 510091, P. R. China
- Department of Infectious Disease, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, P. R. China
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Key Laboratory of Vascular Injury and Repair Research, Ningxia Medical University, Yinchuan 750004, P. R. China
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Wang X, Liu J, Chen J, Xu X, Zhong Y, Xu Y, Lu P, Zhou J, Lin Z, Yang B, Yang C. Loss-of-function mutations in CST6 cause dry skin, desquamation and abnormal keratosis without hypotrichosis. Clin Genet 2023; 103:301-309. [PMID: 36371786 DOI: 10.1111/cge.14265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 11/15/2022]
Abstract
Cystatin M/E (encoded by the CST6 gene) is a cysteine protease inhibitor, that exerts regulatory and protective effects against uncontrolled proteolysis mainly by directly regulating cathepsin V, cathepsin L, and legumain activities. Previous studies have suggested that CST6 may exert a regulatory role in epidermal differentiation and hair follicle formation by inhibiting the activity of respective cognate target proteases. However, until recently, studies have revealed that loss- or gain-of-function of the CST6 gene causes dry skin with hypotrichosis in humans. Here, we reported two siblings of Chinese origin with dry skin, desquamation and abnormal keratosis without hypotrichosis. By applying whole-exome sequencing, we identified homozygous loss-of-function mutation c.251G > A (p.Gly84Asp) in the CST6 gene as the underlying genetic cause. Further fluorimetric enzyme assays demonstrated the mutant cystatin M/E protein lost its inhibitory function on the protease activity of cathepsins. Moreover, the corresponding mutation in mice resulted in excessive cornification, desquamation, impaired skin barrier function, and abnormal proliferation and differentiation of keratinocytes. In conclusion, the homozygous missense mutation c.251G > A in CST6 gene resulted in dry skin, desquamation, as well as abnormal keratosis of the skin, promoting our understanding of the role of protease-antiprotease balance in human skin disorders.
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Affiliation(s)
- Xuan Wang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jun Liu
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Junyi Chen
- Dermatology Hospital, Southern Medical University, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Xueyan Xu
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Yadan Zhong
- Dermatology Hospital, Southern Medical University, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yingping Xu
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Ping Lu
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Zhimiao Lin
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Bin Yang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Chao Yang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
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Sun L, Li T, Zhou J, Li W, Wu Z, Niu R, Cheng J, Asare‐Yeboah K, He Z. A Green Binary Solvent Method to Control Organic Semiconductor Crystallization. ChemistrySelect 2023. [DOI: 10.1002/slct.202203927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Li Sun
- School of Mechanical and Electrical Engineering Jinling Institute of Technology Nanjing Jiangsu 210014 China
| | - Tianyu Li
- School of Mechanical and Electrical Engineering Jinling Institute of Technology Nanjing Jiangsu 210014 China
| | - Jiajian Zhou
- School of Mechanical and Electrical Engineering Jinling Institute of Technology Nanjing Jiangsu 210014 China
| | - Wenhao Li
- School of Mechanical and Electrical Engineering Jinling Institute of Technology Nanjing Jiangsu 210014 China
| | - Zhongming Wu
- School of Mechanical and Electrical Engineering Jinling Institute of Technology Nanjing Jiangsu 210014 China
| | - Ruikun Niu
- School of Mechanical and Electrical Engineering Jinling Institute of Technology Nanjing Jiangsu 210014 China
| | - Jinxiang Cheng
- School of Mechanical and Electrical Engineering Jinling Institute of Technology Nanjing Jiangsu 210014 China
| | - Kyeiwaa Asare‐Yeboah
- Department of Electrical and Computer Engineering Penn State Behrend Erie PA 16563 USA
| | - Zhengran He
- Department of Electrical and Computer Engineering The University of Alabama Tuscaloosa AL 35487 USA
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Weng JW, Yu J, Jin F, Peng YG, Zhou JJ, Chen Y, Zhang J, Hei MY. [Clinical characteristics of 14 cases of neonatal tracheotomy in neonatal intensive care unit]. Zhonghua Er Ke Za Zhi 2022; 60:815-819. [PMID: 35922194 DOI: 10.3760/cma.j.cn112140-20220226-00152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Objective: To analyze the clinical characteristics of neonatal tracheotomy in neonatal intensive care unit (NICU). Methods: This single-center retrospective study included 14 neonates admitted to NICU of Beijing Children's Hospital, Capital Medical University from January 2016 to August 2021, and were<28 days of age on admission, who met the criteria of tracheotomy and finally completed the procedure. The clinical characteristics including age, weight, duration of ventilation, etiology of tracheotomy, length of hospital stay and prognosis were summarized and analyzed. Wilcoxon signed-rank test was used to compare the weight gain velocity and the duration of ventilation before and after tracheotomy. Paired t-test was used to compare the hospitalization length before and after tracheotomy. Spearman correlation was used to analyze the correlation between the clinical characteristics and outcomes. Results: For the 14 neonates, the gestational age was (38±4) weeks and birth weight was (2 824±949) g. Nine of them were male. The age on transportation was 16 (6, 25) d. A total of 10 neonates were on invasive ventilation on admission, the other 4 were on nasal continuous positive airway pressure support. Bilateral vocal cord paralysis (7 cases) was the commonest cause of tracheotomy. The age on operation was 33 (22, 44) d. There were statistically significant differences in duration of ventilation and weight gain velocity before and after operation (19.00 (10.50, 34.00) vs. 0.86 (0.06, 3.25) d, 1.66 (-0.16, 5.54) vs. 4.69 (2.30, 9.32) g/(kg·d), Z=3.01 and -1.98, both P<0.05). The total hospital stay in NICU was (37±12) d. One neonate died during hospitalization. The existence of pneumonia on admission was positively correlated to NICU stay length (r=0.57, P=0.027), the pre-operational weight gain velocity was negatively correlated to the post-operational NICU stay length (r=-0.73, P=0.020). There were 4 neonates de-cannulated during 7-38 months after the tracheotomy, and 5 neonates still wearing the tracheal cannulation during 15-66 months after the tracheotomy. Two neonates died and 2 neonates lost follow-up after discharge. All neonates could not vocalize normally before de-cannulation, and the language development obviously lagged behind the normal age group after de-cannulation. Conclusions: Bilateral vocal cord paralysis is the commonest cause of neonatal tracheotomy. The benefit of tracheotomy for NICU neonates with surgical indications is obvious, especially in facilitating extubation and improving weight gain.
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Affiliation(s)
- J W Weng
- Department of Neonatology, Neonatal Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - J Yu
- Department of Neonatology, Neonatal Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - F Jin
- Department of Neonatology, Neonatal Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - Y G Peng
- Center for Clinical Epidemiology and Evidence-based Medicine, National Center for Children's Health,Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - J J Zhou
- Department of Neonatology, Neonatal Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - Y Chen
- Department of Neonatology, Neonatal Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - J Zhang
- Department of Otorhinolaryngology, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - M Y Hei
- Department of Neonatology, Neonatal Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
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Huang H, Huang G, Tan Z, Hu Y, Shan L, Zhou J, Zhang X, Ma S, Lv W, Huang T, Liu Y, Wang D, Zhao X, Lin Y, Rong Z. Engineered Cas12a-Plus nuclease enables gene editing with enhanced activity and specificity. BMC Biol 2022; 20:91. [PMID: 35468792 PMCID: PMC9040236 DOI: 10.1186/s12915-022-01296-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/12/2022] [Indexed: 11/23/2022] Open
Abstract
Background The CRISPR-Cas12a (formerly Cpf1) system is a versatile gene-editing tool with properties distinct from the broadly used Cas9 system. Features such as recognition of T-rich protospacer-adjacent motif (PAM) and generation of sticky breaks, as well as amenability for multiplex editing in a single crRNA and lower off-target nuclease activity, broaden the targeting scope of available tools and enable more accurate genome editing. However, the widespread use of the nuclease for gene editing, especially in clinical applications, is hindered by insufficient activity and specificity despite previous efforts to improve the system. Currently reported Cas12a variants achieve high activity with a compromise of specificity. Here, we used structure-guided protein engineering to improve both editing efficiency and targeting accuracy of Acidaminococcus sp. Cas12a (AsCas12a) and Lachnospiraceae bacterium Cas12a (LbCas12a). Results We created new AsCas12a variant termed “AsCas12a-Plus” with increased activity (1.5~2.0-fold improvement) and specificity (reducing off-targets from 29 to 23 and specificity index increased from 92% to 94% with 33 sgRNAs), and this property was retained in multiplex editing and transcriptional activation. When used to disrupt the oncogenic BRAFV600E mutant, AsCas12a-Plus showed less off-target activity while maintaining comparable editing efficiency and BRAFV600E cancer cell killing. By introducing the corresponding substitutions into LbCas12a, we also generated LbCas12a-Plus (activity improved ~1.1-fold and off-targets decreased from 20 to 12 while specificity index increased from 78% to 89% with 15 sgRNAs), suggesting this strategy may be generally applicable across Cas12a orthologs. We compared Cas12a-Plus, other variants described in this study, and the reported enCas12a-HF, enCas12a, and Cas12a-ultra, and found that Cas12a-Plus outperformed other variants with a good balance for enhanced activity and improved specificity. Conclusions Our discoveries provide alternative AsCas12a and LbCas12a variants with high specificity and activity, which expand the gene-editing toolbox and can be more suitable for clinical applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01296-1.
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Affiliation(s)
- Hongxin Huang
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Guanjie Huang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Zhihong Tan
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Yongfei Hu
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Lin Shan
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Xin Zhang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Shufeng Ma
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Weiqi Lv
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Tao Huang
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China.,Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Yuchen Liu
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Dong Wang
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoyang Zhao
- Department of Development, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ying Lin
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China. .,Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Zhili Rong
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China. .,Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China. .,Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
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10
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Tao J, Zhou J, Liu Z, Yang B. Two related female patients with familial facial pigmentary demarcation lines. J Cosmet Dermatol 2022; 21:5279-5281. [PMID: 35373475 DOI: 10.1111/jocd.14960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Jingjing Tao
- Aesthetic Department Dermatology Hospital Southern Medical University Guangzhou China
| | - Jiajian Zhou
- Aesthetic Department Dermatology Hospital Southern Medical University Guangzhou China
| | - Zhenfeng Liu
- Aesthetic Department Dermatology Hospital Southern Medical University Guangzhou China
| | - Bin Yang
- Aesthetic Department Dermatology Hospital Southern Medical University Guangzhou China
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11
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Jin F, Weng JW, Zhou JJ, Chen Y, Zhang J, Hei MY. [Clinical characteristics and outcomes of 111 neonates with upper airway obstruction admitted via transportation]. Zhonghua Er Ke Za Zhi 2022; 60:88-93. [PMID: 35090223 DOI: 10.3760/cma.j.cn112140-20210701-00547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Objectives: To analyze the clinical characteristics and outcomes of neonates with upper airway obstruction (UAO) who were admitted via transportation, hence to provide more evidence-based information for the clinical management of UAO. Methods: This was a single center retrospective study. Patients were hospitalized in Beijing Children's Hospital from January 1, 2016 to May 31, 2021 with age <28 days or postmenstrual age (PMA) ≤44 weeks, and UAO as the first diagnosis. The general information of patients, obstructed sites in the upper airway, treatment, complications and prognosis were analyzed. The outcomes of surgical UAO vs. non-surgical UAO were analyzed by 2 by 2 χ2 test. Results: A total of 111 cases were analyzed (2.3% of the total NICU hospitalized 4 826 infants in the same period), in which 62 (55.9%) were boys and 101 (91.0%) were term infants, and their gestational age was (38.7±2.0) weeks, birth weight (3 207±585) g, PMA on admission (40.8±2.5) weeks and weight on admission was (3 221±478) g. There were 92 cases (82.9%) with symptoms of UAO presenting on postnatal day 1, and 35 cases (31.5%) had extra-uterine growth retardation on admission. The diagnosis of UAO and the obstructive site was confirmed in 25 cases (22.5%) before transportation. There were 24 cases (21.6%), 71 cases (64.0%), and 16 cases (14.4%) who had UAO due to nasal, throat, and neck problems, respectively. The top 5 diagnosis of UAO were vocal cord paralysis (28 cases), bilateral choanal atresia (20 cases), laryngomalacia (15 cases), pharynx and larynx cysts (7 cases), and subglottic hemangioma (6 cases). The diagnosis and treatment of all the patients followed a multidisciplinary approach consisted of neonatal intensive care unit, ear-nose-throat department and medical image departments. A total of 102 cases (91.9%) underwent both bronchofiberscope and fiber nasopharyngoscope investigation. Seventy cases (63.1%) required ventilation. Among the 58 cases (52.3%) who required surgical intervention, 16 had tracheotomy. For cases with vs. without surgical intervention, the rate of cure and (or) improvement were 94.8% (55/58) vs. 54.7% (29/53), and the rate of being discharged against medical arrangement were 1.7% (1/58) vs. 45.3% (24/53) (χ²=24.21 and 30.11, both P<0.01). Conclusions: Neonatal UAO may locate at various sites of the upper airway. The overall prognosis of neonatal UAO is favorable. A multidisciplinary approach is necessary for efficient evaluation and appropriate surgical intervention.
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Affiliation(s)
- F Jin
- Department of Neonatology, Neonatal Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - J W Weng
- Department of Neonatology, Neonatal Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - J J Zhou
- Department of Neonatology, Neonatal Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Y Chen
- Department of Neonatology, Neonatal Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - J Zhang
- Department of Otorhinolaryngology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - M Y Hei
- Department of Neonatology, Neonatal Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
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12
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Zhou JJ, Wang SF. [Introduction of landmarking approach and its application in dynamic prediction]. Zhonghua Liu Xing Bing Xue Za Zhi 2022; 43:112-117. [PMID: 35130661 DOI: 10.3760/cma.j.cn112338-20210122-00051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Conventional prediction model, as a static prediction model, can be only used to predict the probability of the occurrence of an event during the observation period using the information available at baseline survey. However, based on current clinical demands, dynamic prediction, which obtains prediction probabilities for both baseline survey and later time points given the history of the events and covariates up to that time, is gaining a growing attention. As a dynamic prediction model, the landmarking approach is simple, easy to use, computationally efficient and has a comparable performance of joint modeling, which makes it to be widely used in recent researches. Because of its limited application in China, this paper makes a brief introduction of its ideas and basic application to further promote its applications in clinical dynamic prediction.
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Affiliation(s)
- J J Zhou
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - S F Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
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13
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Zhang Y, Shi Y, Lin J, Li X, Yang B, Zhou J. Immune Cell Infiltration Analysis Demonstrates Excessive Mast Cell Activation in Psoriasis. Front Immunol 2021; 12:773280. [PMID: 34887864 PMCID: PMC8650163 DOI: 10.3389/fimmu.2021.773280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/04/2021] [Indexed: 12/21/2022] Open
Abstract
Psoriasis represents multiple inflammatory processes and exaggerated physiological responses to epithelial damage by innate and adaptive immune components, thus it is critical to compare the immune cell niche in disease and healthy skin. Here, we inferred the proportions of different immune cell types in psoriatic and healthy skin using the CIBERSORT algorithm with expression profiles as input. As a result, we observed a dramatic change of immune cell profiles in psoriatic skin compared with healthy skin. Interestingly, the resting mast cells is almost eliminated in psoriatic skin. In contrast, the activated mast cells are enriched in psoriatic skin, indicating that mast cells activation may play an important role in psoriasis pathogenesis. In addition, we found that the proportion of the resting mast cells gradually come back to the normal level in lesioned skin upon etanercept treatment, suggesting that mast cells play a critical role in immune cell niche maintenance. Further experiments validated a significant decrease in mast cell population and an excessive mast cell activation in psoriatic skin compared with healthy skin. In conclusion, our integrative analyses of the immune cell profiles and the corresponding marker genes expression provide a better understanding of the inflammation response in psoriasis and important clues for clinical applications.
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Affiliation(s)
- Yongjun Zhang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Yanqiang Shi
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Jingxia Lin
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Xuefei Li
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Bin Yang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou, China
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14
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Zhang W, Sun R, Zhang Y, Hu R, Li Q, Wu W, Cao X, Zhou J, Pei J, Yuan P. Cabazitaxel suppresses colorectal cancer cell growth via enhancing the p53 antitumor pathway. FEBS Open Bio 2021; 11:3032-3050. [PMID: 34496154 PMCID: PMC8564099 DOI: 10.1002/2211-5463.13290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 07/15/2021] [Accepted: 09/07/2021] [Indexed: 11/25/2022] Open
Abstract
There were approximately 1.93 million new cases and 940 000 deaths from colorectal cancer in 2020. The first‐line chemotherapeutic drugs for colorectal cancer are mainly based on 5‐fluorouracil, although the use of these drugs is limited by the development of drug resistance. Consequently, there is a need for novel chemotherapeutic drugs for the efficient treatment of colorectal cancer patients. In the present study, we screened 160 drugs approved by the Food and Drug Administration and identified that cabazitaxel (CBT), a microtube inhibitor, can suppress colony formation and cell migration of colorectal cancer cells in vitro. CBT also induces G2/M phase arrest and apoptosis of colorectal cancer cells. Most importantly, it inhibits the growth of colorectal cancer cell xenograft tumors in vivo. Transcriptome analysis by RNA‐sequencing revealed that Tub family genes are abnormally expressed in CBT‐treated colorectal cancer cells. The expression of several p53 downstream genes that are associated with cell cycle arrest, apoptosis, and inhibition of angiogenesis and metastasis is induced by CBT in colorectal cancer cells. Overall, our results suggests that CBT suppresses colorectal cancer by upregulating the p53 pathway, and thus CBT may have potential as an alternative chemotherapeutic drug for colorectal cancer.
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Affiliation(s)
- Wen Zhang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Guangdong Institute of Gastroenterology, Guangzhou, China
| | - Ruiqian Sun
- Guangdong Country Garden School, Foshan City, China
| | - Yongjun Zhang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Rong Hu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Guangdong Institute of Gastroenterology, Guangzhou, China
| | - Qian Li
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Guangdong Institute of Gastroenterology, Guangzhou, China
| | - Weili Wu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Guangdong Institute of Gastroenterology, Guangzhou, China
| | - Xinyu Cao
- Institute of Clinical Medical Sciences,, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Jianfeng Pei
- Center for Quantitative Biology,, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Ping Yuan
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Guangdong Institute of Gastroenterology, Guangzhou, China
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15
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Huang H, Hu Y, Huang G, Ma S, Feng J, Wang D, Lin Y, Zhou J, Rong Z. Tag-seq: a convenient and scalable method for genome-wide specificity assessment of CRISPR/Cas nucleases. Commun Biol 2021; 4:830. [PMID: 34215845 PMCID: PMC8253812 DOI: 10.1038/s42003-021-02351-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 06/08/2021] [Indexed: 12/26/2022] Open
Abstract
Genome-wide identification of DNA double-strand breaks (DSBs) induced by CRISPR-associated protein (Cas) systems is vital for profiling the off-target events of Cas nucleases. However, current methods for off-target discovery are tedious and costly, restricting their widespread applications. Here we present an easy alternative method for CRISPR off-target detection by tracing the integrated oligonucleotide Tag using next-generation-sequencing (CRISPR-Tag-seq, or Tag-seq). Tag-seq enables rapid and convenient profiling of nuclease-induced DSBs by incorporating the optimized double-stranded oligodeoxynucleotide sequence (termed Tag), adapters, and PCR primers. Moreover, we employ a one-step procedure for library preparation in Tag-seq, which can be applied in the routine workflow of a molecular biology laboratory. We further show that Tag-seq successfully determines the cleavage specificity of SpCas9 variants and Cas12a/Cpf1 in a large-scale manner, and discover the integration sites of exogenous genes introduced by the Sleeping Beauty transposon. Our results demonstrate that Tag-seq is an efficient and scalable approach to genome-wide identification of Cas-nuclease-induced off-targets. Hongxin Huang and Yongfei Hu et al. develop Tag-seq, a streamlined sequencing method to examine off-target editing by CRISPR-Cas systems. The authors validate Tag-seq in multiple cell lines, demonstrating its broad utility and flexibility in identifying off-target genome editing.
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Affiliation(s)
- Hongxin Huang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Yongfei Hu
- Dermatology Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Guanjie Huang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China
| | - Shufeng Ma
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China
| | - Jianqi Feng
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China
| | - Dong Wang
- Dermatology Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ying Lin
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China.
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou, China.
| | - Zhili Rong
- Dermatology Hospital, Southern Medical University, Guangzhou, China. .,Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, China. .,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.
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16
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Huang Y, Qiao Y, Zhao Y, Li Y, Yuan J, Zhou J, Sun H, Wang H. Large scale RNA-binding proteins/LncRNAs interaction analysis to uncover lncRNA nuclear localization mechanisms. Brief Bioinform 2021; 22:6287336. [PMID: 34056657 DOI: 10.1093/bib/bbab195] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 12/25/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are key regulators of major biological processes and their functional modes are dictated by their subcellular localization. Relative nuclear enrichment of lncRNAs compared to mRNAs is a prevalent phenomenon but the molecular mechanisms governing their nuclear retention in cells remain largely unknown. Here in this study, we harness the recently released eCLIP data for a large number of RNA-binding proteins (RBPs) in K562 and HepG2 cells and utilize multiple bioinformatics methods to comprehensively survey the roles of RBPs in lncRNA nuclear retention. We identify an array of splicing RBPs that bind to nuclear-enriched lincRNAs (large intergenic non-coding RNAs) thus may act as trans-factors regulating their nuclear retention. Further analyses reveal that these RBPs may bind with distinct core motifs, flanking sequence compositions, or secondary structures to drive lincRNA nuclear retention. Moreover, network analyses uncover potential co-regulatory RBP clusters and the physical interaction between HNRNPU and SAFB2 proteins in K562 cells is further experimentally verified. Altogether, our analyses reveal previously unknown factors and mechanisms that govern lincRNA nuclear localization in cells.
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Affiliation(s)
- Yile Huang
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yulong Qiao
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yu Zhao
- Department of Orthaepedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yuying Li
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jie Yuan
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jiajian Zhou
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Department of Orthaepedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
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17
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Zhang W, Zhou JJ, Liu GZ, Wang SF, Li LM. [A study on the online medical consulting websites based on the personal computer side]. Zhonghua Liu Xing Bing Xue Za Zhi 2021; 42:303-308. [PMID: 33626620 DOI: 10.3760/cma.j.cn112338-20200120-00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Online medical consulting, acting as the primary type of Internet medical market, has been developing dramatically in the past ten years and begins to take shape. This study collected available information to describe service content status and service provider for online medical consulting websites. The current online medical consulting sites are mainly comprehensive medical consultation websites. The most common consulting provision from is combining graphics and text, which might not meet users' primary demand. The registered physicians are mostly the ones with junior position and work in the eastern and south-central parts of China. Activities of the registered physicians vary across the departments, but with extremely low initiatives.
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Affiliation(s)
- W Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - J J Zhou
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - G Z Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - S F Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - L M Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
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18
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Li S, Lu BP, Feng J, Zhou JJ, Xie ZZ, Liang C, Li XR, Huang Y, Yu XB. Clone, expression and plasminogen binding property of three fructose-1,6-bisphosphate aldolases from Clonorchis sinensis. Trop Biomed 2020; 37:852-863. [PMID: 33612738 DOI: 10.47665/tb.37.4.852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fructose-1,6-bisphosphate aldolase (FbA), a well characterized glycometabolism enzyme, has been found to participate in other important processes besides the classic catalysis. To understand the important functions of three fructose-1,6-bisphosphate aldolases from Clonorchis sinensis (CsFbAs, CsFbA-1/2/3) in host-parasite interplay, the open reading frames of CsFbAs were cloned into pET30a (+) vector and the resulting recombinant plasmids were transformed into Escherichia coli BL21 (DE3) for expression of the proteins. Purified recombinant CsFbAs proteins (rCsFbAs) were approximately 45.0 kDa on 12% SDS-PAGE and could be probed with each rat anti-rCsFbAs sera by western blotting analysis. ELISA and ligand blot overlay indicated that rCsFbAs of 45.0 kDa as well as native CsFbAs of 39.5 kDa from total worm extracts and excretory-secretory products of Clonorchis sinensis (CsESPs) could bind to human plasminogen, and the binding could be efficiently inhibited by lysine analog ε-aminocaproic acid. Our results suggested that as both the components of CsESPs and the plasminogen binding proteins, three CsFbAs might be involved in preventing the formation of the blood clot so that Clonorchis sinensis could acquire enough nutrients from host tissue for their successful survival and colonization in the host. Our work will provide us with new information about the biological function of three CsFbAs and their roles in hostparasite interplay.
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Affiliation(s)
- S Li
- School of Basic Medicine, Henan University of Chinese Medicine, Zhengzhou 450046, China.,Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - B P Lu
- School of Basic Medicine, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - J Feng
- Zhengzhou YIHE Hospital Affiliated to Henan University, Zhengzhou 450047, China
| | - J J Zhou
- Zhengzhou Key Laboratory for Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450047, China
| | - Z Z Xie
- Department of Clinical Laboratory, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - C Liang
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - X R Li
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - Y Huang
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
| | - X B Yu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Key Laboratory for Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
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19
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Li X, Lin J, Hu Y, Zhou J. PARMAP: A Pan-Genome-Based Computational Framework for Predicting Antimicrobial Resistance. Front Microbiol 2020; 11:578795. [PMID: 33193203 PMCID: PMC7642336 DOI: 10.3389/fmicb.2020.578795] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/24/2020] [Indexed: 11/17/2022] Open
Abstract
Antimicrobial resistance (AMR) has emerged as one of the most urgent global threats to public health. Accurate detection of AMR phenotypes is critical for reducing the spread of AMR strains. Here, we developed PARMAP (Prediction of Antimicrobial Resistance by MAPping genetic alterations in pan-genome) to predict AMR phenotypes and to identify AMR-associated genetic alterations based on the pan-genome of bacteria by utilizing machine learning algorithms. When we applied PARMAP to 1,597 Neisseria gonorrhoeae strains, it successfully predicted their AMR phenotypes based on a pan-genome analysis. Furthermore, it identified 328 genetic alterations in 23 known AMR genes and discovered many new AMR-associated genetic alterations in ciprofloxacin-resistant N. gonorrhoeae, and it clearly indicated the genetic heterogeneity of AMR genes in different subtypes of resistant N. gonorrhoeae. Additionally, PARMAP performed well in predicting the AMR phenotypes of Mycobacterium tuberculosis and Escherichia coli, indicating the robustness of the PARMAP framework. In conclusion, PARMAP not only precisely predicts the AMR of a population of strains of a given species but also uses whole-genome sequencing data to prioritize candidate AMR-associated genetic alterations based on their likelihood of contributing to AMR. Thus, we believe that PARMAP will accelerate investigations into AMR mechanisms in other human pathogens.
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Affiliation(s)
- Xuefei Li
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Jingxia Lin
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Yongfei Hu
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou, China
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20
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Zhang LN, Zhou JJ, Zhang J, Wang ZY, Zheng HH, Gan MF. [Multiple primary lung adenocarcinoma with different mutations of EGFR gene: report of a case]. Zhonghua Bing Li Xue Za Zhi 2020; 49:855-857. [PMID: 32746560 DOI: 10.3760/cma.j.cn112151-20191209-00786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- L N Zhang
- Department of Pathology, Taizhou Hospital of Zhejiang Province, Affiliated to Wenzhou Medical University, Linhai 317000, China
| | - J J Zhou
- Department of Pathology, Taizhou Hospital of Zhejiang Province, Affiliated to Wenzhou Medical University, Linhai 317000, China
| | - J Zhang
- Department of Thoracic Surgery, Taizhou Hospital of Zhejiang Province, Affiliated to Wenzhou Medical University, Linhai 317000, China
| | - Z Y Wang
- Department of Pathology, Taizhou Hospital of Zhejiang Province, Affiliated to Wenzhou Medical University, Linhai 317000, China
| | - H H Zheng
- Department of Pathology, Taizhou Hospital of Zhejiang Province, Affiliated to Wenzhou Medical University, Linhai 317000, China
| | - M F Gan
- Department of Pathology, Taizhou Hospital of Zhejiang Province, Affiliated to Wenzhou Medical University, Linhai 317000, China
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21
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Chuan A, Zhou JJ, Hou RM, Stevens CJ, Bogdanovych A. Virtual reality for acute and chronic pain management in adult patients: a narrative review. Anaesthesia 2020; 76:695-704. [PMID: 32720308 DOI: 10.1111/anae.15202] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2020] [Indexed: 12/01/2022]
Abstract
Virtual reality is a computer-generated environment that immerses the user in an interactive artificial world. This ability to distract from reality has been utilised for the purposes of providing pain relief from noxious stimuli. As technology rapidly matures, there is potential for anaesthetists and pain physicians to incorporate virtual reality devices as non-pharmacological therapy in a multimodal pain management strategy. This systematic narrative review evaluates clinical studies that used virtual reality in adult patients for management of acute and chronic pain. A literature search found 690 citations, out of which 18 studies satisfied the inclusion criteria. Studies were assessed for quality using the Jadad and Nottingham-Ottawa Scales. Agreement on scores between independent assessors was 0.87 (95%CI 0.73-0.94). Studies investigated virtual reality use: intra-operatively; for labour analgesia; for wound dressing changes; and in multiple chronic pain conditions. Twelve studies showed reduced pain scores in acute or chronic pain with virtual reality therapy, five studies showed no superiority to control treatment arms and in one study, the virtual reality exposure group had a worsening of acute pain scores. Studies were heterogeneous in: methods; patient population; and type of virtual reality used. These limitations suggest the evidence-base in adult patients is currently immature and more rigorous studies are required to validate the use of virtual reality as a non-pharmacological adjunct in multimodal pain management.
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Affiliation(s)
- A Chuan
- Faculty of Medicine, University of New South Wales Sydney and Ingham Institute of Applied Medical Research, Sydney, NSW, Australia.,Department of Anaesthesia, Liverpool Hospital, Sydney, NSW, Australia
| | - J J Zhou
- Department of Anaesthesia, Liverpool Hospital, Sydney, NSW, Australia
| | - R M Hou
- Faculty of Medicine, University of New South Wales Sydney and Ingham Institute of Applied Medical Research, Sydney, NSW, Australia.,Department of Pain Medicine, Liverpool Hospital, Sydney, NSW, Australia
| | - C J Stevens
- MARCS Institute for Brain, Behaviour and Development, Western Sydney University, Sydney, NSW, Australia
| | - A Bogdanovych
- MARCS Institute for Brain, Behaviour and Development, Western Sydney University, Sydney, Australia
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22
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Sun X, Ren Z, Cun Y, Zhao C, Huang X, Zhou J, Hu R, Su X, Ji L, Li P, Mak K, Gao F, Yang Y, Xu H, Ding J, Cao N, Li S, Zhang W, Lan P, Sun H, Wang J, Yuan P. Hippo-YAP signaling controls lineage differentiation of mouse embryonic stem cells through modulating the formation of super-enhancers. Nucleic Acids Res 2020; 48:7182-7196. [PMID: 32510157 PMCID: PMC7367178 DOI: 10.1093/nar/gkaa482] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/21/2020] [Accepted: 05/28/2020] [Indexed: 02/07/2023] Open
Abstract
Hippo-YAP signaling pathway functions in early lineage differentiation of pluripotent stem cells, but the detailed mechanisms remain elusive. We found that knockout (KO) of Mst1 and Mst2, two key components of the Hippo signaling in mouse embryonic stem cells (ESCs), resulted in a disruption of differentiation into mesendoderm lineage. To further uncover the underlying regulatory mechanisms, we performed a series of ChIP-seq experiments with antibodies against YAP, ESC master transcription factors and some characterized histone modification markers as well as RNA-seq assays using wild type and Mst KO samples at ES and day 4 embryoid body stage respectively. We demonstrate that YAP is preferentially co-localized with super-enhancer (SE) markers such as Nanog, Sox2, Oct4 and H3K27ac in ESCs. The hyper-activation of nuclear YAP in Mst KO ESCs facilitates the binding of Nanog, Sox2 and Oct4 as well as H3K27ac modification at the loci where YAP binds. Moreover, Mst depletion results in novel SE formation and enhanced liquid-liquid phase-separated Med1 condensates on lineage associated genes, leading to the upregulation of these genes and the distortion of ESC differentiation. Our study reveals a novel mechanism on how Hippo-YAP signaling pathway dictates ESC lineage differentiation.
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Affiliation(s)
| | | | - Yixian Cun
- Department of Medical Bioinformatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510275, China
| | - Cai Zhao
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510275, China
| | - Xianglin Huang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510275, China
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou, China
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong
| | - Rong Hu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong 510655, China
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong
| | - Xiaoxi Su
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong
- China Hong Kong Children's Hospital, Hong Kong SAR
| | - Lu Ji
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong
| | - Peng Li
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - King Lun Kingston Mak
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou, China
| | - Feng Gao
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China
- Guangdong Institute of Gastroenterology, Guangzhou, Guangdong 510655, China
| | - Yi Yang
- Department of Medical Bioinformatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510275, China
| | - He Xu
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510275, China
| | - Junjun Ding
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510275, China
- Department of Histology and embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Nan Cao
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510275, China
| | - Shuo Li
- Department of Medical Bioinformatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou 510275, China
| | - Wensheng Zhang
- Cam-Su Genomic Resource Center, Soochow University, Suzhou 215123, China
| | - Ping Lan
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong
| | - Jinkai Wang
- Correspondence may also be addressed to Jinkai Wang. Tel: +86 2087335142; Fax: +86 2087331209;
| | - Ping Yuan
- To whom correspondence should be addressed. Tel: +86 18819239657; Fax: +86 2038254166;
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23
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Zhang M, Lai Y, Krupalnik V, Guo P, Guo X, Zhou J, Xu Y, Yu Z, Liu L, Jiang A, Li W, Abdul MM, Ma G, Li N, Fu X, Lv Y, Jiang M, Tariq M, Kanwal S, Liu H, Xu X, Zhang H, Huang Y, Wang L, Chen S, Babarinde IA, Luo Z, Wang D, Zhou T, Ward C, He M, Ibañez DP, Li Y, Zhou J, Yuan J, Feng Y, Arumugam K, Di Vicino U, Bao X, Wu G, Schambach A, Wang H, Sun H, Gao F, Qin B, Hutchins AP, Doble BW, Hartmann C, Cosma MP, Qin Y, Xu GL, Chen R, Volpe G, Chen L, Hanna JH, Esteban MA. β-Catenin safeguards the ground state of mousepluripotency by strengthening the robustness of the transcriptional apparatus. Sci Adv 2020; 6:eaba1593. [PMID: 32832621 PMCID: PMC7439582 DOI: 10.1126/sciadv.aba1593] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 06/05/2020] [Indexed: 05/12/2023]
Abstract
Mouse embryonic stem cells cultured with MEK (mitogen-activated protein kinase kinase) and GSK3 (glycogen synthase kinase 3) inhibitors (2i) more closely resemble the inner cell mass of preimplantation blastocysts than those cultured with SL [serum/leukemia inhibitory factor (LIF)]. The transcriptional mechanisms governing this pluripotent ground state are unresolved. Release of promoter-proximal paused RNA polymerase II (Pol2) is a multistep process necessary for pluripotency and cell cycle gene transcription in SL. We show that β-catenin, stabilized by GSK3 inhibition in medium with 2i, supplies transcriptional coregulators at pluripotency loci. This selectively strengthens pluripotency loci and renders them addicted to transcription initiation for productive gene body elongation in detriment to Pol2 pause release. By contrast, cell cycle genes are not bound by β-catenin, and proliferation/self-renewal remains tightly controlled by Pol2 pause release under 2i conditions. Our findings explain how pluripotency is reinforced in the ground state and also provide a general model for transcriptional resilience/adaptation upon network perturbation in other contexts.
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Affiliation(s)
- Meng Zhang
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Yiwei Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Vladislav Krupalnik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Pengcheng Guo
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xiangpeng Guo
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Jianguo Zhou
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Yan Xu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Zhijun Yu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Longqi Liu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Ao Jiang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenjuan Li
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
- Guangzhou Medical University, Guangzhou 511436, China
| | - Mazid Md. Abdul
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Gang Ma
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Na Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Xiuling Fu
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuan Lv
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Mengling Jiang
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Muqddas Tariq
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Shahzina Kanwal
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Hao Liu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Xueting Xu
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Hui Zhang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yinghua Huang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Lulu Wang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Shuhan Chen
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Isaac A. Babarinde
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhiwei Luo
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
- Guangzhou Medical University, Guangzhou 511436, China
| | - Dongye Wang
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Tiantian Zhou
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Carl Ward
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Minghui He
- Forevergen Biosciences Center, Guangzhou 510000, China
| | - David P. Ibañez
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Yunpan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Jiajian Zhou
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jie Yuan
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yayan Feng
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Karthik Arumugam
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Umberto Di Vicino
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Xichen Bao
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
| | - Guangming Wu
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
| | - Axel Schambach
- Hannover Medical School, Institute of Experimental Hematology, Hannover 30625, Germany
- Division of Hematology and Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Fei Gao
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg DK1870C, Denmark
| | - Baoming Qin
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Andrew P. Hutchins
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Bradley W. Doble
- Departments of Pediatrics and Child Health and Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0W2, Canada
| | - Christine Hartmann
- Department of Bone and Skeletal Research, Institute of Musculoskeletal Medicine, Medical Faculty of the University of Münster, Münster D-48149, Germany
| | - Maria Pia Cosma
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08003, Spain
| | - Yan Qin
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Laboratory of Metabolism and Epigenetics, Institutes of Biomedical Sciences, Medical College of Fudan University, Shanghai 200032, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Giacomo Volpe
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Liang Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Corresponding author. (M.A.E.); (J.H.H.); (L.C.)
| | - Jacob H. Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Corresponding author. (M.A.E.); (J.H.H.); (L.C.)
| | - Miguel A. Esteban
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Corresponding author. (M.A.E.); (J.H.H.); (L.C.)
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Li R, Huang D, Zhu H, Sun QG, Wang Y, Zhang XH, Zhao XY, He J, Liu L, Zhou JJ, Liu H. [The performance of visual photoscreening for Chinese preschool children aged 4 to 5 years]. Zhonghua Yan Ke Za Zhi 2020; 56:189-196. [PMID: 32187947 DOI: 10.3760/cma.j.issn.0412-4081.2020.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To assess the accuracy of photoscreening for detecting refractive amblyopia risk factors (ARFs) in Chinese preschool children aged 4 to 5 years. Methods: A cross-sectional study. Comprehensive ocular examinations were conducted for preschool children in Nanjing, China from September to December, 2016. Photoscreening (Plusoptix A12C) was applied for refractive screening without cycloplegia. Voluntary children and children suspected of eyes abnormalities received cycloplegic retinoscopy (CR). Results of photoscreening and CR were compared using Wilcoxon signed rank test, and Bland-Altman plot were used to assess the agreement between the photoscreener and CR. According to the updated preschool vision screening guidelines from American Association for Pediatric Ophthalmology and Strabismus (AAPOS) in 2013, CR was adopted for identifying children with ARFs, which was considered as a golden standard. Based on the golden standard, the accuracy of 5 sets of referral criteria (including sensitivity standard, Matta/Silbert standard, AAPOS2013 standard, Alaska Blind Child Discovery standard, specificity standard) for photoscreener were tested. Receiver operating characteristics curves were constructed applied to evaluate the quality of the photoscreener in refractive ARFs detection and to find probably the best cut-off points. Results: In total, 1 986 children [mean age, (4.57±0.29) years] received comprehensive examinations, including 1 084 boys and 902 girls. The test ability of photoscreening was 99.04% (1 967/1 986) in the preschool children, and 96.56%(1 827/1 892) of the children got a reliable result within three screening attempts. In 538 children who had data of CR, refractive error of one child exceeded the upper limit of the photoscreener value setting, which was directly categorized as hyperopia, so in the end, 537 children were included to analyze the comparison between the two tests. The measurement values of photoscreening were lower than those of CR in sphere, cylinder and spherical equivalent [(0.75 (0.50, 1.25) D vs. 1.25 (1.00, 1.75) D, Z=-10.36, P<0.01; -0.50 (-0.75, -0.25) D vs. -0.25 (-0.75, 0.00) D, Z=-11.10, P<0.01; 0.63 (0.38, 0.88) D vs. 1.00 (0.75, 1.50) D, Z=-13.33, P<0.01]. The 95% limit of agreement cover rates between the photoscreening and CR in sphere, cylinder and spherical equivalent was 96.28% (517/537), 95.34% (512/537) and 96.65% (519/537), respectively. Based on the golden standard, 47 (8.74%) children had refractive ARFs, and the range of sensitivity, specificity, Youden index, positive predictive values and negative predictive values for detecting refractive ARFs of the 5 common used referral criteria was from 63.83% to 97.87%, from 53.36% to 97.56%, from 0.51 to 0.80, from 16.73% to 74.51% and from 96.57% to 99.62%, respectively. Considering particular refractive ARFs on the basis of the receiver operating characteristic curves, the optimal cut-off point for astigmatism was set at 1.38 D. Conclusion: Photoscreening could be an applicable tool to detect refractive ARFs in preschool children. (Chin J Ophthalmol, 2020, 56: 189-196).
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Affiliation(s)
- R Li
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - D Huang
- Department of Child Healthcare, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - H Zhu
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Q G Sun
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China, is now working at the Department of Ophthalmology, Maternal and Child Healthcare Hospital of Yuhuatai District, Nanjing 210012, China
| | - Y Wang
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - X H Zhang
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - X Y Zhao
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - J He
- the Fourth School of Clinical Medicine of Nanjing Medical University, Nanjing 210029, China, is now working at the Department of Ophthalmology, Subei People's Hospital of Jiangsu Province, Yangzhou 225001, China
| | - L Liu
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - J J Zhou
- the Fourth School of Clinical Medicine of Nanjing Medical University, Nanjing 210029, China
| | - H Liu
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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25
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Hu JJ, Nie SM, Gao Y, Yan XS, Huang JX, Li TL, Liu SS, Mao CX, Zhou JJ, Xu YJ, Wang W, Meng FJ, Feng XQ. [The correlations and prognostic value of neutrophil to lymphocyte ratio, immunophenotype and cytogenetic abnormalities in patients with newly diagnosed multiple myeloma]. Zhonghua Xue Ye Xue Za Zhi 2020; 40:1044-1046. [PMID: 32023739 PMCID: PMC7342691 DOI: 10.3760/cma.j.issn.0253-2727.2019.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- J J Hu
- Department of Hematology, the Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - S M Nie
- Department of Hematology, the Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Y Gao
- Department of Hematology, the Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - X S Yan
- Department of Hematology, the Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - J X Huang
- Department of Hematology, the Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - T L Li
- Department of Hematology, the Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - S S Liu
- Department of Hematology, the Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - C X Mao
- Department of Hematology, the Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - J J Zhou
- Department of Hematology, the Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Y J Xu
- Department of Hematology, the Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - W Wang
- Department of Hematology, the Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - F J Meng
- Department of Hematology, the Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - X Q Feng
- Department of Hematology, the Affiliated Hospital of Qingdao University, Qingdao 266000, China
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Yuan J, Zhou J, Wang H, Sun H. SKmDB: an integrated database of next generation sequencing information in skeletal muscle. Bioinformatics 2019; 35:847-855. [PMID: 30165538 DOI: 10.1093/bioinformatics/bty705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/18/2018] [Accepted: 08/23/2018] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Skeletal muscles have indispensable functions and also possess prominent regenerative ability. The rapid emergence of Next Generation Sequencing (NGS) data in recent years offers us an unprecedented perspective to understand gene regulatory networks governing skeletal muscle development and regeneration. However, the data from public NGS database are often in raw data format or processed with different procedures, causing obstacles to make full use of them. RESULTS We provide SKmDB, an integrated database of NGS information in skeletal muscle. SKmDB not only includes all NGS datasets available in the human and mouse skeletal muscle tissues and cells, but also provide preliminary data analyses including gene/isoform expression levels, gene co-expression subnetworks, as well as assembly of putative lincRNAs, typical and super enhancers and transcription factor hotspots. Users can efficiently search, browse and visualize the information with the well-designed user interface and server side. SKmDB thus will offer wet lab biologists useful information to study gene regulatory mechanisms in the field of skeletal muscle development and regeneration. AVAILABILITY AND IMPLEMENTATION Freely available on the web at http://sunlab.cpy.cuhk.edu.hk/SKmDB. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jie Yuan
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Jiajian Zhou
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Huating Wang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Hao Sun
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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27
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Zhao Y, Zhou J, He L, Li Y, Yuan J, Sun K, Chen X, Bao X, Esteban MA, Sun H, Wang H. MyoD induced enhancer RNA interacts with hnRNPL to activate target gene transcription during myogenic differentiation. Nat Commun 2019; 10:5787. [PMID: 31857580 PMCID: PMC6923398 DOI: 10.1038/s41467-019-13598-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/15/2019] [Indexed: 12/21/2022] Open
Abstract
Emerging evidence supports roles of enhancer RNAs (eRNAs) in regulating target gene. Here, we study eRNA regulation and function during skeletal myoblast differentiation. We provide a panoramic view of enhancer transcription and categorization of eRNAs. Master transcription factor MyoD is crucial in activating eRNA production. Super enhancer (se) generated seRNA-1 and -2 promote myogenic differentiation in vitro and in vivo. seRNA-1 regulates expression levels of two nearby genes, myoglobin (Mb) and apolipoprotein L6 (Apol6), by binding to heterogeneous nuclear ribonucleoprotein L (hnRNPL). A CAAA tract on seRNA-1 is essential in mediating seRNA-1/hnRNPL binding and function. Disruption of seRNA-1-hnRNPL interaction attenuates Pol II and H3K36me3 deposition at the Mb locus, in coincidence with the reduction of its transcription. Furthermore, analyses of hnRNPL binding transcriptome-wide reveal its association with eRNAs is a general phenomenon in multiple cells. Collectively, we propose that eRNA-hnRNPL interaction represents a mechanism contributing to target mRNA activation.
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Affiliation(s)
- Yu Zhao
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jiajian Zhou
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Liangqiang He
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuying Li
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jie Yuan
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kun Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518000, China
| | - Xiaona Chen
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xichen Bao
- Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Miguel A Esteban
- Laboratory of Chromatin and Human Disease, Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
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Zhou J, Huang Y, Ding Y, Yuan J, Wang H, Sun H. lncFunTK: a toolkit for functional annotation of long noncoding RNAs. Bioinformatics 2019; 34:3415-3416. [PMID: 29718162 DOI: 10.1093/bioinformatics/bty339] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 04/25/2018] [Indexed: 11/13/2022] Open
Abstract
Motivation Thousands of long noncoding RNAs (lncRNAs) were newly identified from high throughput RNA-seq data. Functional annotation and prioritization of these lncRNAs for further experimental validation as well as the functional investigation is the bottleneck step for many noncoding RNA studies. Results Here we describe lncFunTK that can run either as standard application or webserver for this purpose. It integrates high throughput sequencing data (i.e. ChIP-seq, CLIP-seq and RNA-seq) to construct the regulatory network associated with lncRNAs. Through the network, it calculates the Functional Information Score (FIS) of each individual lncRNA for prioritizing and inferring its functions through Gene Ontology (GO) terms of neighboring genes. In addition, it also provides utility scripts to support the input data preprocessing and the parameter optimizing. We further demonstrate that lncFunTK can be widely used in various biological systems for lncRNA prioritization and functional annotation. Availability and implementation The lncFunTK standalone version is an open source package and freely available at http://sunlab.cpy.cuhk.edu.hk/lncfuntk under the MIT license. A webserver implementation is also available at http://sunlab.cpy.cuhk.edu.hk/lncfuntk/runlncfuntk.html. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jiajian Zhou
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong SAR, China
| | - Yile Huang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong SAR, China
| | - Yingzhe Ding
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong SAR, China
| | - Jie Yuan
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong SAR, China
| | - Huating Wang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong SAR, China.,Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong SAR, China
| | - Hao Sun
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong SAR, China
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Zhou J, So KK, Li Y, Li Y, Yuan J, Ding Y, Chen F, Huang Y, Liu J, Lee W, Li G, Ju Z, Sun H, Wang H. Elevated H3K27ac in aged skeletal muscle leads to increase in extracellular matrix and fibrogenic conversion of muscle satellite cells. Aging Cell 2019; 18:e12996. [PMID: 31325224 PMCID: PMC6718601 DOI: 10.1111/acel.12996] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 05/24/2019] [Accepted: 06/05/2019] [Indexed: 01/22/2023] Open
Abstract
Epigenetic alterations occur in various cells and tissues during aging, but it is not known if such alterations are also associated with aging in skeletal muscle. Here, we examined the changes of a panel of histone modifications and found H3K27ac (an active enhancer mark) is markedly increased in aged human skeletal muscle tissues. Further analyses uncovered that the H3K27ac increase and enhancer activation are associated with the up‐regulation of extracellular matrix (ECM) genes; this may result in alteration of the niche environment for skeletal muscle stem cells, also called satellite cells (SCs), which causes decreased myogenic potential and fibrogenic conversion of SCs. In mice, treatment of aging muscles with JQ1, an inhibitor of enhancer activation, inhibited the ECM up‐regulation and fibrogenic conversion of SCs and restored their myogenic differentiation potential. Altogether, our findings not only uncovered a novel aspect of skeletal muscle aging that is associated with enhancer remodeling but also implicated JQ1 as a potential treatment approach for restoring SC function in aging muscle.
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Affiliation(s)
- Jiajian Zhou
- Department of Chemical Pathology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Karl K. So
- Department of Chemical Pathology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Yuying Li
- Department of Chemical Pathology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Yang Li
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Department of Orthopaedics and Traumatology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Jie Yuan
- Department of Chemical Pathology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Yingzhe Ding
- Department of Chemical Pathology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Fengyuan Chen
- Department of Chemical Pathology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Yile Huang
- Department of Chemical Pathology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Jin Liu
- Key Laboratory of Regenerative Medicine of Ministry of Education Institute of Aging and Regenerative MedicineJinan University Guangzhou China
| | - Wayne Lee
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Department of Orthopaedics and Traumatology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Gang Li
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Department of Orthopaedics and Traumatology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Zhenyu Ju
- Key Laboratory of Regenerative Medicine of Ministry of Education Institute of Aging and Regenerative MedicineJinan University Guangzhou China
| | - Hao Sun
- Department of Chemical Pathology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
| | - Huating Wang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
- Department of Orthopaedics and Traumatology The Chinese University of Hong Kong, Prince of Wales Hospital Shatin, New Territories Hong Kong SAR China
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30
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Chen J, Xing N, Zhou JJ, Huang WX, Xue DJ. [Effects of different fluid resuscitation methods on hemorheology in pigs during burn shock stage]. Zhonghua Yi Xue Za Zhi 2019; 99:1421-1426. [PMID: 31137132 DOI: 10.3760/cma.j.issn.0376-2491.2019.18.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the impact of different methods of fluid resuscitation on hemorheology during burn shock stage. Methods: Twenty four miniature swines were randomly divided into four groups with 6 in each group (succinylated gelatin group, hydroxyethyl starch group, Parkland group and allogeneic plasma group). Severe burn shock model was established by burning miniature swine with napalm. Two hours after injury, succinylated gelatin, hydroxyethyl starch (130/0.4) and swine allogenic plasma were used as colloid (alternative colloid) in fluid resuscitation according to the burn shock fluid resuscitation formula which is commonly accepted in the field of Burns Surgery. In Parkland group, miniature swines received liquid recovery according to Parkland Formula. The vital signs before and within 48 h after burn were observed by Solar 8000i electrocardiomonitor during the process of transfusion. The infusion speed was adjusted based on the heart rate, blood pressure, urine volume and central venous pressure. The level of hematocrit (HCT), viscosity of plasma (ηp), index of rigidity (IR), red cell assembling index (RCA) and erythrocyte electrophoresis time (EFT) were measured at the time of pre-injury as well as 4, 8, 24 and 48 h post-injury and statistical analysis was performed. Results: HCT in hydroxyethyl starch group and Parkland group at 8 h post-injury were significantly higher than pre-injury [(0.395±0.047) vs (0.333±0.042), (0.379±0.026) vs (0.352±0.019)] (both P<0.05). And compared with pre-injury, HCT in hydroxyethyl starch (130/0.4) group at 48 h decreased significantly (0.232±0.021) vs (0.333±0.042) (P<0.05). HCT in Parkland group at 24, 48 h post-injury were lower than pre-injury [(0.277±0.021), (0.241±0.029) vs (0.352±0.019)] (both P<0.05). Compared with pre-injury, the levels of ηp in Parkland group decreased substantially at 4, 8 and 24 h post-injury [(1.61±0.07), (1.55±0.07) and (1.63±0.07) vs (1.73±0.04) mPa·s] (all P<0.05). Compared with allogeneic plasma group, IR decreased in succinylated gelatin group at 24, 48 h post-injury [(1.10±0.05 vs 1.26±0.07), (1.11±0.05 vs 1.32±0.05)](both P<0.05). RCA in succinylated gelatin group was significantly higher (both P<0.05) at 4 h (6.80±0.87) than pre-injury (5.92±0.43). RCA in hydroxyethyl starch group at 8 h post-injury (6.73±0.56) was significantly higher (both P<0.05) than pre-injury (6.03±0.53). Compared with pre-injury (17.3±1.3 s, 16.4±1.5 s), the levels of EFT in hydroxyethyl starch group (15.5±1.4 s) and Parkland group (13.4±1.2 s) decreased substantially at 48 h post-injury (both P<0.05). Compared with allogeneic plasma group, the level of EFT in succinylated gelatin group at 4 h post-injury (19.5±2.3 s) increased and decreased at 24 h post-injury (12.0±5.7 s) (both P<0.05). Conclusion: During swine burn shock stage, the hemorheological parameters of shock resuscitation with artificial colloid are more stable than those with Parkland formula resuscitation.
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Affiliation(s)
- J Chen
- Ruian Burns Research Institute, the Third Affiliated Hospital of Wenzhou Medical University, Ruian 325200, China
| | - N Xing
- Burn Department of Weihai Municipal Hospital, Weihai 250021, China
| | - J J Zhou
- Ruian Burns Research Institute, the Third Affiliated Hospital of Wenzhou Medical University, Ruian 325200, China
| | - W X Huang
- Ruian Burns Research Institute, the Third Affiliated Hospital of Wenzhou Medical University, Ruian 325200, China
| | - D J Xue
- Ruian Burns Research Institute, the Third Affiliated Hospital of Wenzhou Medical University, Ruian 325200, China
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31
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Chen F, Zhou J, Li Y, Zhao Y, Yuan J, Cao Y, Wang L, Zhang Z, Zhang B, Wang CC, Cheung TH, Wu Z, Wong CCL, Sun H, Wang H. YY1 regulates skeletal muscle regeneration through controlling metabolic reprogramming of satellite cells. EMBO J 2019; 38:embj.201899727. [PMID: 30979776 DOI: 10.15252/embj.201899727] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 02/04/2023] Open
Abstract
Skeletal muscle satellite cells (SCs) are adult muscle stem cells responsible for muscle regeneration after acute or chronic injuries. The lineage progression of quiescent SC toward activation, proliferation, and differentiation during the regeneration is orchestrated by cascades of transcription factors (TFs). Here, we elucidate the function of TF Yin Yang1 (YY1) in muscle regeneration. Muscle-specific deletion of YY1 in embryonic muscle progenitors leads to severe deformity of diaphragm muscle formation, thus neonatal death. Inducible deletion of YY1 in SC almost completely blocks the acute damage-induced muscle repair and exacerbates the chronic injury-induced dystrophic phenotype. Examination of SC revealed that YY1 loss results in cell-autonomous defect in activation and proliferation. Mechanistic search revealed that YY1 binds and represses mitochondrial gene expression. Simultaneously, it also stabilizes Hif1α protein and activates Hif1α-mediated glycolytic genes to facilitate a metabolic reprogramming toward glycolysis which is needed for SC proliferation. Altogether, our findings have identified YY1 as a key regulator of SC metabolic reprogramming through its dual roles in modulating both mitochondrial and glycolytic pathways.
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Affiliation(s)
- Fengyuan Chen
- Department of Orthopedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Jiajian Zhou
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Yuying Li
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Yu Zhao
- Department of Orthopedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Jie Yuan
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Yang Cao
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Lijun Wang
- Department of Orthopedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Zongkang Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Baoting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi Chiu Wang
- Department of Obstetrics and Gynecology, Li Ka Shing Institute of Health Sciences, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Tom H Cheung
- The State Key Lab in Molecular Neuroscience, Division of Life Science, Center for Stem Cell Research and Center for Systems Biology and Human Diseases, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhenguo Wu
- The State Key Lab in Molecular Neuroscience, Division of Life Science, Center for Stem Cell Research and Center for Systems Biology and Human Diseases, The Hong Kong University of Science and Technology, Hong Kong, China
| | | | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Department of Orthopedics and Traumatology, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong, China
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32
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Zhou JJ, Luo L. [Hypersomnia and syncope as initial manifestations of neuromyelitis optica spectrum disorder: a case report]. Zhonghua Nei Ke Za Zhi 2019; 58:309-311. [PMID: 30917426 DOI: 10.3760/cma.j.issn.0578-1426.2019.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- J J Zhou
- Department of Neurology, The Hangzhou Xixi Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310023, China
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33
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Hu XQ, Liu Q, Hu JP, Zhou JJ, Zhang X, Peng SY, Peng LJ, Wang XD. Identification and characterization of probiotic yeast isolated from digestive tract of ducks. Poult Sci 2018; 97:2902-2908. [PMID: 29762784 DOI: 10.3382/ps/pey152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/17/2018] [Indexed: 01/27/2023] Open
Abstract
The objective of this study was to isolate and identify yeast strains from the digestive tract of ducks, and evaluate in vitro their potential as probiotics in poultry. The yeast strains were isolated using malt extract agar medium, and identified through morphological, physiological, and biochemical tests as well as sequence homology analyses of 26S rDNA D1/D2 region. A total of 35 yeast strains were isolated from the guts of Cherry Valley meat ducks, including seven strains of Saccharomyces cerevisiae (S. cerevisiae). These seven strains of S. cerevisiae were further screened for their use as alternative yeast probiotics strains for poultry feed. The yeast strains were characterized for their cell surface hydrophobicity, autoaggregation ability, and resistance to high temperature (30°C, 37°C, and 42°C), low pH (2.0, 3.0, and 4.0), bile salts (0.3% and 0.6%), and nutrition starvation (2, 4, 6, 8, 10, and 12 days). The isolates of WHY-2 and WHY-7 had a higher survival percentage at 37°C, pH 2.0, 0.60% poultry bile salts, and 10 days of nutrition starvation, with higher cell surface hydrophobicity and autoaggregation, when compared with the other isolates, suggesting that the isolates WHY-2 and WHY-7, could be used as probiotic candidates. The data obtained in this study could help in selecting probiotic yeast candidates for use in poultry industry.
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Affiliation(s)
- X Q Hu
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, 68 Changqing Garden School Road, Wuhan City, Hubei Province, China, 430023
| | - Q Liu
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, 68 Changqing Garden School Road, Wuhan City, Hubei Province, China, 430023
| | - J P Hu
- Angel Yeast Co., Ltd., 168 East Avenue, Yichang City, Hubei Province, China, 443003
| | - J J Zhou
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, 68 Changqing Garden School Road, Wuhan City, Hubei Province, China, 430023
| | - X Zhang
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, 68 Changqing Garden School Road, Wuhan City, Hubei Province, China, 430023
| | - S Y Peng
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, 68 Changqing Garden School Road, Wuhan City, Hubei Province, China, 430023
| | - L J Peng
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, 68 Changqing Garden School Road, Wuhan City, Hubei Province, China, 430023
| | - X D Wang
- Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, 68 Changqing Garden School Road, Wuhan City, Hubei Province, China, 430023.,Wuhan Yongsheng Duck Industry Co., Ltd, Wuhan City, Hubei Province, China, 430334
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34
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Yao M, Zhou X, Zhou J, Gong S, Hu G, Li J, Huang K, Lai P, Shi G, Hutchins AP, Sun H, Wang H, Yao H. PCGF5 is required for neural differentiation of embryonic stem cells. Nat Commun 2018; 9:1463. [PMID: 29765032 PMCID: PMC5954019 DOI: 10.1038/s41467-018-03781-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/12/2018] [Indexed: 02/06/2023] Open
Abstract
Polycomb repressive complex 1 (PRC1) is an important regulator of gene expression and development. PRC1 contains the E3 ligases RING1A/B, which monoubiquitinate lysine 119 at histone H2A (H2AK119ub1), and has been sub-classified into six major complexes based on the presence of a PCGF subunit. Here, we report that PCGF5, one of six PCGF paralogs, is an important requirement in the differentiation of mouse embryonic stem cells (mESCs) towards a neural cell fate. Although PCGF5 is not required for mESC self-renewal, its loss blocks mESC neural differentiation by activating the SMAD2/TGF-β signaling pathway. PCGF5 loss-of-function impairs the reduction of H2AK119ub1 and H3K27me3 around neural specific genes and keeps them repressed. Our results suggest that PCGF5 might function as both a repressor for SMAD2/TGF-β signaling pathway and a facilitator for neural differentiation. Together, our findings reveal a critical context-specific function for PCGF5 in directing PRC1 to control cell fate. Polycomb-group proteins are key regulators of transcriptional programs that maintain cell identity. Here the authors provide evidence that PCGF5, a subunit of Polycomb Repressor Complex 1, is important for the differentiation of mouse embryonic stem cells towards a neural cell fate.
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Affiliation(s)
- Mingze Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Xueke Zhou
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jiajian Zhou
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, the Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Shixin Gong
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Gongcheng Hu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jiao Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Kaimeng Huang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Ping Lai
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Guang Shi
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Andrew P Hutchins
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, the Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, the Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Hongjie Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China. .,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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35
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Zhang XJ, Cui XM, Chen RY, Sun HT, Zhou JJ, Jiang LD. [The analysis of clinical characteristics and disease activity in ankylosing spondylitis patients with hyperuircemia]. Zhonghua Yi Xue Za Zhi 2018; 98:982-986. [PMID: 29690706 DOI: 10.3760/cma.j.issn.0376-2491.2018.13.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: to investigate the clinical characteristics and disease activity in ankylosing spondylitis (AS) patients with hyperuricemia. Method: Laboratory tests, magnetic resonance imaging, disease activity and functional index of AS patients from Fudan University Zhongshan Hospital were collected. T test, square test were applied to investigate the difference between AS patients with hyperuricemia and AS patients with normal serum uric acid in clinical characteristics and disease activity in AS patients. Result: Among all the AS patients, 23.4% (22/94) patients accompanied with hyperuricemia. AS patients accompanied with hyperuricemia showed significant younger age (28.9±7.9 vs 35.8±11.1, P=0.002); higher serum alanine aminotransferase (33.6±23.6 vs 19.8±12.4, P=0.014), aspartate aminotransferase (23.8±8.7 vs 18.6±9.6, P=0.025) and creatinine (78.4±12.5 vs 69.8±13.3, P=0.009), lower Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) (11.2±8.8 vs 17.9±12.0, P=0.027) and Bath Ankylosing Spondylitis Functional Index (BASFI) (0.7±0.9 vs 1.8±2.2, P=0.002) compared with AS patients whose serum uric acid level is normal. Conclusion: AS Patients with younger age, impaired hepatic and renal funtion and lower scores in BASDAI and BASFI tend to accompany with hyperuricemia.
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Affiliation(s)
- X J Zhang
- Department of Rheumatology, Zhongshan Hospital Fudan University, Shanghai 200030, China
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36
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Peng XL, So KK, He L, Zhao Y, Zhou J, Li Y, Yao M, Xu B, Zhang S, Yao H, Hu P, Sun H, Wang H. MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation. Nucleic Acids Res 2017; 45:8785-8805. [PMID: 28575289 PMCID: PMC5587775 DOI: 10.1093/nar/gkx488] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/26/2017] [Indexed: 12/14/2022] Open
Abstract
Super-enhancers (SEs) are cis-regulatory elements enriching lineage specific key transcription factors (TFs) to form hotspots. A paucity of identification and functional dissection promoted us to investigate SEs during myoblast differentiation. ChIP-seq analysis of histone marks leads to the uncovering of SEs which remodel progressively during the course of differentiation. Further analyses of TF ChIP-seq enable the definition of SE hotspots co-bound by the master TF, MyoD and other TFs, among which we perform in-depth dissection for MyoD/FoxO3 interaction in driving the hotspots formation and SE activation. Furthermore, using Myogenin as a model locus, we elucidate the hierarchical and complex interactions among hotspots during the differentiation, demonstrating SE function is propelled by the physical and functional cooperation among hotspots. Finally, we show MyoD and FoxO3 are key in orchestrating the Myogenin hotspots interaction and activation. Altogether our results identify muscle-specific SEs and provide mechanistic insights into the functionality of SE.
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Affiliation(s)
- Xianlu L Peng
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Karl K So
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Liangqiang He
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Yu Zhao
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Jiajian Zhou
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuying Li
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Mingze Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Guangzhou, China
| | - Bo Xu
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Suyang Zhang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Hongjie Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Guangzhou, China
| | - Ping Hu
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
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Zhou J, Zhang S, Wang H, Sun H. LncFunNet: an integrated computational framework for identification of functional long noncoding RNAs in mouse skeletal muscle cells. Nucleic Acids Res 2017; 45:e108. [PMID: 28379566 PMCID: PMC5499579 DOI: 10.1093/nar/gkx232] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/27/2017] [Indexed: 02/01/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are key regulators of diverse cellular processes. Recent advances in high-throughput sequencing have allowed for an unprecedented discovery of novel lncRNAs. To identify functional lncRNAs from thousands of candidates for further functional validation is still a challenging task. Here, we present a novel computational framework, lncFunNet (lncRNA Functional inference through integrated Network) that integrates ChIP-seq, CLIP-seq and RNA-seq data to predict, prioritize and annotate lncRNA functions. In mouse embryonic stem cells (mESCs), using lncFunNet we not only recovered most of the functional lncRNAs known to maintain mESC pluripotency but also predicted a plethora of novel functional lncRNAs. Similarly, in mouse myoblast C2C12 cells, applying lncFunNet led to prediction of reservoirs of functional lncRNAs in both proliferating myoblasts (MBs) and differentiating myotubes (MTs). Further analyses demonstrated that these lncRNAs are frequently bound by key transcription factors, interact with miRNAs and constitute key nodes in biological network motifs. Further experimentations validated their dynamic expression profiles and functionality during myoblast differentiation. Collectively, our studies demonstrate the use of lncFunNet to annotate and identify functional lncRNAs in a given biological system.
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Affiliation(s)
- Jiajian Zhou
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Suyang Zhang
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Huating Wang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Hao Sun
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
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Yang X, Zhao Y, Sun K, Li Y, Zhou J, Wang J, Sun H, Wang CC, Kwong J, Wang H, Chung TKH. Abstract 3448: LncRNA HAND2-AS1 inactivates neuromedin U (NMU) and inhibits tumor invasion and metastasis in endometrioid endometrial carcinoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
Endometrioid endometrial carcinoma (EEC) is one of the common cause of cancer-related mortality in women. Despite progress in diagnostics and treatment of EEC, its prognosis remains poor. Mounting evidence suggest that long noncoding RNAs (lncRNAs) function in mutiple human cancers. Aberrant lncRNA expression may predict tumor outcome of patients and have served as diagnostic or prognostic markers. In this study, we investigated the expression levels and functions of lncRNAs in EEC.
Methods
Differentially expressed lncRNAs involved in EEC were identified by using publically available RNA-Seq data. The expression of 18 dysregulated lncRNA candidates was verified in 5 NE tissues, 5 EEC tissues and 5 EEC cell lines (HEC1-A, HEC1-B, AN3CA, KLE and RL95-2) by real-time polymerase chain reaction (PCR). Further, we selected the most misexpressed lncRNA and confirmed the expression level of the lncRNA in 59 EEC tissues and 24 NE tissues by real-time PCR and correlated the lncRNA expression levels with the clinical pathological characteristics. The promoter methylation assay was used to analyze the methylation level of the lncRNA in EEC. The lncRNA methylation status was confirmed by bisulfite genomic sequencing. Cell proliferation assays, wound healing assays, and invasion and migration assays were performed to determine the biological functions of the lncRNA in EEC cells. To discover the direct targets of the lncRNA in EEC, we performed RNA-sequence analysis in EEC cells overexpressed with the lncRNA and target genes were further studied by functional studies in vitro (knockdown assay and overexpression rescue assay).
Results
We discovered that HAND2-AS1, a lncRNA transcribed antisense adjacent to Heart and Neural Crest Derivatives Expressed 2 (HAND2), was significantly downregulated lncRNA in EEC. HAND2-AS1 and HAND2 was frequently downregulated in EEC tissues, especially in poor differentiated tumor tissues. Downregulation of HAND2-AS1 and HAND2 was correlated with tumor grade, lymph node metastasis and recurrence of EEC patients. HAND2-AS1 and HAND2 was co-downregulated by promoter hypermethylation in EEC. HAND2-AS1 suppressed EEC cell migration and invasion but not cell growth. Similarly, HAND2 also inhibited EEC cell migration and invasion indicating that HAND2-AS1 and HAND2 have a concordant role in the progression of EEC. Moreover, the anti-tumorigenic effect of HAND2-AS1 was mediated by downregulating NMU, which had an oncogenic role in EEC.
Conclusions
Our findings provide the first evidence that HAND2-AS1 is a critical tumor suppressor in EEC and may constitute a prognostic biomarker in EEC.
Note: This abstract was not presented at the meeting.
Citation Format: Xueying Yang, Yu Zhao, Kun Sun, Yuying Li, Jiajian Zhou, Jianzhang Wang, Hao Sun, Chi Chiu Wang, Joseph Kwong, Huating Wang, Tony Kwok Hung Chung. LncRNA HAND2-AS1 inactivates neuromedin U (NMU) and inhibits tumor invasion and metastasis in endometrioid endometrial carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3448. doi:10.1158/1538-7445.AM2017-3448
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Affiliation(s)
- Xueying Yang
- The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Yu Zhao
- The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Kun Sun
- The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Yuying Li
- The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Jiajian Zhou
- The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Jianzhang Wang
- The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Hao Sun
- The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Chi Chiu Wang
- The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Joseph Kwong
- The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Huating Wang
- The Chinese University of Hong Kong, Hong Kong, Hong Kong
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Abstract
Long intergenic noncoding RNAs (lincRNAs) have emerged as critical participators in gene regulation in myriads of cell types. The development of the whole transcriptome sequencing technology, or RNA-seq , has enabled novel lincRNA detection, but the bioinformatics analysis toward distinguishing reliable ones remains a challenge. Here, we describe the bioinformatics workflow developed for identifying novel lincRNAs step by step, including read alignment, transcriptome assembly and transcript filtering.
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Affiliation(s)
- Xianlu Peng
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kun Sun
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jiajian Zhou
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hao Sun
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Department of Orthopaedics and Traumotology, The Chinese University of Hong Kong, Hong Kong, China.
- 507A, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China.
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40
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Jiang L, Liu W, Zhu A, Zhang J, Zhou J, Wu C. Transcriptome analysis demonstrate widespread differential expression of long noncoding RNAs involve in Larimichthys crocea immune response. Fish Shellfish Immunol 2016; 51:1-8. [PMID: 26892794 DOI: 10.1016/j.fsi.2016.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/19/2016] [Accepted: 02/03/2016] [Indexed: 06/05/2023]
Abstract
Long noncoding RNAs (lncRNAs) are a class of transcripts that longer than 200 bp and do not encode proteins. Recent genome-wide studies of vertebrate transcriptomes have annotated lncRNAs that are expressed in various tissues and development stages. The draft genome and several transcriptome sequencing data sets have been collected for the study of protein-coding genes in large yellow croaker (Larimichthys crocea), but little is known about the expression and functional roles of lncRNAs in this species. In order to obtain a catalog of lncRNAs for large yellow croaker, several RNA-seq datasets were integrated from various tissues including egg, muscle, liver, and spleen. A total of 48,953 high-confidence transcripts were reconstructed in 38,017 loci, recovering the most of expressed reference transcripts while thousands of novel expressed loci have been identified. The tissue expression profile revealed that most lncRNAs were specifically enriched in different tissues. A stringent set of 210 lncRNAs were identified as being specifically expressed in spleen and potentially involved in immune response. Our study first systematically identify lncRNAs in large yellow croaker, benefiting the future genomic study of this species.
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Affiliation(s)
- Lihua Jiang
- National Engineering Research Center of Maricultural Facilities of China, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, China
| | - Wei Liu
- National Engineering Research Center of Maricultural Facilities of China, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, China
| | - Aiyi Zhu
- National Engineering Research Center of Maricultural Facilities of China, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, China
| | - Jianshe Zhang
- National Engineering Research Center of Maricultural Facilities of China, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, China
| | | | - Changwen Wu
- National Engineering Research Center of Maricultural Facilities of China, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, China.
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Fang F, Zhang XL, Luo HH, Zhou JJ, Gong YH, Li WJ, Shi ZW, He Q, Wu Q, Li L, Jiang LL, Cai ZG, Oren-Shamir M, Zhang ZQ, Pang XQ. An Intracellular Laccase Is Responsible for Epicatechin-Mediated Anthocyanin Degradation in Litchi Fruit Pericarp. Plant Physiol 2015; 169:2391-408. [PMID: 26514808 PMCID: PMC4677877 DOI: 10.1104/pp.15.00359] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 10/27/2015] [Indexed: 05/21/2023]
Abstract
In contrast to the detailed molecular knowledge available on anthocyanin synthesis, little is known about its catabolism in plants. Litchi (Litchi chinensis) fruit lose their attractive red color soon after harvest. The mechanism leading to quick degradation of anthocyanins in the pericarp is not well understood. An anthocyanin degradation enzyme (ADE) was purified to homogeneity by sequential column chromatography, using partially purified anthocyanins from litchi pericarp as a substrate. The purified ADE, of 116 kD by urea SDS-PAGE, was identified as a laccase (ADE/LAC). The full-length complementary DNA encoding ADE/LAC was obtained, and a polyclonal antibody raised against a deduced peptide of the gene recognized the ADE protein. The anthocyanin degradation function of the gene was confirmed by its transient expression in tobacco (Nicotiana benthamiana) leaves. The highest ADE/LAC transcript abundance was in the pericarp in comparison with other tissues, and was about 1,000-fold higher than the polyphenol oxidase gene in the pericarp. Epicatechin was found to be the favorable substrate for the ADE/LAC. The dependence of anthocyanin degradation by the enzyme on the presence of epicatechin suggests an ADE/LAC epicatechin-coupled oxidation model. This model was supported by a dramatic decrease in epicatechin content in the pericarp parallel to anthocyanin degradation. Immunogold labeling transmission electron microscopy suggested that ADE/LAC is located mainly in the vacuole, with essential phenolic substances. ADE/LAC vacuolar localization, high expression levels in the pericarp, and high epicatechin-dependent anthocyanin degradation support its central role in pigment breakdown during pericarp browning.
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Affiliation(s)
- Fang Fang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (F.F., X.Z., H.L., J.Z., Y.G., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., Z.Z., X.P.), College of Life Sciences (F.F., X.Z., H.L., J.Z., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., X.P.), and College of Horticulture (Y.G., Z.Z.), South China Agricultural University, Guangzhou 510642, China;Research Institute of Food Science and Engineering Technology, Hezhou University, Hezhou 542899, China (F.F.); andDepartment of Ornamental Horticulture, Agriculture Research Organization, Volcani Centre, Bet Dagan 50250, Israel (M.O.-S.)
| | - Xue-lian Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (F.F., X.Z., H.L., J.Z., Y.G., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., Z.Z., X.P.), College of Life Sciences (F.F., X.Z., H.L., J.Z., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., X.P.), and College of Horticulture (Y.G., Z.Z.), South China Agricultural University, Guangzhou 510642, China;Research Institute of Food Science and Engineering Technology, Hezhou University, Hezhou 542899, China (F.F.); andDepartment of Ornamental Horticulture, Agriculture Research Organization, Volcani Centre, Bet Dagan 50250, Israel (M.O.-S.)
| | - Hong-hui Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (F.F., X.Z., H.L., J.Z., Y.G., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., Z.Z., X.P.), College of Life Sciences (F.F., X.Z., H.L., J.Z., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., X.P.), and College of Horticulture (Y.G., Z.Z.), South China Agricultural University, Guangzhou 510642, China;Research Institute of Food Science and Engineering Technology, Hezhou University, Hezhou 542899, China (F.F.); andDepartment of Ornamental Horticulture, Agriculture Research Organization, Volcani Centre, Bet Dagan 50250, Israel (M.O.-S.)
| | - Jia-jian Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (F.F., X.Z., H.L., J.Z., Y.G., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., Z.Z., X.P.), College of Life Sciences (F.F., X.Z., H.L., J.Z., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., X.P.), and College of Horticulture (Y.G., Z.Z.), South China Agricultural University, Guangzhou 510642, China;Research Institute of Food Science and Engineering Technology, Hezhou University, Hezhou 542899, China (F.F.); andDepartment of Ornamental Horticulture, Agriculture Research Organization, Volcani Centre, Bet Dagan 50250, Israel (M.O.-S.)
| | - Yi-hui Gong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (F.F., X.Z., H.L., J.Z., Y.G., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., Z.Z., X.P.), College of Life Sciences (F.F., X.Z., H.L., J.Z., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., X.P.), and College of Horticulture (Y.G., Z.Z.), South China Agricultural University, Guangzhou 510642, China;Research Institute of Food Science and Engineering Technology, Hezhou University, Hezhou 542899, China (F.F.); andDepartment of Ornamental Horticulture, Agriculture Research Organization, Volcani Centre, Bet Dagan 50250, Israel (M.O.-S.)
| | - Wen-jun Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (F.F., X.Z., H.L., J.Z., Y.G., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., Z.Z., X.P.), College of Life Sciences (F.F., X.Z., H.L., J.Z., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., X.P.), and College of Horticulture (Y.G., Z.Z.), South China Agricultural University, Guangzhou 510642, China;Research Institute of Food Science and Engineering Technology, Hezhou University, Hezhou 542899, China (F.F.); andDepartment of Ornamental Horticulture, Agriculture Research Organization, Volcani Centre, Bet Dagan 50250, Israel (M.O.-S.)
| | - Zhao-wan Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (F.F., X.Z., H.L., J.Z., Y.G., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., Z.Z., X.P.), College of Life Sciences (F.F., X.Z., H.L., J.Z., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., X.P.), and College of Horticulture (Y.G., Z.Z.), South China Agricultural University, Guangzhou 510642, China;Research Institute of Food Science and Engineering Technology, Hezhou University, Hezhou 542899, China (F.F.); andDepartment of Ornamental Horticulture, Agriculture Research Organization, Volcani Centre, Bet Dagan 50250, Israel (M.O.-S.)
| | - Quan He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (F.F., X.Z., H.L., J.Z., Y.G., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., Z.Z., X.P.), College of Life Sciences (F.F., X.Z., H.L., J.Z., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., X.P.), and College of Horticulture (Y.G., Z.Z.), South China Agricultural University, Guangzhou 510642, China;Research Institute of Food Science and Engineering Technology, Hezhou University, Hezhou 542899, China (F.F.); andDepartment of Ornamental Horticulture, Agriculture Research Organization, Volcani Centre, Bet Dagan 50250, Israel (M.O.-S.)
| | - Qing Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (F.F., X.Z., H.L., J.Z., Y.G., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., Z.Z., X.P.), College of Life Sciences (F.F., X.Z., H.L., J.Z., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., X.P.), and College of Horticulture (Y.G., Z.Z.), South China Agricultural University, Guangzhou 510642, China;Research Institute of Food Science and Engineering Technology, Hezhou University, Hezhou 542899, China (F.F.); andDepartment of Ornamental Horticulture, Agriculture Research Organization, Volcani Centre, Bet Dagan 50250, Israel (M.O.-S.)
| | - Lu Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (F.F., X.Z., H.L., J.Z., Y.G., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., Z.Z., X.P.), College of Life Sciences (F.F., X.Z., H.L., J.Z., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., X.P.), and College of Horticulture (Y.G., Z.Z.), South China Agricultural University, Guangzhou 510642, China;Research Institute of Food Science and Engineering Technology, Hezhou University, Hezhou 542899, China (F.F.); andDepartment of Ornamental Horticulture, Agriculture Research Organization, Volcani Centre, Bet Dagan 50250, Israel (M.O.-S.)
| | - Lin-lin Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (F.F., X.Z., H.L., J.Z., Y.G., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., Z.Z., X.P.), College of Life Sciences (F.F., X.Z., H.L., J.Z., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., X.P.), and College of Horticulture (Y.G., Z.Z.), South China Agricultural University, Guangzhou 510642, China;Research Institute of Food Science and Engineering Technology, Hezhou University, Hezhou 542899, China (F.F.); andDepartment of Ornamental Horticulture, Agriculture Research Organization, Volcani Centre, Bet Dagan 50250, Israel (M.O.-S.)
| | - Zhi-gao Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (F.F., X.Z., H.L., J.Z., Y.G., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., Z.Z., X.P.), College of Life Sciences (F.F., X.Z., H.L., J.Z., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., X.P.), and College of Horticulture (Y.G., Z.Z.), South China Agricultural University, Guangzhou 510642, China;Research Institute of Food Science and Engineering Technology, Hezhou University, Hezhou 542899, China (F.F.); andDepartment of Ornamental Horticulture, Agriculture Research Organization, Volcani Centre, Bet Dagan 50250, Israel (M.O.-S.)
| | - Michal Oren-Shamir
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (F.F., X.Z., H.L., J.Z., Y.G., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., Z.Z., X.P.), College of Life Sciences (F.F., X.Z., H.L., J.Z., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., X.P.), and College of Horticulture (Y.G., Z.Z.), South China Agricultural University, Guangzhou 510642, China;Research Institute of Food Science and Engineering Technology, Hezhou University, Hezhou 542899, China (F.F.); andDepartment of Ornamental Horticulture, Agriculture Research Organization, Volcani Centre, Bet Dagan 50250, Israel (M.O.-S.)
| | - Zhao-qi Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (F.F., X.Z., H.L., J.Z., Y.G., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., Z.Z., X.P.), College of Life Sciences (F.F., X.Z., H.L., J.Z., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., X.P.), and College of Horticulture (Y.G., Z.Z.), South China Agricultural University, Guangzhou 510642, China;Research Institute of Food Science and Engineering Technology, Hezhou University, Hezhou 542899, China (F.F.); andDepartment of Ornamental Horticulture, Agriculture Research Organization, Volcani Centre, Bet Dagan 50250, Israel (M.O.-S.)
| | - Xue-qun Pang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources (F.F., X.Z., H.L., J.Z., Y.G., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., Z.Z., X.P.), College of Life Sciences (F.F., X.Z., H.L., J.Z., W.L., Z.S., Q.H., Q.W., L.L., L.J., Z.C., X.P.), and College of Horticulture (Y.G., Z.Z.), South China Agricultural University, Guangzhou 510642, China;Research Institute of Food Science and Engineering Technology, Hezhou University, Hezhou 542899, China (F.F.); andDepartment of Ornamental Horticulture, Agriculture Research Organization, Volcani Centre, Bet Dagan 50250, Israel (M.O.-S.)
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Wu C, Zhang D, Kan M, Lv Z, Zhu A, Su Y, Zhou D, Zhang J, Zhang Z, Xu M, Jiang L, Guo B, Wang T, Chi C, Mao Y, Zhou J, Yu X, Wang H, Weng X, Jin JG, Ye J, He L, Liu Y. The draft genome of the large yellow croaker reveals well-developed innate immunity. Nat Commun 2014; 5:5227. [PMID: 25407894 PMCID: PMC4263168 DOI: 10.1038/ncomms6227] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/10/2014] [Indexed: 12/19/2022] Open
Abstract
The large yellow croaker, Larimichthys crocea, is one of the most economically important marine fish species endemic to China. Its wild stocks have severely suffered from overfishing, and the aquacultured species are vulnerable to various marine pathogens. Here we report the creation of a draft genome of a wild large yellow croaker using a whole-genome sequencing strategy. We estimate the genome size to be 728 Mb with 19,362 protein-coding genes. Phylogenetic analysis shows that the stickleback is most closely related to the large yellow croaker. Rapidly evolving genes under positive selection are significantly enriched in pathways related to innate immunity. We also confirm the existence of several genes and identify the expansion of gene families that are important for innate immunity. Our results may reflect a well-developed innate immune system in the large yellow croaker, which could aid in the development of wild resource preservation and mariculture strategies.
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Affiliation(s)
- Changwen Wu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Di Zhang
- Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
| | - Mengyuan Kan
- Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhengmin Lv
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Aiyi Zhu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yongquan Su
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Daizhan Zhou
- Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jianshe Zhang
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zhou Zhang
- Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
| | - Meiying Xu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Lihua Jiang
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Baoying Guo
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Ting Wang
- Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai 200031, China
| | - Changfeng Chi
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yong Mao
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Jiajian Zhou
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Xinxiu Yu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Hailing Wang
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Xiaoling Weng
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jason Gang Jin
- ShanghaiBio Corporation, 675 US Highway One, North Brunswick, New Jersey 08902, USA
| | - Junyi Ye
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Lin He
- Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yun Liu
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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Cui YL, Zhou JJ, Gao LR, Zhu CQ, Jiang X, Fu SL, Gong H. Utilization of excess NADH in 2,3-butanediol-deficient Klebsiella pneumoniae for 1,3-propanediol production. J Appl Microbiol 2014; 117:690-8. [PMID: 24961176 DOI: 10.1111/jam.12588] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/09/2014] [Accepted: 06/19/2014] [Indexed: 11/27/2022]
Abstract
AIMS To utilize excess NADH for 1,3-propanediol production by 2,3-butanediol-deficient mutants, the effect of dhaT overexpression in two distinct 2,3-butanediol-deficient mutants was investigated. METHODS AND RESULTS Two 2,3-butanediol-deficient mutants, KG1-3 (blocking of the 2,3-butanediol pathway only) and KG1-5 (blocking of both of 2,3-butanediol and lactate pathways) were constructed. Our results showed that although the intracellular redox balance (NADH/NAD(+)) was extremely high at the end of fermentation for both mutants, the status of intracellular redox in KG1-5 was maintained at a normal level following the first stage of fermentation. Analysis of cell growth and metabolite formation confirmed the inhibition of excess lactate in 2,3-butanediol pathway-deficient mutants. Furthermore, dhaT was overexpressed in two 2,3-butanediol-deficient mutants (KG1-3T and KG1-5T). In KG1-5T, the intracellular redox balance was restored to normal and 1,3-propanediol production increased. The yield of 1,3-propanediol from glycerol in KG1-5T was also restored to a normal level of 0·6. CONCLUSIONS The excess NADH in both the 2,3-butanediol- and lactate-deficient mutants can be used by overexpresstion of dhaT. SIGNIFICANCE AND IMPACT OF STUDY The metabolic flux tended to increase lactate production by the abolishment of the 2,3-butanediol pathway in Klebsiella pneumoniae, and the high accumulation of lactate prevented the cell from using excess NADH, thereby inhibiting cell growth and 1,3-propanediol production.
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Affiliation(s)
- Y L Cui
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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44
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Terrapon N, Li C, Robertson HM, Ji L, Meng X, Booth W, Chen Z, Childers CP, Glastad KM, Gokhale K, Gowin J, Gronenberg W, Hermansen RA, Hu H, Hunt BG, Huylmans AK, Khalil SMS, Mitchell RD, Munoz-Torres MC, Mustard JA, Pan H, Reese JT, Scharf ME, Sun F, Vogel H, Xiao J, Yang W, Yang Z, Yang Z, Zhou J, Zhu J, Brent CS, Elsik CG, Goodisman MAD, Liberles DA, Roe RM, Vargo EL, Vilcinskas A, Wang J, Bornberg-Bauer E, Korb J, Zhang G, Liebig J. Molecular traces of alternative social organization in a termite genome. Nat Commun 2014; 5:3636. [PMID: 24845553 DOI: 10.1038/ncomms4636] [Citation(s) in RCA: 268] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 03/13/2014] [Indexed: 01/28/2023] Open
Abstract
Although eusociality evolved independently within several orders of insects, research into the molecular underpinnings of the transition towards social complexity has been confined primarily to Hymenoptera (for example, ants and bees). Here we sequence the genome and stage-specific transcriptomes of the dampwood termite Zootermopsis nevadensis (Blattodea) and compare them with similar data for eusocial Hymenoptera, to better identify commonalities and differences in achieving this significant transition. We show an expansion of genes related to male fertility, with upregulated gene expression in male reproductive individuals reflecting the profound differences in mating biology relative to the Hymenoptera. For several chemoreceptor families, we show divergent numbers of genes, which may correspond to the more claustral lifestyle of these termites. We also show similarities in the number and expression of genes related to caste determination mechanisms. Finally, patterns of DNA methylation and alternative splicing support a hypothesized epigenetic regulation of caste differentiation.
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Affiliation(s)
- Nicolas Terrapon
- 1] Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität, Münster D48149, Germany [2] [3]
| | - Cai Li
- 1] China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China [2] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350, Denmark [3]
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Lu Ji
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xuehong Meng
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Warren Booth
- 1] Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA [2]
| | - Zhensheng Chen
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Karl M Glastad
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Kaustubh Gokhale
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Johannes Gowin
- 1] Behavioural Biology, University of Osnabrück, Osnabrück D49076, Germany [2]
| | - Wulfila Gronenberg
- Department of Neuroscience, University of Arizona, Tucson, Arizona 85721, USA
| | - Russell A Hermansen
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA
| | - Haofu Hu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Brendan G Hunt
- 1] School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA [2]
| | - Ann Kathrin Huylmans
- 1] Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität, Münster D48149, Germany [2]
| | - Sayed M S Khalil
- 1] Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA [2] Department of Microbial Molecular Biology, Agricultural Genetic Engineering Research Institute, Giza 12619, Egypt
| | - Robert D Mitchell
- Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Monica C Munoz-Torres
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Julie A Mustard
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Hailin Pan
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Justin T Reese
- Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Michael E Scharf
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Fengming Sun
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena D-07745, Germany
| | - Jin Xiao
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Wei Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhikai Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Zuoquan Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiajian Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiwei Zhu
- Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Colin S Brent
- Arid Land Agricultural Research Center, United States Department of Agriculture, Maricopa, Arizona 85138, USA
| | - Christine G Elsik
- 1] Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA [2] Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | | | - David A Liberles
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA
| | - R Michael Roe
- Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Edward L Vargo
- Department of Entomology and W. M Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Andreas Vilcinskas
- Institut für Phytopathologie und Angewandte Zoologie, Justus-Liebig-Universität Giessen, Giessen D35390, Germany
| | - Jun Wang
- 1] China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China [2] Department of Biology, University of Copenhagen, Copenhagen DK-1165, Denmark [3] Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, 21589 Jeddah, Saudi Arabia [4] Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China [5] Department of Medicine, University of Hong Kong, Hong Kong
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität, Münster D48149, Germany
| | - Judith Korb
- 1] Behavioural Biology, University of Osnabrück, Osnabrück D49076, Germany [2]
| | - Guojie Zhang
- 1] China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China [2] Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Jürgen Liebig
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA
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45
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Siciliano P, He XL, Woodcock C, Pickett JA, Field LM, Birkett MA, Kalinova B, Gomulski LM, Scolari F, Gasperi G, Malacrida AR, Zhou JJ. Identification of pheromone components and their binding affinity to the odorant binding protein CcapOBP83a-2 of the Mediterranean fruit fly, Ceratitis capitata. Insect Biochem Mol Biol 2014; 48:51-62. [PMID: 24607850 PMCID: PMC4003389 DOI: 10.1016/j.ibmb.2014.02.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 02/17/2014] [Accepted: 02/18/2014] [Indexed: 05/27/2023]
Abstract
The Mediterranean fruit fly (or medfly), Ceratitis capitata (Wiedemann; Diptera: Tephritidae), is a serious pest of agriculture worldwide, displaying a very wide larval host range with more than 250 different species of fruit and vegetables. Olfaction plays a key role in the invasive potential of this species. Unfortunately, the pheromone communication system of the medfly is complex and still not well established. In this study, we report the isolation of chemicals emitted by sexually mature individuals during the "calling" period and the electrophysiological responses that these compounds elicit on the antennae of male and female flies. Fifteen compounds with electrophysiological activity were isolated and identified in male emissions by gas chromatography coupled to electroantennography (GC-EAG). Within the group of 15 identified compounds, 11 elicited a response in antennae of both sexes, whilst 4 elicited a response only in female antennae. The binding affinity of these compounds, plus 4 additional compounds known to be behaviourally active from other studies, was measured using C. capitata OBP, CcapOBP83a-2. This OBP has a high homology to Drosophila melanogaster OBPs OS-E and OS-F, which are associated with trichoid sensilla and co-expressed with the well-studied Drosophila pheromone binding protein LUSH. The results provide evidence of involvement of CcapOBP83a-2 in the medfly's odorant perception and its wider specificity for (E,E)-α-farnesene, one of the five major compounds in medfly male pheromone emission. This represents the first step in the clarification of the C. capitata and pheromone reception pathway, and a starting point for further studies aimed towards the creation of new powerful attractants or repellents applicable in the actual control strategies.
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Affiliation(s)
- P Siciliano
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Herts. AL5 2JQ, United Kingdom; Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 9, 27100 Pavia, Italia
| | - X L He
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Herts. AL5 2JQ, United Kingdom
| | - C Woodcock
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Herts. AL5 2JQ, United Kingdom
| | - J A Pickett
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Herts. AL5 2JQ, United Kingdom
| | - L M Field
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Herts. AL5 2JQ, United Kingdom
| | - M A Birkett
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Herts. AL5 2JQ, United Kingdom
| | - B Kalinova
- Institute of Organic Chemistry and Biochemistry of the AS CR, v.v.i., Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
| | - L M Gomulski
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 9, 27100 Pavia, Italia
| | - F Scolari
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 9, 27100 Pavia, Italia
| | - G Gasperi
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 9, 27100 Pavia, Italia
| | - A R Malacrida
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 9, 27100 Pavia, Italia
| | - J J Zhou
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Herts. AL5 2JQ, United Kingdom.
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46
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Farias LR, Paula DP, Zhou JJ, Liu R, Pappas GJ, Moraes MCB, Laumann RA, Borges M, Birkett MA, Pickett JA, Field LM, Báo SN. Identification and Expression Profile of Two Putative Odorant-Binding Proteins from the Neotropical Brown Stink Bug, Euschistus heros (Fabricius) (Hemiptera: Pentatomidae). Neotrop Entomol 2014; 43:106-14. [PMID: 27193516 DOI: 10.1007/s13744-013-0187-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 12/02/2013] [Indexed: 06/05/2023]
Abstract
This work presents the first identification of putative odorant-binding proteins (OBPs) from a member of the Pentatomidae, i.e. the brown stink bug Euschistus heros (Fabricius), an important pest of soybean in Brazil. Antennae from both sexes of E. heros adults (12 days old and unmated) were used to construct a cDNA library, from which two transcripts encoding putative E. heros OBPs (EherOBPs) were identified. The expression levels of EherOBP1 and EherOBP2 were found to be higher in male antennae than in female and there was difference in expression in legs, wings, and abdomens of the two sexes. The histolocalization of EherOBP1 and EherOBP2 transcripts in antennae also showed a sexual dimorphism in the chemoreception system, with different expression sites in the antennal segments between males and females, occurring predominantly at the base of the sensillum. The implications of these findings for stink bug chemoreception are discussed.
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Affiliation(s)
- L R Farias
- Instituto de Ciências Biológicas, Univ de Brasília, Campus Universitário Darcy Ribeiro, Brasília, DF, Brasil.
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil.
| | - D P Paula
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
| | - J J Zhou
- Dept of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - R Liu
- Dept of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - G J Pappas
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
| | - M C B Moraes
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
| | - R A Laumann
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
| | - M Borges
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brasil
| | - M A Birkett
- Dept of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - J A Pickett
- Dept of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - L M Field
- Dept of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - S N Báo
- Instituto de Ciências Biológicas, Univ de Brasília, Campus Universitário Darcy Ribeiro, Brasília, DF, Brasil
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47
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Liu ZR, Zhang H, Wu JQ, Zhou JJ, Ji YH. PKA phosphorylation reshapes the pharmacological kinetics of BmK AS, a unique site-4 sodium channel-specific modulator. Sci Rep 2014; 4:3721. [PMID: 24430351 PMCID: PMC5379197 DOI: 10.1038/srep03721] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 12/19/2013] [Indexed: 01/14/2023] Open
Abstract
Although modulation of the activity of voltage-gated sodium channels (VGSCs) by protein kinase A (PKA) phosphorylation has been investigated in multiple preparations, the pharmacological sensitivity of VGSCs to scorpion toxins after PKA phosphorylation has rarely been approached. In this study, the effects of BmK AS, a sodium channel-specific modulator from Chinese scorpion Buthus martensi Karsch, on the voltage-dependent activation and inactivation of Nav1.2 were examined before and after PKA activation. After PKA phosphorylation, the pattern of dose-dependent modulation of BmK AS, on both Nav1.2α and Nav1.2 (α + β1) was reshaped. Meanwhile, the shifts in voltage-dependency of activation and inactivation induced by BmK AS were attenuated. The results suggested that PKA might play a role in different patterns how β-like toxins such as BmK AS modulate gating properties and peak currents of VGSCs.
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Affiliation(s)
- Z R Liu
- 1] Department of Pharmacology, Institute of Medical Science, Shanghai Jiao Tong University School of Medicine, South Chongqing Road 280, Shanghai 200025, P.R.China [2] Lab of Neuropharmacology and Neurotoxicology, Shanghai University, Nanchen Road 333, Shanghai 200436, P.R. China
| | - H Zhang
- Lab of Neuropharmacology and Neurotoxicology, Shanghai University, Nanchen Road 333, Shanghai 200436, P.R. China
| | - J Q Wu
- Lab of Neuropharmacology and Neurotoxicology, Shanghai University, Nanchen Road 333, Shanghai 200436, P.R. China
| | - J J Zhou
- Lab of Neuropharmacology and Neurotoxicology, Shanghai University, Nanchen Road 333, Shanghai 200436, P.R. China
| | - Y H Ji
- 1] Lab of Neuropharmacology and Neurotoxicology, Shanghai University, Nanchen Road 333, Shanghai 200436, P.R. China [2] Shanghai Chongmin Xinhua Translational Institute of Cancer Pain, Nanmen Road 25, Shanghai 202151, P.R. China
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48
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Zhou JJ, Tian J, Fang DY, Liang Y, Yan HJ, Zhou JM, Gao HL, Fu CY, Liu Y, Ni HZ, Ke CW, Jiang LF. Analysis of antigen epitopes and molecular pathogenic characteristics of the 2009 H1N1 pandemic influenza A virus in China. Acta Virol 2011; 55:195-202. [PMID: 21978153 DOI: 10.4149/av_2011_03_195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In order to further predict the epidemic trend and develop vaccines for 2009 H1N1 virus, we monitored its epitopes and molecular pathogenic characteristics during the epidemic process. We also analyzed the similarity of antigenic and genetic characteristics among the novel 2009 H1N1, representative seasonal H1N1 strains, and vaccine strains. 2009 H1N1 isolates had high similarity of hemagglutinin (HA) antigenic sites with H1N1 viruses isolated before 1940 and up to 80.0% similarity with 1918 H1N1. The elderly people born before 1940 have relatively low 2009 H1N1 infection rate, which might be responsible for their previous infection with either 1918 H1N1 virus or an early progeny. Compared to seasonal H1N1 vaccine strains from 1999 to 2010, the HA, neuraminidase (NA), and nucleoprotein (NP) proteins of the isolates had highly conserved CTL epitopes (60.5-65.8%, 69.6-82.6%, and 76.7%, respectively). The seriousness and mortality rate of 2009 H1N1 infections were similar to seasonal influenza, which may be related to the molecular characteristics of low toxicity of 2009 H1N1 and cross-T-cell immunity, due to vaccination or exposure to seasonal H1N1 virus. Some strains of 2009 H1N1 acquired mutations at antigenic and glycosylation sites. It is of particular interest that Haishu/SWL110/10 and Beijing/SE2649/09, isolated after November 2009, gained a new glycosylation site at the position 179 of HA protein, near the RBD. Thus, in the future, vaccination with glycosylated 2009 H1N1 virus may prevent the seasonal epidemic caused by strains with glycosylation site mutation near the receptor binding domain (RBD).
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Affiliation(s)
- J J Zhou
- Department of Microbiology, Sun Yat-sen University, Guangzhou, People's Republic of China
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49
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Nygaard S, Zhang G, Schiøtt M, Li C, Wurm Y, Hu H, Zhou J, Ji L, Qiu F, Rasmussen M, Pan H, Hauser F, Krogh A, Grimmelikhuijzen CJP, Wang J, Boomsma JJ. The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. Genome Res 2011; 21:1339-48. [PMID: 21719571 DOI: 10.1101/gr.121392.111] [Citation(s) in RCA: 177] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We present a high-quality (>100× depth) Illumina genome sequence of the leaf-cutting ant Acromyrmex echinatior, a model species for symbiosis and reproductive conflict studies. We compare this genome with three previously sequenced genomes of ants from different subfamilies and focus our analyses on aspects of the genome likely to be associated with known evolutionary changes. The first is the specialized fungal diet of A. echinatior, where we find gene loss in the ant's arginine synthesis pathway, loss of detoxification genes, and expansion of a group of peptidase proteins. One of these is a unique ant-derived contribution to the fecal fluid, which otherwise consists of "garden manuring" fungal enzymes that are unaffected by ant digestion. The second is multiple mating of queens and ejaculate competition, which may be associated with a greatly expanded nardilysin-like peptidase gene family. The third is sex determination, where we could identify only a single homolog of the feminizer gene. As other ants and the honeybee have duplications of this gene, we hypothesize that this may partly explain the frequent production of diploid male larvae in A. echinatior. The fourth is the evolution of eusociality, where we find a highly conserved ant-specific profile of neuropeptide genes that may be related to caste determination. These first analyses of the A. echinatior genome indicate that considerable genetic changes are likely to have accompanied the transition from hunter-gathering to agricultural food production 50 million years ago, and the transition from single to multiple queen mating 10 million years ago.
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Affiliation(s)
- Sanne Nygaard
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
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50
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Zhou JJ, Pelka S, Lange K, Palmer CGS, Sinsheimer JS. Dissecting prenatal, postnatal, and inherited effects: ART and design. Genet Epidemiol 2011; 35:437-46. [PMID: 21638309 DOI: 10.1002/gepi.20591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 03/31/2011] [Accepted: 04/14/2011] [Indexed: 11/11/2022]
Abstract
With the failure of common variants alone to explain the bulk of trait heritability, it becomes more important to understand the contribution of maternally inherited effects, prenatal effects, and postnatal environmental effects. These effects can be disentangled by studying families containing children conceived by assisted reproductive technologies (ART). We propose and develop a model that is an extension of the variance component model commonly used in pedigree analysis. Our model is flexible enough to allow any number of family members and degrees of relationship; thus, researchers can use both small and extended families simultaneously. Simulations demonstrate that our method has appropriate statistical properties and is robust to model misspecification and accurate in the presence of missing data. Most importantly, our method is able to disentangle maternally inherited effects from prenatal effects, which are confounded in traditional family studies. Our analyses also provide guidance to researchers designing studies that will use ART families to clarify genetic and environmental factors underlying traits.
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Affiliation(s)
- J J Zhou
- Department of Biomathematics, The University of California-Los Angeles, CA 90095, USA
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