1
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Hao J, Liu C, Gu Z, Yang X, Lan X, Guo X. Dysregulation of Wnt/β-catenin signaling contributes to intestinal inflammation through regulation of group 3 innate lymphoid cells. Nat Commun 2024; 15:2820. [PMID: 38561332 PMCID: PMC10985070 DOI: 10.1038/s41467-024-45616-1] [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: 06/14/2023] [Accepted: 01/30/2024] [Indexed: 04/04/2024] Open
Abstract
RORγt+ group 3 innate lymphoid cells (ILC3s) are essential for intestinal homeostasis. Dysregulation of ILC3s has been found in the gut of patients with inflammatory bowel disease and colorectal cancer, yet the specific mechanisms still require more investigation. Here we observe increased β-catenin in intestinal ILC3s from inflammatory bowel disease and colon cancer patients compared with healthy donors. In contrast to promoting RORγt expression in T cells, activation of Wnt/β-catenin signaling in ILC3s suppresses RORγt expression, inhibits its proliferation and function, and leads to a deficiency of ILC3s and subsequent intestinal inflammation in mice. Activated β-catenin and its interacting transcription factor, TCF-1, cannot directly suppress RORγt expression, but rather alters global chromatin accessibility and inhibits JunB expression, which is essential for RORγt expression in ILC3s. Together, our findings suggest that dysregulated Wnt/β-catenin signaling impairs intestinal ILC3s through TCF-1/JunB/RORγt regulation, further disrupting intestinal homeostasis, and promoting inflammation and cancer.
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Affiliation(s)
- Jiacheng Hao
- Institute for Immunology, Tsinghua University, 100084, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
- Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, 100084, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Chang Liu
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Zhijie Gu
- Institute for Immunology, Tsinghua University, 100084, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
- Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, 100084, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xuanming Yang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, 200240, Shanghai, China
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Xun Lan
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohuan Guo
- Institute for Immunology, Tsinghua University, 100084, Beijing, China.
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China.
- Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, 100084, Beijing, China.
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2
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Yang Z, Li X, Sheng L, Zhu M, Lan X, Gu F. Multiomics-integrated deep language model enables in silico genome-wide detection of transcription factor binding site in unexplored biosamples. Bioinformatics 2024; 40:btae013. [PMID: 38216534 PMCID: PMC10812877 DOI: 10.1093/bioinformatics/btae013] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/07/2023] [Accepted: 01/11/2024] [Indexed: 01/14/2024] Open
Abstract
MOTIVATION Transcription factor binding sites (TFBS) are regulatory elements that have significant impact on transcription regulation and cell fate determination. Canonical motifs, biological experiments, and computational methods have made it possible to discover TFBS. However, most existing in silico TFBS prediction models are solely DNA-based, and are trained and utilized within the same biosample, which fail to infer TFBS in experimentally unexplored biosamples. RESULTS Here, we propose TFBS prediction by modified TransFormer (TFTF), a multimodal deep language architecture which integrates multiomics information in epigenetic studies. In comparison to existing computational techniques, TFTF has state-of-the-art accuracy, and is also the first approach to accurately perform genome-wide detection for cell-type and species-specific TFBS in experimentally unexplored biosamples. Compared to peak calling methods, TFTF consistently discovers true TFBS in threshold tuning-free way, with higher recalled rates. The underlying mechanism of TFTF reveals greater attention to the targeted TF's motif region in TFBS, and general attention to the entire peak region in non-TFBS. TFTF can benefit from the integration of broader and more diverse data for improvement and can be applied to multiple epigenetic scenarios. AVAILABILITY AND IMPLEMENTATION We provide a web server (https://tftf.ibreed.cn/) for users to utilize TFTF model. Users can train TFTF model and discover TFBS with their own data.
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Affiliation(s)
- Zikun Yang
- Damo Academy, Alibaba Group, Hangzhou 310023, China
- Hupan Lab, Hangzhou 310023, China
| | - Xin Li
- Damo Academy, Alibaba Group, Hangzhou 310023, China
- Hupan Lab, Hangzhou 310023, China
| | - Lele Sheng
- Damo Academy, Alibaba Group, Hangzhou 310023, China
- Hupan Lab, Hangzhou 310023, China
| | - Ming Zhu
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
| | - Xun Lan
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
| | - Fei Gu
- Damo Academy, Alibaba Group, Hangzhou 310023, China
- Hupan Lab, Hangzhou 310023, China
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3
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Zheng Y, Jiang H, Yang N, Shen S, Huang D, Jia L, Ling J, Xu L, Li M, Yu K, Ren X, Cui Y, Lan X, Lin S, Lin X. Glioma-derived ANXA1 suppresses the immune response to TLR3 ligands by promoting an anti-inflammatory tumor microenvironment. Cell Mol Immunol 2024; 21:47-59. [PMID: 38049523 PMCID: PMC10757715 DOI: 10.1038/s41423-023-01110-0] [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: 04/01/2023] [Accepted: 11/07/2023] [Indexed: 12/06/2023] Open
Abstract
A highly immunosuppressive tumor microenvironment (TME) and the presence of the blood‒brain barrier are the two major obstacles to eliciting an effective immune response in patients with high-grade glioma (HGG). Here, we tried to enhance the local innate immune response in relapsed HGG by intracranially injecting poly(I:C) to establish a robust antitumor immune response in this registered clinical trial (NCT03392545). During the follow-up, 12/27 (44.4%) patients who achieved tumor control concomitant with survival benefit were regarded as responders in our study. We found that the T-cell receptor (TCR) repertoire in the TME was reshaped after poly(I:C) treatment. Based on the RNA-seq analysis of tumor samples, the expression of annexin A1 (ANXA1) was significantly upregulated in the tumor cells of nonresponders, which was further validated at the protein level. In vitro and in vivo experiments showed that ANXA1 could induce the production of M2-like macrophages and microglia via its surface receptor formyl peptide receptor 1 (FPR1) to establish a Treg cell-driven immunosuppressive TME and suppress the antitumor immune response facilitated by poly(I:C). The ANXA1/FPR1 signaling axis can inhibit the innate immune response of glioma patients by promoting an anti-inflammatory and Treg-driven TME. Moreover, ANXA1 could serve as a reliable predictor of response to poly(I:C), with a notable predictive accuracy rate of 92.3%. In light of these notable findings, this study unveils a new perspective of immunotherapy for gliomas.
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Affiliation(s)
- Yu Zheng
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Haihui Jiang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China. National Clinical Research Center for Neurological Diseases, Center of Brain Tumor, Beijing Institute for Brain Disorders and Beijing Key Laboratory of Brain Tumor, Beijing, 100070, China
- Department of Neurosurgery, Peking University Third Hospital, Peking University, Beijing, 100191, China
| | - Naixue Yang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Shaoping Shen
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China. National Clinical Research Center for Neurological Diseases, Center of Brain Tumor, Beijing Institute for Brain Disorders and Beijing Key Laboratory of Brain Tumor, Beijing, 100070, China
| | - Daosheng Huang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Lemei Jia
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Jing Ling
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Longchen Xu
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Mingxiao Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China. National Clinical Research Center for Neurological Diseases, Center of Brain Tumor, Beijing Institute for Brain Disorders and Beijing Key Laboratory of Brain Tumor, Beijing, 100070, China
| | - Kefu Yu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China. National Clinical Research Center for Neurological Diseases, Center of Brain Tumor, Beijing Institute for Brain Disorders and Beijing Key Laboratory of Brain Tumor, Beijing, 100070, China
| | - Xiaohui Ren
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China. National Clinical Research Center for Neurological Diseases, Center of Brain Tumor, Beijing Institute for Brain Disorders and Beijing Key Laboratory of Brain Tumor, Beijing, 100070, China
| | - Yong Cui
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China. National Clinical Research Center for Neurological Diseases, Center of Brain Tumor, Beijing Institute for Brain Disorders and Beijing Key Laboratory of Brain Tumor, Beijing, 100070, China
| | - Xun Lan
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Song Lin
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China. National Clinical Research Center for Neurological Diseases, Center of Brain Tumor, Beijing Institute for Brain Disorders and Beijing Key Laboratory of Brain Tumor, Beijing, 100070, China.
| | - Xin Lin
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
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4
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Liu X, Liu X, Du Y, Zou D, Tian C, Li Y, Lan X, David CJ, Sun Q, Chen M. Aberrant accumulation of Kras-dependent pervasive transcripts during tumor progression renders cancer cells dependent on PAF1 expression. Cell Rep 2023; 42:112979. [PMID: 37572321 DOI: 10.1016/j.celrep.2023.112979] [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: 01/04/2023] [Revised: 06/05/2023] [Accepted: 07/31/2023] [Indexed: 08/14/2023] Open
Abstract
KRAS is the most commonly mutated oncogene in human cancer, and mutant KRAS is responsible for over 90% of pancreatic ductal adenocarcinoma (PDAC), the most lethal cancer. Here, we show that RNA polymerase II-associated factor 1 complex (PAF1C) is specifically required for survival of PDAC but not normal adult pancreatic cells. We show that PAF1C maintains cancer cell genomic stability by restraining overaccumulation of enhancer RNAs (eRNAs) and promoter upstream transcripts (PROMPTs) driven by mutant Kras. Loss of PAF1C leads to cancer-specific lengthening and accumulation of pervasive transcripts on chromatin and concomitant aberrant R-loop formation and DNA damage, which, in turn, trigger cell death. We go on to demonstrate that the global transcriptional hyperactivation driven by Kras signaling during tumorigenesis underlies the specific demand for PAF1C by cancer cells. Our work provides insights into how enhancer transcription hyperactivation causes general transcription factor addiction during tumorigenesis.
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Affiliation(s)
- Xinhong Liu
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiangzheng Liu
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yingxue Du
- Tsinghua University School of Life Sciences, Beijing 100084, China
| | - Di Zou
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chen Tian
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yong Li
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xun Lan
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Charles J David
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Qianwen Sun
- Tsinghua University School of Life Sciences, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Mo Chen
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China.
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5
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Li J, Lan X. Perspective on new cell-free DNA technologies for early cancer detection. Cancer Biol Med 2023; 21:j.issn.2095-3941.2023.0159. [PMID: 37553805 PMCID: PMC10884532 DOI: 10.20892/j.issn.2095-3941.2023.0159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/14/2023] [Indexed: 08/10/2023] Open
Affiliation(s)
- Jie Li
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
| | - Xun Lan
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
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6
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Zhao M, Qin W, Zhang S, Qi F, Li X, Lan X. Assessing the construction of a Healthy City in China: a conceptual framework and evaluation index system. Public Health 2023; 220:88-95. [PMID: 37285608 DOI: 10.1016/j.puhe.2023.04.020] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/05/2023] [Accepted: 04/21/2023] [Indexed: 06/09/2023]
Abstract
OBJECTIVES COVID-19 has brought challenges to the health of all mankind. It is particularly important to promote the construction of a 'Healthy China' and build a 'healthy community'. The aims of this study were to construct a reasonable conceptual framework for the Healthy City concept and to assess Healthy City construction in China. STUDY DESIGN This study combined qualitative and quantitative research. METHODS This study proposes the concept model of 'nature-human body-Healthy City' and accordingly constructs an evaluation index system for the construction of a Healthy City that integrates five dimensions, namely, the medical level, economic basis, cultural development, social services, and ecological environment to explore the spatial and temporal heterogeneity of Healthy City construction in China. Finally, the influencing factors of Healthy City construction patterns are explored using GeoDetector. RESULTS (1) The pace of Healthy City construction is generally on the rise; (2) the construction of Healthy Cities exhibits significant global spatial autocorrelation and gradually increasing agglomeration. The spatial distribution of cold hotspot areas was relatively stable; (3) medical and health progress is an important factor; the level of economic development is the leading support; the endowment of resources and environment is the basic condition; public service support provides important support; and scientific and technological innovation capabilities provide technical support for the construction of a Healthy City. CONCLUSIONS The spatial heterogeneity of Healthy City construction in China is evident, and the state of spatial distribution is relatively stable. The spatial pattern of Healthy City construction is shaped by a combination of factors. Our research will provide a scientific basis for promoting the construction of Healthy Cities and helping to implement the Health China Strategy.
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Affiliation(s)
- M Zhao
- School of Resources and Environmental Engineering, Ludong University, Yantai, 264025, PR China
| | - W Qin
- School of Resources and Environmental Engineering, Ludong University, Yantai, 264025, PR China.
| | - S Zhang
- School of Resources and Environmental Engineering, Ludong University, Yantai, 264025, PR China
| | - F Qi
- School of Resources and Environmental Engineering, Ludong University, Yantai, 264025, PR China
| | - X Li
- School of Resources and Environmental Engineering, Ludong University, Yantai, 264025, PR China
| | - X Lan
- School of Resources and Environmental Engineering, Ludong University, Yantai, 264025, PR China
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7
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Li J, Sun X, Yang H, Chen J, Bu Z, Ji J, Lan X. Integrated analysis toolkit for dissecting whole-genome-wide features of cell-free DNA. Clin Transl Med 2023; 13:e1212. [PMID: 36855790 PMCID: PMC9975452 DOI: 10.1002/ctm2.1212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/13/2023] [Accepted: 02/19/2023] [Indexed: 03/02/2023] Open
Affiliation(s)
- Jie Li
- Department of Basic Medical SciencesSchool of Medicine, Tsinghua UniversityBeijingChina
- MOE Key Laboratory of BioinformaticsTsinghua UniversityBeijingChina
| | - Xin Sun
- Department of Basic Medical SciencesSchool of Medicine, Tsinghua UniversityBeijingChina
- Peking‐Tsinghua‐NIBS Joint Graduate ProgramTsinghua UniversityBeijingChina
- MOE Key Laboratory of BioinformaticsTsinghua UniversityBeijingChina
| | - Heli Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Center of Gastrointestinal Cancer, Peking University Cancer Hospital & InstituteBeijingChina
| | - Jiahui Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Center of Gastrointestinal Cancer, Peking University Cancer Hospital & InstituteBeijingChina
| | - Zhaode Bu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Center of Gastrointestinal Cancer, Peking University Cancer Hospital & InstituteBeijingChina
- Center of Gastrointestinal CancerPeking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian DistrictBeijingChina
| | - Jiafu Ji
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Center of Gastrointestinal Cancer, Peking University Cancer Hospital & InstituteBeijingChina
- Center of Gastrointestinal CancerPeking University Cancer Hospital & Institute, No. 52 Fucheng Road, Haidian DistrictBeijingChina
| | - Xun Lan
- Department of Basic Medical SciencesSchool of Medicine, Tsinghua UniversityBeijingChina
- Tsinghua‐Peking Joint Center for Life SciencesTsinghua UniversityBeijingChina
- MOE Key Laboratory of BioinformaticsTsinghua UniversityBeijingChina
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8
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Chen H, Wang X, Lan X, Yu T, Li L, Tang S, Liu S, Jiang F, Wang L, Zhang J. A radiomics model development via the associations with genomics features in predicting axillary lymph node metastasis of breast cancer: a study based on a public database and single-centre verification. Clin Radiol 2023; 78:e279-e287. [PMID: 36623978 DOI: 10.1016/j.crad.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/17/2022] [Accepted: 11/29/2022] [Indexed: 12/27/2022]
Abstract
AIM To evaluate the predictive performance of the radiomics model in predicting axillary lymph node (ALN) metastasis through the associations between radiomics features and genomic features in patients with breast cancer. MATERIALS AND METHODS Patients with breast cancer were enrolled retrospectively from a public database (111 patients as training group) and one hospital (15 patients as external validation group). The genomics features from transcriptome data and radiomics features from dynamic contrast-enhanced magnetic resonance imaging (MRI) were collected. Firstly, overlapping genes were identified using the Kyoto Encyclopedia of Genes and Genomes and differentially expressed gene analysis, while radiomics features were reduced using a data-driven method. Then, the associations between overlapping genes and retained radiomics features were assessed to obtain key pairs of radiomics-genomics features. Furthermore, the least absolute shrinkage and selection operator (LASSO) algorithm was used to detect the key-pairs features. Finally, radiomics and genomics models were constructed to predict ALN metastasis. RESULTS After using the hybrid data- and gene-driven selection method, key pairs of features were detected, which consisted of six radiomic features associated with four genomic features. The radiomics model exhibited comparable performance to the genomics model in predicting ALN metastasis (radiomic model: area under the curve [AUC] = 0.71, sensitivity = 77%, specificity = 56%; genomic model: AUC = 0.72, sensitivity = 85%, specificity = 74%). The four genomic features were enriched in six pathways and related to metabolism and human diseases. CONCLUSION The radiomics model established using the gene-driven hybrid selection method could predict ALN metastasis in breast cancer, which showed comparable performance to the genomics model.
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Affiliation(s)
- H Chen
- Department of Radiology, Chongqing University Cancer Hospital, Chongqing, PR China
| | - X Wang
- Department of Radiology, Chongqing University Cancer Hospital, Chongqing, PR China
| | - X Lan
- Department of Radiology, Chongqing University Cancer Hospital, Chongqing, PR China
| | - T Yu
- Department of Radiology, Chongqing University Cancer Hospital, Chongqing, PR China
| | - L Li
- Department of Radiology, Chongqing University Cancer Hospital, Chongqing, PR China
| | - S Tang
- Department of Radiology, Chongqing University Cancer Hospital, Chongqing, PR China
| | - S Liu
- Department of Radiology, Chongqing University Cancer Hospital, Chongqing, PR China
| | - F Jiang
- Department of Radiology, Chongqing University Cancer Hospital, Chongqing, PR China
| | - L Wang
- Department of Radiology, Chongqing University Cancer Hospital, Chongqing, PR China
| | - J Zhang
- Department of Radiology, Chongqing University Cancer Hospital, Chongqing, PR China.
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9
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Ji F, Chen L, Chen Z, Luo B, Wang Y, Lan X. TCR repertoire and transcriptional signatures of circulating tumour-associated T cells facilitate effective non-invasive cancer detection. Clin Transl Med 2022; 12:e853. [PMID: 36134717 PMCID: PMC9494610 DOI: 10.1002/ctm2.853] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/11/2022] [Accepted: 04/15/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Fansen Ji
- Tsinghua-Peking Center for Life Sciences, MOE Key Laboratory of Tsinghua University, Beijing, China.,School of Medicine, Tsinghua University, Beijing, China
| | - Lin Chen
- School of Medicine, Tsinghua University, Beijing, China.,General Surgery Department, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Zhizhuo Chen
- School of Life Science, Tsinghua University, Beijing, China
| | - Bin Luo
- General Surgery Department, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Yongwang Wang
- Department of Anesthesiology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xun Lan
- Tsinghua-Peking Center for Life Sciences, MOE Key Laboratory of Tsinghua University, Beijing, China.,School of Medicine, Tsinghua University, Beijing, China
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10
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Sun K, Xu R, Ma F, Yang N, Li Y, Sun X, Jin P, Kang W, Jia L, Xiong J, Hu H, Tian Y, Lan X. scRNA-seq of gastric tumor shows complex intercellular interaction with an alternative T cell exhaustion trajectory. Nat Commun 2022; 13:4943. [PMID: 35999201 PMCID: PMC9399107 DOI: 10.1038/s41467-022-32627-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [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: 03/29/2021] [Accepted: 08/10/2022] [Indexed: 11/15/2022] Open
Abstract
The tumor microenvironment (TME) in gastric cancer (GC) has been shown to be important for tumor control but the specific characteristics for GC are not fully appreciated. We generated an atlas of 166,533 cells from 10 GC patients with matched paratumor tissues and blood. Our results show tumor-associated stromal cells (TASCs) have upregulated activity of Wnt signaling and angiogenesis, and are negatively correlated with survival. Tumor-associated macrophages and LAMP3+ DCs are involved in mediating T cell activity and form intercellular interaction hubs with TASCs. Clonotype and trajectory analysis demonstrates that Tc17 (IL-17+CD8+ T cells) originate from tissue-resident memory T cells and can subsequently differentiate into exhausted T cells, suggesting an alternative pathway for T cell exhaustion. Our results indicate that IL17+ cells may promote tumor progression through IL17, IL22, and IL26 signaling, highlighting the possibility of targeting IL17+ cells and associated signaling pathways as a therapeutic strategy to treat GC. Gastric cancer can vary in tumour stage and immune cell involvement. Here the authors compare gene expression in immune cell types from the blood and the tumour site from GC patients using single cell and TCR sequencing and show that IL17+CD8+ T cells have a phenotype related to that seen with exhausted cells.
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Affiliation(s)
- Keyong Sun
- School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Runda Xu
- School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Fuhai Ma
- Department of Pancreatic and Gastric Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, 100021, Beijing, China.,Department of General Surgery, Department of Gastrointestinal Surgery, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, 100730, Beijing, China
| | - Naixue Yang
- School of Medicine, Tsinghua University, 100084, Beijing, China.,Peking-Tsinghua-NIBS Joint Graduate Program, Tsinghua University, 100084, Beijing, China
| | - Yang Li
- Department of Pancreatic and Gastric Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, 100021, Beijing, China
| | - Xiaofeng Sun
- School of Medicine, Tsinghua University, 100084, Beijing, China.,Centre for Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Peng Jin
- Department of Pancreatic and Gastric Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, 100021, Beijing, China
| | - Wenzhe Kang
- Department of Pancreatic and Gastric Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, 100021, Beijing, China
| | - Lemei Jia
- School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Jianping Xiong
- Department of Pancreatic and Gastric Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, 100021, Beijing, China
| | - Haitao Hu
- Department of Pancreatic and Gastric Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, 100021, Beijing, China
| | - Yantao Tian
- Department of Pancreatic and Gastric Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, 100021, Beijing, China.
| | - Xun Lan
- School of Medicine, Tsinghua University, 100084, Beijing, China. .,Peking-Tsinghua-NIBS Joint Graduate Program, Tsinghua University, 100084, Beijing, China. .,Centre for Life Sciences, Tsinghua University, 100084, Beijing, China. .,MOE Key Laboratory of Bioinformatics, Tsinghua University, 100084, Beijing, China.
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11
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Abstract
Personalized immunotherapy, such as cancer vaccine and TCR-T methods, demands rapid screening of TCR-pMHC interactions. While several screening approaches have been developed, their throughput is limited. Here, the Yeast Agglutination Mediated TCR antigen Discovery system (YAMTAD) was designed and demonstrated to allow fast and unbiased library-on-library screening of TCR-pMHC interactions. Our proof-of-principle study achieved high sensitivity and specificity in identifying antigens for a given TCR and identifying TCRs recognizing a given pMHC for modest library sizes. Finally, the enrichment of high-affinity TCR-pMHC interactions by YAMTAD in library-on-library screening was demonstrated. Given the high throughput (106–108 × 106–108 in theory) and simplicity (identifying TCR-pMHC interactions without purification of TCR and pMHC) of YAMTAD, this study provides a rapid but effective platform for TCR-pMHC interaction screening, with valuable applications in future personalized immunotherapy.
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Affiliation(s)
- Lihui Wang
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China.,MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Xun Lan
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing, China. .,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China. .,MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.
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12
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Meng J, Jiang YZ, Zhao S, Tao Y, Zhang T, Wang X, Zhang Y, Sun K, Yuan M, Chen J, Wei Y, Lan X, Chen M, David CJ, Chang Z, Guo X, Pan D, Chen M, Shao ZM, Kang Y, Zheng H. Tumor-derived Jagged1 promotes cancer progression through immune evasion. Cell Rep 2022; 38:110492. [PMID: 35263601 DOI: 10.1016/j.celrep.2022.110492] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 07/27/2021] [Revised: 12/09/2021] [Accepted: 02/14/2022] [Indexed: 12/13/2022] Open
Abstract
Immune checkpoint inhibitor (ICI) therapy is generating remarkable responses in individuals with cancer, but only a small portion of individuals with breast cancer respond well. Here we report that tumor-derived Jagged1 is a key regulator of the tumor immune microenvironment. Jagged1 promotes tumorigenesis in multiple spontaneous mammary tumor models. Through Jagged1-induced Notch activation, tumor cells increase expression and secretion of multiple cytokines to help recruit macrophages into the tumor microenvironment. Educated macrophages crosstalk with tumor-infiltrating T cells to inhibit T cell proliferation and tumoricidal activity. In individuals with triple-negative breast cancer, a high expression level of Jagged1 correlates with increased macrophage infiltration and decreased T cell activity. Co-administration of an ICI PD-1 antibody with a Notch inhibitor significantly inhibits tumor growth in breast cancer models. Our findings establish a distinct signaling cascade by which Jagged1 promotes adaptive immune evasion of tumor cells and provide several possible therapeutic targets.
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Affiliation(s)
- Jingjing Meng
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yi-Zhou Jiang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shen Zhao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuwei Tao
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Tengjiang Zhang
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xuxiang Wang
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yuan Zhang
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Keyong Sun
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Min Yuan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jin Chen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yong Wei
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Xun Lan
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Mo Chen
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Charles J David
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zhijie Chang
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaohuan Guo
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Deng Pan
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Meng Chen
- National Cancer Data Center, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhi-Ming Shao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Cancer Metabolism and Growth Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA; Ludwig Institute for Cancer Research, Princeton Branch, Princeton, NJ 08544, USA.
| | - Hanqiu Zheng
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
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13
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Cao C, Shou J, Sun Z, Zhou A, Lan X, Shang B, Jiang W, Guo L, Zheng S, Bi X. Phenotypical screening on metastatic PRCC-TFE3 fusion translocation renal cell carcinoma organoids reveals potential therapeutic agents. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)01205-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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14
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Luo Q, Yu Y, Lan X. SIGNET: single-cell RNA-seq-based gene regulatory network prediction using multiple-layer perceptron bagging. Brief Bioinform 2022; 23:bbab547. [PMID: 34962260 PMCID: PMC8769917 DOI: 10.1093/bib/bbab547] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 10/01/2021] [Revised: 11/13/2021] [Accepted: 11/25/2021] [Indexed: 11/17/2022] Open
Abstract
High-throughput single-cell RNA-seq data have provided unprecedented opportunities for deciphering the regulatory interactions among genes. However, such interactions are complex and often nonlinear or nonmonotonic, which makes their inference using linear models challenging. We present SIGNET, a deep learning-based framework for capturing complex regulatory relationships between genes under the assumption that the expression levels of transcription factors participating in gene regulation are strong predictors of the expression of their target genes. Evaluations based on a variety of real and simulated scRNA-seq datasets showed that SIGNET is more sensitive to ChIP-seq validated regulatory interactions in different types of cells, particularly rare cells. Therefore, this process is more effective for various downstream analyses, such as cell clustering and gene regulatory network inference. We demonstrated that SIGNET is a useful tool for identifying important regulatory modules driving various biological processes.
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Affiliation(s)
- Qinhuan Luo
- School of Medicine, Tsinghua University, Beijing, China
| | - Yongzhen Yu
- School of Medicine, Tsinghua University, Beijing, China
| | - Xun Lan
- School of Medicine,and the Tsinghua-Peking Center for Life science, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
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15
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Gao R, Zu W, Liu Y, Li J, Li Z, Wen Y, Wang H, Yuan J, Cheng L, Zhang S, Zhang Y, Zhang S, Liu W, Lan X, Liu L, Li F, Zhang Z. Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis. Virulence 2021; 12:1209-1226. [PMID: 34030593 PMCID: PMC8158041 DOI: 10.1080/21505594.2021.1911477] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/28/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C > T. Analyses of intra-host population diversity revealed that intra-host quasispecies' composition varies with time during the early onset of symptoms, which implicates viral evolution during infection. Network analysis of co-occurring SNPs revealed the most abundant non-synonymous SNP 22,638 in the S glycoprotein RBD region and 28,144 in the ORF8 region. Furthermore, SARS-CoV-2 variations differ in an individual's respiratory tissue (nose, throat, BALF, or sputum), suggesting independent compartmentalization of SARS-CoV-2 populations in patients. The positive selection analysis of the SARS-CoV-2 genome uncovered the positive selected amino acid G251V on ORF3a. Alternative allele frequency spectrum (AAFS) of all variants revealed that ORF8 could bear alternate alleles with high frequency. Overall, the results show the quasispecies' profile of SARS-CoV-2 in the respiratory tract in the first two months after the outbreak.
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Affiliation(s)
- Rongsui Gao
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Wenhong Zu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Yang Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Junhua Li
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Zeyao Li
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yanling Wen
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Haiyan Wang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Jing Yuan
- Department of Infectious Diseases, Shenzhen Third People’s Hospital, National Clinical Research Center for Infectious Disease, Shenzhen, Guangdong Province, China
| | - Lin Cheng
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Shengyuan Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Yu Zhang
- National Supercomputing Center in Shenzhen (Shenzhen Cloud Computing Center), Shenzhen, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center, Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Weilong Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Xun Lan
- Department of Basic Medical Sciences at School of Medicine, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Lei Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Feng Li
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
- Shenzhen Research Center for Communicable Disease Diagnosis and Treatment of Chinese Academy of Medical Science, Shenzhen, Guangdong Province, China
- Guangdong Key Laboratory for Anti-infection Drug Quality Evaluation, Shenzhen, Guangdong Province, China
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16
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Wang PP, Dong HL, Sun H, Pang XX, Cai CJ, Bai D, Li F, Yang MY, Lan X, Zeng G. [Association between dietary vitamin A intake and gestational diabetes mellitus in the first trimester]. Zhonghua Yu Fang Yi Xue Za Zhi 2021; 55:1293-1298. [PMID: 34749471 DOI: 10.3760/cma.j.cn112150-20201023-01305] [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] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the relationship between dietary vitamin A intake and its sources in the first trimester and gestational diabetes mellitus (GDM). Methods: A prospective study was conducted to select women at 6-14 weeks of gestation in an obstetric clinic of a maternal and child health care medical institution in Chengdu in 2017. The types and quantities of food during the first trimester were collected by 3-day 24-hour dietary recalls. Dietary vitamin A intake was calculated based on the Chinese Food Composition Table (2018), and it was divided into animal and plant vitamin A intakes according to its food sources. An oral glucose tolerance test was performed at 24-28 weeks of gestation to diagnose GDM according to the Chinese guidelines for diagnosis and treatment of gestational diabetes mellitus (2014). According to the estimated average requirement (EAR) and recommended nutrient intake (RNI), dietary vitamin A intake was divided into low-level group (<EAR), medium-level group (EAR-RNI) and high-level group (>RNI). Animal and plant vitamin A intakes were divided into four groups (Q1-Q4) according to the quartile method, respectively. The association between dietary vitamin A intake, its different sources of vitamin A intake and GDM in the first trimester was analyzed by log-binomial regression models. Results: A total of 1 298 valid samples were finally included. The average dietary vitamin A intake, animal and plant vitamin A intakes in the first trimester were 341.1 (227.8-501.0) μgRAE/d, 139.3 (69.6-195.3) μgRAE/d and 184.2 (99.4-301.1) μgRAE/d, respectively. After adjusting for confounding factors, log-binomial regression analysis showed that the risk of GDM in high-level group of dietary vitamin A intake was lower than that in low-level group [RR (95%CI):0.53 (0.36-0.80)]. Pregnant women in the highest quartile of animal vitamin A intake had a lower risk of GDM than those in the lowest quartile [RR (95%CI):0.66 (0.47-0.95)]. No relationship between plant vitamin A intake and GDM was found. Conclusion: Dietary vitamin A intake in the first trimester is associated with the occurrence of GDM, and higher intake than RNI may reduce the risk of GDM. Higher vitamin A intake from animal-derived food is associated with decreased risk of GDM.
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Affiliation(s)
- P P Wang
- Department of Nutrition and Food Safety, West China School of Public Health/West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - H L Dong
- Department of Nutrition and Food Safety, West China School of Public Health/West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - H Sun
- Department of Nutrition and Food Safety, West China School of Public Health/West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - X X Pang
- Department of Nutrition and Food Safety, West China School of Public Health/West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - C J Cai
- Department of Nutrition and Food Safety, West China School of Public Health/West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - D Bai
- Department of Nutrition and Food Safety, West China School of Public Health/West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - F Li
- Department of Nutrition and Food Safety, West China School of Public Health/West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - M Y Yang
- Department of Nutrition and Food Safety, West China School of Public Health/West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - X Lan
- Department of Nutrition and Food Safety, West China School of Public Health/West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - G Zeng
- Department of Nutrition and Food Safety, West China School of Public Health/West China Fourth Hospital, Sichuan University, Chengdu 610041, China
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17
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Pang H, Jiang Y, Li J, Wang Y, Nie M, Xiao N, Wang S, Song Z, Ji F, Chang Y, Zheng Y, Yao K, Yao L, Li S, Li P, Song L, Lan X, Xu Z, Hu Z. Aberrant NAD + metabolism underlies Zika virus-induced microcephaly. Nat Metab 2021; 3:1109-1124. [PMID: 34385701 DOI: 10.1038/s42255-021-00437-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 07/07/2021] [Indexed: 12/18/2022]
Abstract
Zika virus (ZIKV) infection during pregnancy can cause microcephaly in newborns, yet the underlying mechanisms remain largely unexplored. Here, we reveal extensive and large-scale metabolic reprogramming events in ZIKV-infected mouse brains by performing a multi-omics study comprising transcriptomics, proteomics, phosphoproteomics and metabolomics approaches. Our proteomics and metabolomics analyses uncover dramatic alteration of nicotinamide adenine dinucleotide (NAD+)-related metabolic pathways, including oxidative phosphorylation, TCA cycle and tryptophan metabolism. Phosphoproteomics analysis indicates that MAPK and cyclic GMP-protein kinase G signaling may be associated with ZIKV-induced microcephaly. Notably, we demonstrate the utility of our rich multi-omics datasets with follow-up in vivo experiments, which confirm that boosting NAD+ by NAD+ or nicotinamide riboside supplementation alleviates cell death and increases cortex thickness in ZIKV-infected mouse brains. Nicotinamide riboside supplementation increases the brain and body weight as well as improves the survival in ZIKV-infected mice. Our study provides a comprehensive resource of biological data to support future investigations of ZIKV-induced microcephaly and demonstrates that metabolic alterations can be potentially exploited for developing therapeutic strategies.
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Affiliation(s)
- Huanhuan Pang
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Yisheng Jiang
- State Key Laboratory of Molecular Developmental Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Li
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Yushen Wang
- School of Life Sciences, Tsinghua University, Beijing, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (the PHOENIX Center), Beijing, China
| | - Meng Nie
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Nan Xiao
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Shuo Wang
- State Key Laboratory of Molecular Developmental Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhihong Song
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Fansen Ji
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Yafei Chang
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zheng
- State Key Laboratory of Molecular Developmental Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ke Yao
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - LiAng Yao
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Shao Li
- Institute of TCM-X, MOE Key Laboratory of Bioinformatics / Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, China
| | - Peng Li
- School of Life Sciences, Tsinghua University, Beijing, China
- Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
- Shanghai Qi Zhi Institute, Shanghai, China
| | - Lei Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (the PHOENIX Center), Beijing, China.
| | - Xun Lan
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China.
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Parkinson's Disease Center, Beijing Institute for Brain Disorders, Beijing, China.
| | - Zeping Hu
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.
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18
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Lan X, Basu S, Schwietzke S, Bruhwiler LMP, Dlugokencky EJ, Michel SE, Sherwood OA, Tans PP, Thoning K, Etiope G, Zhuang Q, Liu L, Oh Y, Miller JB, Pétron G, Vaughn BH, Crippa M. Improved Constraints on Global Methane Emissions and Sinks Using δ 13C-CH 4. Global Biogeochem Cycles 2021; 35:e2021GB007000. [PMID: 34219915 PMCID: PMC8244052 DOI: 10.1029/2021gb007000] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/14/2021] [Accepted: 05/03/2021] [Indexed: 06/13/2023]
Abstract
We study the drivers behind the global atmospheric methane (CH4) increase observed after 2006. Candidate emission and sink scenarios are constructed based on proposed hypotheses in the literature. These scenarios are simulated in the TM5 tracer transport model for 1984-2016 to produce three-dimensional fields of CH4 and δ 13C-CH4, which are compared with observations to test the competing hypotheses in the literature in one common model framework. We find that the fossil fuel (FF) CH4 emission trend from the Emissions Database for Global Atmospheric Research 4.3.2 inventory does not agree with observed δ 13C-CH4. Increased FF CH4 emissions are unlikely to be the dominant driver for the post-2006 global CH4 increase despite the possibility for a small FF emission increase. We also find that a significant decrease in the abundance of hydroxyl radicals (OH) cannot explain the post-2006 global CH4 increase since it does not track the observed decrease in global mean δ 13C-CH4. Different CH4 sinks have different fractionation factors for δ 13C-CH4, thus we can investigate the uncertainty introduced by the reaction of CH4 with tropospheric chlorine (Cl), a CH4 sink whose abundance, spatial distribution, and temporal changes remain uncertain. Our results show that including or excluding tropospheric Cl as a 13 Tg/year CH4 sink in our model changes the magnitude of estimated fossil emissions by ∼20%. We also found that by using different wetland emissions based on a static versus a dynamic wetland area map, the partitioning between FF and microbial sources differs by 20 Tg/year, ∼12% of estimated fossil emissions.
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Affiliation(s)
- X. Lan
- Cooperative Institute for Research in Environmental SciencesUniversity of Colorado BoulderBoulderCOUSA
- Global Monitoring LaboratoryNational Oceanic and Atmospheric AdministrationBoulderCOUSA
| | - S. Basu
- Earth System Science Interdisciplinary CenterUniversity of MarylandCollege ParkMDUSA
- Global Modeling and Assimilation OfficeNational Aeronautics and Space Administration Goddard Space Flight CenterGreenbeltMDUSA
| | - S. Schwietzke
- Cooperative Institute for Research in Environmental SciencesUniversity of Colorado BoulderBoulderCOUSA
- Environmental Defense FundBerlinGermany
| | - L. M. P. Bruhwiler
- Global Monitoring LaboratoryNational Oceanic and Atmospheric AdministrationBoulderCOUSA
| | - E. J. Dlugokencky
- Global Monitoring LaboratoryNational Oceanic and Atmospheric AdministrationBoulderCOUSA
| | - S. E. Michel
- Institute of Arctic and Alpine ResearchUniversity of Colorado BoulderBoulderCOUSA
| | - O. A. Sherwood
- Institute of Arctic and Alpine ResearchUniversity of Colorado BoulderBoulderCOUSA
- Department of Earth and Environmental SciencesDalhousie UniversityHalifaxNova ScotiaCanada
| | - P. P. Tans
- Global Monitoring LaboratoryNational Oceanic and Atmospheric AdministrationBoulderCOUSA
| | - K. Thoning
- Global Monitoring LaboratoryNational Oceanic and Atmospheric AdministrationBoulderCOUSA
| | - G. Etiope
- Istituto Nazionale di Geofisica e VulcanologiaRomeItaly
- Faculty of Environmental Science and EngineeringBabes Bolyai UniversityCluj-NapocaRomania
| | - Q. Zhuang
- Department of Earth, Atmospheric, and Planetary SciencesPurdue UniversityWest LafayetteINUSA
| | - L. Liu
- Department of Earth, Atmospheric, and Planetary SciencesPurdue UniversityWest LafayetteINUSA
| | - Y. Oh
- Global Monitoring LaboratoryNational Oceanic and Atmospheric AdministrationBoulderCOUSA
- Department of Earth, Atmospheric, and Planetary SciencesPurdue UniversityWest LafayetteINUSA
| | - J. B. Miller
- Global Monitoring LaboratoryNational Oceanic and Atmospheric AdministrationBoulderCOUSA
| | - G. Pétron
- Cooperative Institute for Research in Environmental SciencesUniversity of Colorado BoulderBoulderCOUSA
- Global Monitoring LaboratoryNational Oceanic and Atmospheric AdministrationBoulderCOUSA
| | - B. H. Vaughn
- Institute of Arctic and Alpine ResearchUniversity of Colorado BoulderBoulderCOUSA
| | - M. Crippa
- Joint Research CentreEuropean CommissionIspraItaly
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19
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Lu J, Wang X, Sun K, Lan X. Chrom-Lasso: a lasso regression-based model to detect functional interactions using Hi-C data. Brief Bioinform 2021; 22:6278150. [PMID: 34013331 PMCID: PMC8574949 DOI: 10.1093/bib/bbab181] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/13/2021] [Indexed: 01/02/2023] Open
Abstract
Hi-C is a genome-wide assay based on Chromosome Conformation Capture and high-throughput sequencing to decipher 3D chromatin organization in the nucleus. However, computational methods to detect functional interactions utilizing Hi-C data face challenges including the correction for various sources of biases and the identification of functional interactions with low counts of interacting fragments. We present Chrom-Lasso, a lasso linear regression model that removes complex biases assumption-free and identifies functional interacting loci with increased power by combining information of local reads distribution surrounding the area of interest. We showed that interacting regions identified by Chrom-Lasso are more enriched for 5C validated interactions and functional GWAS hits than that of GOTHiC and Fit-Hi-C. To further demonstrate the ability of Chrom-Lasso to detect interactions of functional importance, we performed time-series Hi-C and RNA-seq during T cell activation and exhaustion. We showed that the dynamic changes in gene expression and chromatin interactions identified by Chrom-Lasso were largely concordant with each other. Finally, we experimentally confirmed Chrom-Lasso’s finding that Erbb3 was co-regulated with distinct neighboring genes at different states during T cell activation. Our results highlight Chrom-Lasso’s utility in detecting weak functional interaction between cis-regulatory elements, such as promoters and enhancers.
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Affiliation(s)
- Jingzhe Lu
- School of Medicine, Tsinghua University, Beijing, China
| | - Xu Wang
- School of Medicine and the Tsinghua-Peking Center for Life science, Tsinghua University, Beijing, China
| | - Keyong Sun
- School of Medicine and the Tsinghua-Peking Center for Life science, Tsinghua University, Beijing, China
| | - Xun Lan
- School of Medicine and the Tsinghua-Peking Center for Life science, Tsinghua University, Beijing, China
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20
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Yang N, Ji F, Cheng L, Lu J, Sun X, Lin X, Lan X. Knockout of immunotherapy prognostic marker genes eliminates the effect of the anti-PD-1 treatment. NPJ Precis Oncol 2021; 5:37. [PMID: 33963274 PMCID: PMC8105367 DOI: 10.1038/s41698-021-00175-2] [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: 10/27/2020] [Accepted: 04/05/2021] [Indexed: 12/26/2022] Open
Abstract
The efficacy of immunotherapy is largely patient-specific due to heterogeneity in tumors. Combining statistic power from a variety of immunotherapies across cancer types, we found four biological pathways significantly correlated with patient survival following immunotherapy. The expression of immunotherapy prognostic marker genes (IPMGs) in these pathways can predict the patient survival with high accuracy not only in the TCGA cohort (89.36%) but also in two other independent cohorts (80.91%), highlighting that the activity of the IPMGs can reflect the sensitivity of the tumor immune microenvironment (TIME) to immunotherapies. Using mouse models, we show that knockout of one of the IPMGs, MALT1, which is critical for the T-cell receptor signaling, can eliminate the antitumor effect of anti-PD-1 treatment completely by impairing the activation of CD8+ T cells. Notably, knockout of another IPMG, CLEC4D, a C-type lectin receptor that expressed on myeloid cells, also reduced the effect of anti-PD-1 treatment potentially through maintaining the immunosuppressive effects of myeloid cells. Our results suggest that priming TIME via activating the IPMGs may increase the response rate and the effect of immune checkpoint blockers.
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Affiliation(s)
- Naixue Yang
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing, China.,Peking-Tsinghua-NIBS Joint Graduate Program, Tsinghua University, Beijing, China
| | - Fansen Ji
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Liqing Cheng
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Institute for Immunology, School of Medicine, Tsinghua University, Beijing, China
| | - Jingzhe Lu
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing, China
| | - Xiaofeng Sun
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xin Lin
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing, China. .,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China. .,Institute for Immunology, School of Medicine, Tsinghua University, Beijing, China.
| | - Xun Lan
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing, China. .,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.
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21
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Chen H, Liu N, Xu R, Chen X, Zhang Y, Hu R, Lan X, Tang Z, Lin G. Quantitative proteomics analysis reveals the response mechanism of peanut (Arachis hypogaea L.) to imbibitional chilling stress. Plant Biol (Stuttg) 2021; 23:517-527. [PMID: 33502082 DOI: 10.1111/plb.13238] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
Imbibitional chilling stress inhibits normal seed germination and seedling establishment and leads to large losses in peanut production. This is a major limiting factor when sowing peanut earlier and further north. To reveal the response mechanism of peanut to imbibitional chilling stress, a Tandem Mass Tag (TMT)-based quantitative proteomics analysis was conducted to identify differentially accumulated proteins (DAPs) under imbibitional chilling stress. Hormone profiling and transcriptional analysis were performed to confirm the proteomics data. Further seed priming analysis with exogenous cytokinins was conducted to validate the role of cytokinins in alleviating imbibitional chilling injury. A total of 5029 proteins were identified and quantified in all of the experimental groups. Among these, 104 proteins were DAPs as compared with the control. Enrichment analysis revealed that these DAPs were significant in various molecular functional and biological processes, especially for biosynthesis and metabolism of plant hormones. Hormone profiling and transcription analysis suggested that the reduced abundance of cytokinin oxidase may be caused by down-regulation of gene expression of the corresponding genes and leads to an elevated content of cytokinins under chilling stress. Seed priming analysis suggested that exogenous application of cytokinins may alleviate injury caused by imbibitional chilling. Our study provides a comprehensive proteomics analysis of peanut under imbibitional chilling stress, suggesting the role of plant hormones in the response mechanism. The results provide a better understanding of the imbibitional chilling stress response mechanism in peanut that will aid in peanut production.
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Affiliation(s)
- H Chen
- Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People's Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Fuzhou, China
| | - N Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People's Republic of China, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - R Xu
- Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People's Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Fuzhou, China
| | - X Chen
- Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People's Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Fuzhou, China
| | - Y Zhang
- Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People's Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Fuzhou, China
| | - R Hu
- Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People's Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Fuzhou, China
| | - X Lan
- Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People's Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Fuzhou, China
| | - Z Tang
- Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People's Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Fuzhou, China
| | - G Lin
- Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People's Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Fuzhou, China
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22
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Ma J, Gong S, He Y, Gao W, Hao W, Lan X. Effects of oral sialic acid on gut development, liver function and gut microbiota in mice. Lett Appl Microbiol 2021; 73:20-25. [PMID: 33386625 DOI: 10.1111/lam.13447] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 12/09/2020] [Revised: 12/27/2020] [Accepted: 12/28/2020] [Indexed: 12/27/2022]
Abstract
Sialic acid (N-acetylneuraminic acid), a 9-carbon monosaccharide, has been widely studied in immunology, oncology and neurology. However, the effects of sialic acid on organ and intestinal development, liver function and gut microbiota were rarely studied. In this study, we found that oral sialic acid tended to increase the relative weight of liver and decreased the serum aspartate aminotransferase (GPT) activity. In addition, sialic acid treatment markedly reduced gut villus length, depth, the ratio of villus length/depth (L/D), areas, width and the number of goblet cells. Furthermore, gut microbes were changed in response to oral sialic acid, such as Staphylococcus lentus, Corynebacterium stationis, Corynebacterium urealyticum, Jeotgalibaca sp_PTS2502, Ignatzschineria indica, Sporosarcina pasteurii, Sporosarcina sp_HW10C2, Facklamia tabacinasalis, Oblitimonas alkaliphila, Erysipelatoclostridium ramosum, Blautia sp_YL58, Bacteroids thetaiotaomicron, Morganella morganii, Clostridioides difficile, Helicobacter tryphlonius, Clostridium sp_Clone47, Alistipes finegoldii, [pseudomonas]_geniculata and Pseudomonas parafulva at the species level. In conclusion, oral sialic acid altered the intestinal pathological state and microbial compositions, and the effect of sialic acid on host health should be further studied.
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Affiliation(s)
- J Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - S Gong
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Y He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - W Gao
- Animal Husbandry and Aquatic Affairs Center of Shimen County, Changde, Hunan, China
| | - W Hao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - X Lan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
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23
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Zhang C, An H, Hu J, Li J, Zhang W, Lan X, Deng H, Zhang JR. MetR is a molecular adaptor for pneumococcal carriage in the healthy upper airway. Mol Microbiol 2021; 116:438-458. [PMID: 33811693 DOI: 10.1111/mmi.14724] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 11/26/2022]
Abstract
Streptococcus pneumoniae resides in the human upper airway as a commensal but also causes pneumonia, bacteremia, meningitis, and otitis media. It remains unclear how pneumococci adapt to nutritional conditions of various host niches. We here show that MetR, a LysR family transcriptional regulator, serves as a molecular adaptor for pneumococcal fitness, particularly in the upper airway. The metR mutant of strain D39 rapidly disappeared from the nasopharynx but was marginally attenuated in the lungs and bloodstream of mice. RNA-seq and ChIP-seq analyses showed that MetR broadly regulates transcription of the genes involved in methionine synthesis and other functions under methionine starvation. Genetic and biochemical analyses confirmed that MetR is essential for the activation of methionine synthesis but not uptake. Co-infection of influenza virus partially restored the colonization defect of the metR mutant. These results strongly suggest that MetR is particularly evolved for pneumococcal carriage in the upper airway of healthy individuals where free methionine is severely limited, but it becomes dispensable where environmental methionine is relatively more abundant (e.g., inflamed upper airway and sterile sites). To the best of our knowledge, MetR represents the first known regulator particularly for pneumococcal carriage in healthy individuals.
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Affiliation(s)
- Chengwang Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Haoran An
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Jiao Hu
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Jing Li
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Wenhao Zhang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xun Lan
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jing-Ren Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
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24
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Dai Y, Qiang W, Gui Y, Tan X, Pei T, Lin K, Cai S, Sun L, Ning G, Wang J, Guo H, Sun Y, Cheng J, Xie L, Lan X, Wang D. A large-scale transcriptional study reveals inhibition of COVID-19 related cytokine storm by traditional Chinese medicines. Sci Bull (Beijing) 2021; 66:884-888. [PMID: 33457042 PMCID: PMC7803147 DOI: 10.1016/j.scib.2021.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/25/2020] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Affiliation(s)
- Yifei Dai
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.,Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Weijie Qiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Yu Gui
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xue Tan
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tianli Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Kequan Lin
- High Performance Computing Department, National Supercomputing Center in Shenzhen, Shenzhen 518055, China
| | - Siwei Cai
- Department of Electronic and Computer Engineering, College of Engineering, Drexel University, Philadelphia 19104, USA
| | - Liang Sun
- Dongli District Jinqiao Street Community Health Service Center, Tianjin 300300, China
| | - Guochen Ning
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jianxun Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Hongyan Guo
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| | - Yimin Sun
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| | - Jing Cheng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.,National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China.,State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing 100084, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China.,Medical Systems Biology Research Center, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lan Xie
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China.,State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing 100084, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China.,Medical Systems Biology Research Center, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xun Lan
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Dong Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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25
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Tang Q, Zhang Y, Yang Y, Hu H, Lan X, Pan C. The KMT2A gene: mRNA differential expression in the ovary and a novel 13-nt nucleotide sequence variant associated with litter size in cashmere goats. Domest Anim Endocrinol 2021; 74:106538. [PMID: 32896800 DOI: 10.1016/j.domaniend.2020.106538] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 12/16/2022]
Abstract
A genome-wide association study had shown that lysine methyltransferase 2A (KMT2A), which encodes the histone 3 lysine 4 methyltransferase and reportedly can regulate gametogenesis, steroidogenesis, and development as well as other biological processes, is a potential candidate gene influencing litter size in the dairy goat, suggesting its key function in animal reproduction. Here, we aimed to explore the genetic effects of the KMT2A gene on litter size in females of the Chinese indigenous cashmere goat, using a large sample size (n > 1,000), based on their levels of RNA transcription and DNA variation. First, mRNA expression levels of this gene in ovarian tissues between the low-prolific group (first-born litter size = 1) and high-prolific group (first-born litter size ≥2) were significantly different, revealing the potential functioning of KMT2A in goat prolific. Moreover, a novel 13-nt nucleotide sequence variant was identified in Shaanbei white cashmere goats (n = 1,616). In accordance with the independent chi-square (χ2) analysis, the distribution of genotypes (P = 2.57 × 10-9) and allelotypes (P = 3.00 × 10-7) between the low- and high-prolific groups differed significantly, indicating the 13-nt mutation was associated with litter size. Further analysis showed that the insertion/insertion (II) genotype was significantly different with insertion/deletion (ID) (P = 1.76 × 10-9) and deletion/deletion (DD) (P = 7.00 × 10-6), with goats having the DD genotype producing an average litter size larger than the other genotypes. Taken together, these findings suggest KMT2A can serve as a candidate gene for breeding goats, which may have implications for improving the future development of the goat industry.
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Affiliation(s)
- Q Tang
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, No. 22 Xinong Road, Yangling, Shaanxi, 712100, PR China
| | - Y Zhang
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, No. 22 Xinong Road, Yangling, Shaanxi, 712100, PR China
| | - Y Yang
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, No. 22 Xinong Road, Yangling, Shaanxi, 712100, PR China
| | - H Hu
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, No. 22 Xinong Road, Yangling, Shaanxi, 712100, PR China
| | - X Lan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, No. 22 Xinong Road, Yangling, Shaanxi, 712100, PR China
| | - C Pan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, No. 22 Xinong Road, Yangling, Shaanxi, 712100, PR China.
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26
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Xu L, Zhang H, Xu H, Yang H, Zhang L, Zhang W, Gu F, Lan X. The coSIR model predicts effective strategies to limit the spread of SARS-CoV-2 variants with low severity and high transmissibility. Nonlinear Dyn 2021; 105:2757-2773. [PMID: 34334951 PMCID: PMC8300993 DOI: 10.1007/s11071-021-06705-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/04/2021] [Indexed: 05/05/2023]
Abstract
UNLABELLED Multiple new variants of SARS-CoV-2 have been identified as the COVID-19 pandemic spreads across the globe. However, most epidemic models view the virus as static and unchanging and thus fail to address the consequences of the potential evolution of the virus. Here, we built a competitive susceptible-infected-removed (coSIR) model to simulate the competition between virus strains of differing severities or transmissibility under various virus control policies. The coSIR model predicts that although the virus is extremely unlikely to evolve into a "super virus" that causes an increased fatality rate, virus variants with less severe symptoms can lead to potential new outbreaks and can cost more lives over time. The present model also demonstrates that the protocols restricting the transmission of the virus, such as wearing masks and social distancing, are the most effective strategy in reducing total mortality. A combination of adequate testing and strict quarantine is a powerful alternative to policies such as mandatory stay-at-home orders, which may have an enormous negative impact on the economy. In addition, building Mobile Cabin Hospitals can be effective and efficient in reducing the mortality rate of highly infectious virus strains. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11071-021-06705-8.
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Affiliation(s)
- Longchen Xu
- School of Life Sciences, Tsinghua University, Beijing, 100084 China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Haohang Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084 China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Hengyi Xu
- Eight-Year MD Program, Peking Union Medical College, Beijing, 100084 China
| | - Han Yang
- DAMO, Alibaba Cloud Intelligence Business Group, Alibaba Group, Hangzhou, 310052 China
| | - Lei Zhang
- DAMO, Alibaba Cloud Intelligence Business Group, Alibaba Group, Hangzhou, 310052 China
| | - Wei Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084 China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Fei Gu
- DAMO, Alibaba Cloud Intelligence Business Group, Alibaba Group, Hangzhou, 310052 China
| | - Xun Lan
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084 China
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing, 100084 China
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084 China
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27
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Li Y, He Y, Peng J, Su Z, Li Z, Zhang B, Ma J, Zhuo M, Zou D, Liu X, Liu X, Wang W, Huang D, Xu M, Wang J, Deng H, Xue J, Xie W, Lan X, Chen M, Zhao Y, Wu W, David CJ. Mutant Kras co-opts a proto-oncogenic enhancer network in inflammation-induced metaplastic progenitor cells to initiate pancreatic cancer. Nat Cancer 2021; 2:49-65. [PMID: 35121887 DOI: 10.1038/s43018-020-00134-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/29/2020] [Indexed: 02/07/2023]
Abstract
Kras-activating mutations display the highest incidence in pancreatic ductal adenocarcinoma. Pancreatic inflammation accelerates mutant Kras-driven tumorigenesis in mice, suggesting high selectivity in the cells that oncogenic Kras transforms, although the mechanisms dictating this specificity are poorly understood. Here we show that pancreatic inflammation is coupled to the emergence of a transient progenitor cell population that is readily transformed in the presence of mutant KrasG12D. These progenitors harbor a proto-oncogenic transcriptional program driven by a transient enhancer network. KrasG12D mutations lock this enhancer network in place, providing a sustained Kras-dependent oncogenic program that drives tumors throughout progression. Enhancer co-option occurs through functional interactions between the Kras-activated transcription factors Junb and Fosl1 and pancreatic lineage transcription factors, potentially accounting for inter-tissue specificity of oncogene transformation. The pancreatic ductal adenocarcinoma cell of origin thus provides an oncogenic transcriptional program that fuels tumor progression beyond initiation, accounting for the intra-tissue selectivity of Kras transformation.
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Affiliation(s)
- Yong Li
- Tsinghua University School of Medicine, Beijing, China
| | - Yi He
- Tsinghua University School of Medicine, Beijing, China
| | - Junya Peng
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Zhendong Su
- Tsinghua University School of Medicine, Beijing, China
- Peking University-Tsinghua Center for Life Sciences, Beijing, China
| | - Zeyao Li
- Tsinghua University School of Life Sciences, Beijing, China
| | - Bingjie Zhang
- Tsinghua University School of Life Sciences, Beijing, China
| | - Jing Ma
- Tsinghua University School of Life Sciences, Beijing, China
| | - Meilian Zhuo
- Tsinghua University School of Medicine, Beijing, China
| | - Di Zou
- Tsinghua University School of Medicine, Beijing, China
| | - Xinde Liu
- Tsinghua University School of Medicine, Beijing, China
| | - Xinhong Liu
- Tsinghua University School of Medicine, Beijing, China
| | - Wenze Wang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Dan Huang
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Mengyue Xu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Jianbin Wang
- Tsinghua University School of Medicine, Beijing, China
- Peking University-Tsinghua Center for Life Sciences, Beijing, China
| | - Haiteng Deng
- Tsinghua University School of Life Sciences, Beijing, China
| | - Jing Xue
- State Key Laboratory of Oncogenes and Related Genes, Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Xie
- Peking University-Tsinghua Center for Life Sciences, Beijing, China
- Tsinghua University School of Life Sciences, Beijing, China
| | - Xun Lan
- Tsinghua University School of Medicine, Beijing, China
- Peking University-Tsinghua Center for Life Sciences, Beijing, China
| | - Mo Chen
- Tsinghua University School of Medicine, Beijing, China
| | - Yupei Zhao
- Peking University-Tsinghua Center for Life Sciences, Beijing, China.
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China.
| | - Wenming Wu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China.
| | - Charles J David
- Tsinghua University School of Medicine, Beijing, China.
- Peking University-Tsinghua Center for Life Sciences, Beijing, China.
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Tian C, Liu L, Zheng M, Ye Z, Chen R, Lan X. MiR-503 Contributes to Glucocorticoid Sensitivity in Acute Lymphoblastic Leukaemia via Targeting WNT3A. Folia Biol (Praha) 2021; 67:199-207. [PMID: 35439853] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Abnormal accumulation of lymphoblasts in the blood and bone marrow is the main characteristic of acute lymphoblastic leukaemia (ALL). Glucocorticoids are effective drugs for ALL, while glucocorticoid resistance is an obstacle to ALL therapy. MicroRNAs (miRNAs) are implicated in the drug resistance and modulate the response of ALL to glucocorticoids. The role of miR-503 in glucocorticoid sensitivity of ALL was investigated in this study. Firstly, T-leukaemic cells were isolated from patients with ALL. The human ALL cell line (CCRF/CEM) was incubated with dexamethasone to establish a glucocorticoid- resistant ALL cell line (CCRF/CEM-R). Data from MTT showed that IC50 (50% inhibitory concentration) of dexamethasone in T-leukaemic cells isolated from glucocorticoid-resistant ALL patients or CCRF/CEM-R was increased compared with IC50 in T-leukaemic cells isolated from glucocorticoid- sensitive ALL patients or CCRF/CEM. MiR- 503 was down-regulated in glucocorticoid-resistant leukaemic cells and CCRF/CEM-R. Secondly, overexpression of miR-503 sensitized CCRF/CEM-R to dexamethasone. Moreover, over-expression of miR- 503 also promoted the sensitivity of ALL cells to dexamethasone. Thirdly, miR-503 bound to WNT3A mRNA and negatively regulated the expression of WNT3A. Over-expression of miR-503 reduced protein expression of nuclear β-catenin, and over-expression of WNT3A attenuated the miR-503 overexpression- induced decrease in nuclear β-catenin. Lastly, the over-expression of miR-503-induced increased sensitivity of ALL-resistant cells and CCRF/ CEM-R to dexamethasone was attenuated by overexpression of WNT3A. In conclusion, miR-503 targeted WNT3A mRNA to sensitize ALL cells to glucocorticoids through inactivation of the Wnt/β-catenin pathway.
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Affiliation(s)
- C Tian
- Department of Paediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, China
| | - L Liu
- Department of Paediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, China
| | - M Zheng
- Department of Obstetrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, China
| | - Z Ye
- Department of Paediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, China
| | - R Chen
- Department of Paediatrics, Shunde Women's and Children's Hospital of Guangdong Medical University, Foshan, Guangdong Province, China
| | - X Lan
- Department of Paediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, China
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Li J, Xu M, Peng J, Wang J, Zhao Y, Wu W, Lan X. Novel technologies in cfDNA analysis and potential utility in clinic. Chin J Cancer Res 2021; 33:708-718. [PMID: 35125814 PMCID: PMC8742177 DOI: 10.21147/j.issn.1000-9604.2021.06.07] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/05/2021] [Indexed: 12/05/2022] Open
Abstract
The profiling of plasma cell-free DNA (cfDNA) is becoming a valuable tool rapidly for tumor diagnosis, monitoring and prognosis. Diverse plasma cfDNA technologies have been in routine or emerging use, including analyses of mutations, copy number alterations, gene fusions and DNA methylation. Recently, new technologies in cfDNA analysis have been developed in laboratories, and potentially reflect the status of epigenetic modification, the immune microenvironment and the microbiome in tumor tissues. In this review, the authors discuss the principles, methods and effects of the current cfDNA assays and provide an overview of studies that may inform clinical applications in the near future.
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Affiliation(s)
- Jie Li
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Mengyue Xu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Junya Peng
- Department of Medical Research, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Jingqiao Wang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Yupei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Department of State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
- Yupei Zhao. Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China.
| | - Wenming Wu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
- Department of State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China
- Wenming Wu. Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China.
| | - Xun Lan
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Xun Lan. Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
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30
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Huang X, Wang J, Li J, Liu Y, Liu X, Li Z, Kurniyati K, Deng Y, Wang G, Ralph JD, De Ste Croix M, Escobar-Gonzalez S, Roberts RJ, Veening JW, Lan X, Oggioni MR, Li C, Zhang JR. Prevalence of phase variable epigenetic invertons among host-associated bacteria. Nucleic Acids Res 2020; 48:11468-11485. [PMID: 33119758 PMCID: PMC7672463 DOI: 10.1093/nar/gkaa907] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 05/08/2020] [Revised: 09/28/2020] [Accepted: 10/23/2020] [Indexed: 12/14/2022] Open
Abstract
Type I restriction-modification (R-M) systems consist of a DNA endonuclease (HsdR, HsdM and HsdS subunits) and methyltransferase (HsdM and HsdS subunits). The hsdS sequences flanked by inverted repeats (referred to as epigenetic invertons) in certain Type I R-M systems undergo invertase-catalyzed inversions. Previous studies in Streptococcus pneumoniae have shown that hsdS inversions within clonal populations produce subpopulations with profound differences in the methylome, cellular physiology and virulence. In this study, we bioinformatically identified six major clades of the tyrosine and serine family invertases homologs from 16 bacterial phyla, which potentially catalyze hsdS inversions in the epigenetic invertons. In particular, the epigenetic invertons are highly enriched in host-associated bacteria. We further verified hsdS inversions in the Type I R-M systems of four representative host-associated bacteria and found that each of the resultant hsdS allelic variants specifies methylation of a unique DNA sequence. In addition, transcriptome analysis revealed that hsdS allelic variations in Enterococcus faecalis exert significant impact on gene expression. These findings indicate that epigenetic switches driven by invertases in the epigenetic invertons broadly operate in the host-associated bacteria, which may broadly contribute to bacterial host adaptation and virulence beyond the role of the Type I R-M systems against phage infection.
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Affiliation(s)
- Xueting Huang
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Juanjuan Wang
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jing Li
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yanni Liu
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xue Liu
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, CH 1015, Switzerland
| | - Zeyao Li
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kurni Kurniyati
- Department of Oral and Craniofacial Molecular Biology, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Yijie Deng
- Department of Oral and Craniofacial Molecular Biology, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Guilin Wang
- W. M. Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT 06520, USA
| | - Joseph D Ralph
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Megan De Ste Croix
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Sara Escobar-Gonzalez
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | | | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, CH 1015, Switzerland
| | - Xun Lan
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Marco R Oggioni
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Chunhao Li
- Department of Oral and Craniofacial Molecular Biology, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jing-Ren Zhang
- Department of Basic Medical Science, School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
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31
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Lan X, Liu F, Ma J, Chang Y, Lan X, Xiang L, Shen X, Zhou F, Zhao Q. Leukocyte immunoglobulin-like receptor A3 is increased in IBD patients and functions as an anti-inflammatory modulator. Clin Exp Immunol 2020; 203:286-303. [PMID: 33006756 PMCID: PMC7806419 DOI: 10.1111/cei.13529] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/19/2022] Open
Abstract
Growing evidence shows that a homozygous 6·7-kb deletion of the novel anti-inflammatory molecule leukocyte immunoglobulin-like receptor A3 (LILRA3) is associated with many autoimmune disorders. However, its effects on pathogenesis of inflammatory bowel disease (IBD) have yet not been clarified. LILRA3 is mainly expressed in monocytes, whereas its effects on biological behaviors of monocytes have not been systematically reported. In our study, to investigate the association between LILRA3 polymorphism and IBD susceptibility, LILRA3 polymorphism was assessed in 378 IBD patients and 509 healthy controls. Quantitative real time PCR (qRT-PCR), Western blot and immunohistochemistry (IHC) were employed to detect the LILRA3 expression in IBD patient blood and intestinal samples. The human U937 monocyte cell line was employed to establish LILRA3 over-expressing cells and the effects of LILRA3 on the biological behaviors of U937 cells were systematically explored. Although no association of the polymorphism with IBD development was found, LILRA3 expression was markedly increased in IBD patients compared with healthy controls. Over-expression of LILRA3 in monocytes led to significant decreases in secretion of interferon (IFN)-γ, tumor necrosis factor (TNF)-α and interleukin (IL)-6. Additionally, LILRA3 abated monocyte migration by reducing the expression of several chemokines and enhanced monocyte phagocytosis by increasing CD36 expression. Furthermore, LILRA3 promoted monocyte proliferation through a combination of Akt and extracellular receptor kinase/mitogen-activated protein kinase (Erk/MEK) signaling pathways. We report for the first time, to our knowledge, that LILRA3 is related to IBD and functions as an anti-inflammatory modulator in U937 cells.
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Affiliation(s)
- X Lan
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - F Liu
- Department of Gastroenterology, Xuhui District Central Hospital, Shanghai, China
| | - J Ma
- Department of Health Related Product Evaluation, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Y Chang
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - X Lan
- Pathology department, National Shanghai Center for New Drug Safety Evaluation and Research, Shanghai, China
| | - L Xiang
- Department of Infectious Disease, Xiangxi Autonomous Prefecture People's Hospital, Xiangxi, China
| | - X Shen
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - F Zhou
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Q Zhao
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, China
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32
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Yang Z, Lan X, Huang Z, Yang Y, Tang Y, Jing H, Wang J, Zhang J, Wang X, Gao J, Wang J, Xuan L, Fang Y, Ying J, LI Y, Huang X, Wang S. Development and External Validation of a Nomogram to Predict N2 or N3 Disease in Breast Cancer Patients with One to Three Positive Sentinel Lymph Nodes. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.1054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Dai Y, Qiang W, Lin K, Gui Y, Lan X, Wang D. An immune-related gene signature for predicting survival and immunotherapy efficacy in hepatocellular carcinoma. Cancer Immunol Immunother 2020; 70:967-979. [PMID: 33089373 DOI: 10.1007/s00262-020-02743-0] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [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: 07/01/2020] [Accepted: 10/12/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) ranks the fourth in terms of cancer-related mortality globally. Herein, in this research, we attempted to develop a novel immune-related gene signature that could predict survival and efficacy of immunotherapy for HCC patients. METHODS The transcriptomic and clinical data of HCC samples were downloaded from The Cancer Genome Atlas (TCGA) and GSE14520 datasets, followed by acquiring immune-related genes from the ImmPort database. Afterwards, an immune-related gene-based prognostic index (IRGPI) was constructed using the Least Absolute Shrinkage and Selection Operator (LASSO) regression model. Kaplan-Meier survival curves as well as time-dependent receiver operating characteristic (ROC) curve were performed to evaluate its predictive capability. Besides, both univariate and multivariate analyses on overall survival for the IRGPI and multiple clinicopathologic factors were carried out, followed by the construction of a nomogram. Finally, we explored the possible correlation of IRGPI with immune cell infiltration or immunotherapy efficacy. RESULTS Analysis of 365 HCC samples identified 11 differentially expressed immune-related genes, which were selected to establish the IRGPI. Notably, it can predict the survival of HCC patients more accurately than published biomarkers. Furthermore, IRGPI can predict the infiltration of immune cells in the tumor microenvironment of HCC, as well as the response of immunotherapy. CONCLUSION Collectively, the currently established IRGPI can accurately predict survival, reflect the immune microenvironment, and predict the efficacy of immunotherapy among HCC patients.
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Affiliation(s)
- Yifei Dai
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Weijie Qiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Kequan Lin
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yu Gui
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Xun Lan
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China.
| | - Dong Wang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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34
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Dong HL, Cai CJ, Bai D, Pang XX, Lan X, Zhang YQ, Zhang J, Zhou FM, Sun H, Zeng G. [Association between dietary glycemic load during first trimester and the risk of gestational diabetes mellitus: a prospective study]. Zhonghua Liu Xing Bing Xue Za Zhi 2020; 41:1352-1358. [PMID: 32867449 DOI: 10.3760/cma.j.cn112338-20190909-00659] [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 explore the effects of dietary glycemic load (GL) during first trimester on the risk of gestational diabetes mellitus (GDM). Methods: A prospective study was conducted among healthy women with singleton pregnancy at 8-14 weeks of gestation in a maternity out-patient clinic of maternal-and-child health care institution in Chengdu, Sichuan province. Information on dietary intake during the first trimester was collected through a 3-day 24-hour dietary recall. Glycemic index (GI) values were obtained from China Food Composition Tables (Standard Edition) and International Tables of Glycemic Index and Glycemic Load Values (2008). Dietary GL and GLs of staple foods were calculated based on GI values and the amount of carbohydrate consumed per day. Diagnostic criteria of GDM was followed the Guidelines for Diagnosis and Treatment of Pregnancy Diabetes in China (2014), and used on participants who underwent an oral glucose tolerant test during 24-28 weeks of gestation. Log-binomial regression models were used to explore the associations between both quartiles of dietary GL, GLs of staple foods and the risks of GDM,respectively. Results: The medians of dietary GL and GL of staple foods were 145.70 (113.23-180.85) and 121.05 (89.08-155.70), respectively. The median GL of both rice and tubers were 73.14 (43.89-107.50) and 3.43 (0.00-9.84), respectively. After adjusting for the age at pregnancy, pre-pregnancy body mass index and other confounding factors, results of log-binomial regressions analysis showed that when compared with the lowest quartile of dietary GL group, the third and highest quartiles of dietary GL groups increased the risk of GDM (RR=1.47, 95%CI: 1.20-1.80; RR=1.31, 95%CI: 1.04-1.64), respectively. Compared with the lowest quartile of GL of staple foods, the third and highest quartiles of GL of staple foods groups also increased the risk of GDM (RR=1.28, 95%CI: 1.04-1.58; RR=1.27, 95%CI: 1.02-1.60), respectively. The third and highest quartiles of GL of rice groups increased the risk of GDM (RR=1.30, 95%CI: 1.06-1.59; RR=1.28, 95%CI: 1.03-1.59), respectively, than the lowest quartile of GL of rice group. When compared with the lowest quartile of GL of tubers group, the highest quartile of GL of tubers group increased the risk of GDM (RR=1.30, 95%CI: 1.09-1.54). However, we did not notice the effects of wheat GL and coarse grain GL on the risk of GDM. Conclusions: A positive association was found between dietary glycemic load and the risk of GDM. Higher dietary glycemic load, especially in rice and tubers during first trimester, seemed to have increased the risk of GDM.
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Affiliation(s)
- H L Dong
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - C J Cai
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - D Bai
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - X X Pang
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - X Lan
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Y Q Zhang
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - J Zhang
- Department of Clinical Nutrition, Sichuan Provincial Hospital for Women and Children, Chengdu 610045, China
| | - F M Zhou
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - H Sun
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - G Zeng
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
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Huang HL, Gnanasegaran G, Paez D, Fanti S, Hacker M, Sathekge M, Bom HS, Cerci JJ, Chiti A, Lan X, Herrmann K, Scott AM, Vinjamuri S, Dorbala S, Estrada E, Pellet O, Orellana P, El-Haj N, Giammarile F, Abdel-Wahab M, Bomanji J. Nuclear medicine services after COVID-19: gearing up back to normality. Eur J Nucl Med Mol Imaging 2020; 47:2048-2053. [PMID: 32367256 PMCID: PMC7197920 DOI: 10.1007/s00259-020-04848-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- H L Huang
- Institute of Nuclear Medicine, University College London Hospital, 5th Floor, 235 Euston Road, London, UK.,Department of Nuclear Medicine and Molecular Imaging, Division of Radiological Sciences, Singapore General Hospita, Bukit Merah, Singapore
| | | | - D Paez
- Division of Human Health, International Atomic Energy Agency, Vienna, Austria
| | - S Fanti
- Department of Oncology, Division of Nuclear Medicine, University of Bologna, Bologna, Italy
| | - M Hacker
- Department of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna General Hospital, Vienna, Austria
| | - M Sathekge
- Nuclear Medicine Department, University of Pretoria and Steve Biko Academic Hospital, Pretoria, South Africa
| | - H S Bom
- Department of Nuclear Medicine, Chonnam National University, Seoul, South Korea
| | - J J Cerci
- PET/CT Department at Quanta Diagnostics and Therapy, Curitiba, Brazil
| | - A Chiti
- Humanitas University and Humanitas Research Centre, Milan, Italy
| | - X Lan
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - K Herrmann
- Department of Nuclear Medicine, Universitätsklinikum Essen, Essen, Germany
| | - A M Scott
- Department of Molecular Imaging and Therapy, Austin Health, Melbourne, Australia
| | - S Vinjamuri
- Royal Liverpool University Hospital, Liverpool, L7 8XP, UK
| | - S Dorbala
- Division of Nuclear Medicine and Molecular Imaging, Department of Radiology, Brigham and Women's Hospital, Boston, MA, USA
| | - E Estrada
- Division of Human Health, International Atomic Energy Agency, Vienna, Austria
| | - O Pellet
- Division of Human Health, International Atomic Energy Agency, Vienna, Austria
| | - P Orellana
- Division of Human Health, International Atomic Energy Agency, Vienna, Austria
| | - N El-Haj
- Division of Human Health, International Atomic Energy Agency, Vienna, Austria
| | - F Giammarile
- Division of Human Health, International Atomic Energy Agency, Vienna, Austria
| | - M Abdel-Wahab
- Division of Human Health, International Atomic Energy Agency, Vienna, Austria
| | - Jamshed Bomanji
- Institute of Nuclear Medicine, University College London Hospital, 5th Floor, 235 Euston Road, London, UK.
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Helgeson S, Kukhon F, Lan X, Patel N. UTILITY OF ENDOBRONCHIAL ULTRASOUND-GUIDED LYMPH NODE BIOPSY IN RADIOGRAPHIC STAGE 1 LUNG CANCER. Chest 2020. [DOI: 10.1016/j.chest.2020.05.269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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37
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Huang HL, Gnanasegaran G, Paez D, Fanti S, Hacker M, Sathekge M, Bom HS, Cerci JJ, Chiti A, Lan X, Herrmann K, Scott AM, Vinjamuri S, Dorbala S, Estrada E, Pellet O, Orellana P, El-Haj N, Giammarile F, Abdel-Wahab M, Bomanji J. Correction to: Nuclear medicine services after COVID-19: gearing up back to normality. Eur J Nucl Med Mol Imaging 2020; 47:2220. [PMID: 32462399 PMCID: PMC7252414 DOI: 10.1007/s00259-020-04884-x] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The authors P. Orellana and N. El-Haj were inadvertently deleted in the original paper.
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Affiliation(s)
- H L Huang
- Institute of Nuclear Medicine, University College London Hospital, 5th Floor, 235 Euston Road, London, UK
- Department of Nuclear Medicine and Molecular Imaging, Division of Radiological Sciences, Singapore General Hospital, Bukit Merah, Singapore
| | | | - D Paez
- Division of Human Health, International Atomic Energy Agency, Vienna, Austria
| | - S Fanti
- Department of Oncology, Division of Nuclear Medicine, University of Bologna, Bologna, Italy
| | - M Hacker
- Department of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna General Hospital, Vienna, Austria
| | - M Sathekge
- NuclearMedicine Department, University of Pretoria and Steve Biko Academic Hospital, Pretoria, South Africa
| | - H S Bom
- Department of Nuclear Medicine, Chonnam National University, Seoul, South Korea
| | - J J Cerci
- PET/CT Department at Quanta Diagnostics and Therapy, Curitiba, Brazil
| | - A Chiti
- Humanitas University and Humanitas Research Centre, Milan, Italy
| | - X Lan
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - K Herrmann
- Department of Nuclear Medicine, Universitätsklinikum Essen, Essen, Germany
| | - A M Scott
- Department of Molecular Imaging and Therapy, Austin Health, Melbourne, Australia
| | - S Vinjamuri
- Royal Liverpool University Hospital, Liverpool, L7 8XP, UK
| | - S Dorbala
- Division of Nuclear Medicine and Molecular Imaging, Department of Radiology, Brigham and Women's Hospital, Boston, MA, USA
| | - E Estrada
- Division of Human Health, International Atomic Energy Agency, Vienna, Austria
| | - O Pellet
- Division of Human Health, International Atomic Energy Agency, Vienna, Austria
| | - P Orellana
- Division of Human Health, International Atomic Energy Agency, Vienna, Austria
| | - N El-Haj
- Division of Human Health, International Atomic Energy Agency, Vienna, Austria
| | - F Giammarile
- Division of Human Health, International Atomic Energy Agency, Vienna, Austria
| | - M Abdel-Wahab
- Division of Human Health, International Atomic Energy Agency, Vienna, Austria
| | - Jamshed Bomanji
- Institute of Nuclear Medicine, University College London Hospital, 5th Floor, 235 Euston Road, London, UK.
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38
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Dai Y, Qiang W, Yu X, Cai S, Lin K, Xie L, Lan X, Wang D. Guizhi Fuling Decoction inhibiting the PI3K and MAPK pathways in breast cancer cells revealed by HTS 2 technology and systems pharmacology. Comput Struct Biotechnol J 2020; 18:1121-1136. [PMID: 32489526 PMCID: PMC7260686 DOI: 10.1016/j.csbj.2020.05.004] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023] Open
Abstract
As one of the classical traditional Chinese medicine (TCM) prescriptions in treating gynecological tumors, Guizhi Fuling Decoction (GFD) has been used to treat breast cancer (BRCA). Nonetheless, the potential molecular mechanism remains unclear so far. Therefore, systems pharmacology was used in combination with high throughput sequencing-based high throughput screening (HTS2) assay and bioinformatic technologies in this study to investigate the molecular mechanisms of GFD in treating BRCA. By computationally analyzing 76 active ingredients in GFD, 38 potential therapeutic targets were predicted and significantly enriched in the "pathways in cancer". Meanwhile, experimental analysis was carried out to examine changes in the expression levels of 308 genes involved in the "pathways in cancer" in BRCA cells treated by five herbs of GFD utilizing HTS2 platform, and 5 key therapeutic targets, including HRAS, EGFR, PTK2, SOS1, and ITGB1, were identified. The binding mode of active compounds to these five targets was analyzed by molecular docking and molecular dynamics simulation. It was found after integrating the computational and experimental data that, GFD possessed the anti-proliferation, pro-apoptosis, and anti-angiogenesis activities mainly through regulating the PI3K and the MAPK signaling pathways to inhibit BRCA. Besides, consistent with the TCM theory about the synergy of Cinnamomi Ramulus (Guizhi) by Cortex Moutan (Mudanpi) in GFD, both of these two herbs acted on the same targets and pathways. Taken together, the combined application of computational systems pharmacology techniques and experimental HTS2 platform provides a practical research strategy to investigate the functional and biological mechanisms of the complicated TCM prescriptions.
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Affiliation(s)
- Yifei Dai
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Weijie Qiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Xiankuo Yu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Siwei Cai
- Department of Electronic and Computer Engineering, College of Engineering, Drexel University, Philadelphia 19104, USA
| | - Kequan Lin
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lan Xie
- Medical Systems Biology Research Center, School of Medicine, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| | - Xun Lan
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Dong Wang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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39
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Deng L, Yao P, Li L, Ji F, Zhao S, Xu C, Lan X, Jiang P. p53-mediated control of aspartate-asparagine homeostasis dictates LKB1 activity and modulates cell survival. Nat Commun 2020; 11:1755. [PMID: 32273511 PMCID: PMC7145870 DOI: 10.1038/s41467-020-15573-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [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: 08/28/2019] [Accepted: 03/17/2020] [Indexed: 12/31/2022] Open
Abstract
Asparagine synthetase (ASNS) catalyses the ATP-dependent conversion of aspartate to asparagine. However, both the regulation and biological functions of asparagine in tumour cells remain largely unknown. Here, we report that p53 suppresses asparagine synthesis through the transcriptional downregulation of ASNS expression and disrupts asparagine-aspartate homeostasis, leading to lymphoma and colon tumour growth inhibition in vivo and in vitro. Moreover, the removal of asparagine from culture medium or the inhibition of ASNS impairs cell proliferation and induces p53/p21-dependent senescence and cell cycle arrest. Mechanistically, asparagine and aspartate regulate AMPK-mediated p53 activation by physically binding to LKB1 and oppositely modulating LKB1 activity. Thus, we found that p53 regulates asparagine metabolism and dictates cell survival by generating an auto-amplification loop via asparagine-aspartate-mediated LKB1-AMPK signalling. Our findings highlight a role for LKB1 in sensing asparagine and aspartate and connect asparagine metabolism to the cellular signalling transduction network that modulates cell survival.
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Affiliation(s)
- Longfei Deng
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, 100084, Beijing, China.,School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Pengbo Yao
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, 100084, Beijing, China.,School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Le Li
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, 100084, Beijing, China.,School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Fansen Ji
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, 100084, Beijing, China.,School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Shuang Zhao
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, 100084, Beijing, China.,School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Chang Xu
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, 100084, Beijing, China.,School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xun Lan
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, 100084, Beijing, China.,School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Peng Jiang
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, 100084, Beijing, China. .,School of Life Sciences, Tsinghua University, 100084, Beijing, China.
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40
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Zu W, Zhang H, Lan X, Tan X. Genome-wide evolution analysis reveals low CpG contents of fast-evolving genes and identifies antiviral microRNAs. J Genet Genomics 2020; 47:49-60. [DOI: 10.1016/j.jgg.2019.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/11/2019] [Accepted: 12/03/2019] [Indexed: 01/28/2023]
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41
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Wang Z, Zhang X, Jiang E, Yan H, Zhu H, Chen H, Liu J, Qu L, Pan C, Lan X. InDels within caprine IGF2BP1 intron 2 and the 3'-untranslated regions are associated with goat growth traits. Anim Genet 2019; 51:117-121. [PMID: 31625179 DOI: 10.1111/age.12871] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2019] [Indexed: 12/31/2022]
Abstract
Insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) is involved in the Hedgehog pathway and has been shown to regulate the RNA stability of several growth-related target genes. It is located in a quantitative trait locus showing a strong association with traits related to body size in ducks. Fibroblast growth factor receptor 1 (FGFR1) also participates in Hedgehog signaling pathways and has been reported to be associated with organic growth and development. FGFR1-knockout mice have been shown to have severe postnatal growth defects, including an approximately 50% reduction in body weight and bone mass. Meanwhile, nonsense-mediated mRNA decay factor (SMG6) can maintain genomic stability, which is associated with organic growth and development. Therefore, we hypothesized that IGF2BP1, FGFR1 and SMG6 genes may play important roles in the growth traits of goats. In this study, the existence of two insertion/deletion (InDel) variants within IGF2BP1, one InDel within FGFR1 and two InDels within SMG6 was verified and their correlation with growth traits was analyzed in 2429 female Shaanbei white cashmere goats. Results showed both the 15 bp InDel in intron 2 and the 5 bp InDel in the 3' regulatory region within IGF2BP1 were significantly associated with growth traits (P < 0.05) and goats with the combinatorial homozygous insertion genotypes of these two loci had the highest body weight (P = 0.046). The other InDels within FGFR1 and SMG6 were not obviously associated with growth traits (P > 0.05). Therefore, the two InDels in IGF2BP1 were vital mutations affecting goat growth traits.
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Affiliation(s)
- Z Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - X Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - E Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - H Yan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.,College of Life Sciences, Yulin College, Yulin, Shaanxi, 719000, China.,Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin College, Yulin, Shaanxi, 719000, China
| | - H Zhu
- College of Life Sciences, Yulin College, Yulin, Shaanxi, 719000, China.,Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin College, Yulin, Shaanxi, 719000, China
| | - H Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - J Liu
- College of Life Sciences, Yulin College, Yulin, Shaanxi, 719000, China.,Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin College, Yulin, Shaanxi, 719000, China
| | - L Qu
- College of Life Sciences, Yulin College, Yulin, Shaanxi, 719000, China.,Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin College, Yulin, Shaanxi, 719000, China
| | - C Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - X Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
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42
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Luo M, Bai J, Liu B, Yan P, Zuo F, Sun H, Sun Y, Xu X, Song Z, Yang Y, Massagué J, Lan X, Lu Z, Chen YG, Deng H, Xie W, Xi Q. H3K18ac Primes Mesendodermal Differentiation upon Nodal Signaling. Stem Cell Reports 2019; 13:642-656. [PMID: 31564646 PMCID: PMC6830056 DOI: 10.1016/j.stemcr.2019.08.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 11/19/2018] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 01/17/2023] Open
Abstract
Cellular responses to transforming growth factor β (TGF-β) depend on cell context. Here, we explored how TGF-β/nodal signaling crosstalks with the epigenome to promote mesendodermal differentiation. We find that expression of a group of mesendodermal genes depends on both TRIM33 and nodal signaling in embryoid bodies (EBs) but not in embryonic stem cells (ESCs). Only in EBs, TRIM33 binds these genes in the presence of expanded H3K18ac marks. Furthermore, the H3K18ac landscape at mesendodermal genes promotes TRIM33 recruitment. We reveal that HDAC1 binds to active gene promoters and interferes with TRIM33 recruitment to mesendodermal gene promoters. However, the TRIM33-interacting protein p300 deposits H3K18ac and further enhances TRIM33 recruitment. ATAC-seq data demonstrate that TRIM33 primes mesendodermal genes for activation by maintaining chromatin accessibility at their regulatory regions. Altogether, our study suggests that HDAC1 and p300 are key factors linking the epigenome through TRIM33 to the cell context-dependent nodal response during mesendodermal differentiation. The H3K18ac landscape changes at gene promoters during mesendodermal differentiation Histone acetylation facilitates TRIM33 recruitment to the chromatin HDAC1 and p300 are the key factors for nodal signaling crosstalk with epigenome Chromatin accessibility at mesendodermal genes depends on TRIM33
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Affiliation(s)
- Maoguo Luo
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianbo Bai
- Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Bofeng Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Beijing 100084, China
| | - Peiqiang Yan
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Feifei Zuo
- Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hongyao Sun
- Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ye Sun
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xuanhao Xu
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhihong Song
- Department of Basic Medical Sciences, Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yang Yang
- Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Joan Massagué
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Xun Lan
- Department of Basic Medical Sciences, Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zhi Lu
- Key Laboratory of Bioinformatics and the Center of Biomedical Analysis, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ye-Guang Chen
- The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haiteng Deng
- Key Laboratory of Bioinformatics and the Center of Biomedical Analysis, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xie
- Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Beijing 100084, China
| | - Qiaoran Xi
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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43
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Yamamoto R, Wilkinson AC, Ooehara J, Lan X, Lai CY, Nakauchi Y, Pritchard JK, Nakauchi H. Large-Scale Clonal Analysis Resolves Aging of the Mouse Hematopoietic Stem Cell Compartment. Cell Stem Cell 2019; 22:600-607.e4. [PMID: 29625072 PMCID: PMC5896201 DOI: 10.1016/j.stem.2018.03.013] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/26/2017] [Accepted: 03/15/2018] [Indexed: 12/28/2022]
Abstract
Aging is linked to functional deterioration and hematological diseases. The hematopoietic system is maintained by hematopoietic stem cells (HSCs), and dysfunction within the HSC compartment is thought to be a key mechanism underlying age-related hematopoietic perturbations. Using single-cell transplantation assays with five blood-lineage analysis, we previously identified myeloid-restricted repopulating progenitors (MyRPs) within the phenotypic HSC compartment in young mice. Here, we determined the age-related functional changes to the HSC compartment using over 400 single-cell transplantation assays. Notably, MyRP frequency increased dramatically with age, while multipotent HSCs expanded modestly within the bone marrow. We also identified a subset of functional cells that were myeloid restricted in primary recipients but displayed multipotent (five blood-lineage) output in secondary recipients. We have termed this cell type latent-HSCs, which appear exclusive to the aged HSC compartment. These results question the traditional dogma of HSC aging and our current approaches to assay and define HSCs. Single-cell transplantation reveals dramatic age-related changes in HSC composition MyRPs/MySCs increase with age as a frequency of whole BM cells and the HSC compartment Latent-HSCs were identified exclusively in the aged bone marrow Latent-HSCs have restricted potential in primary, but not secondary, transplants
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Affiliation(s)
- Ryo Yamamoto
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA; Division of Stem Cell Therapy, Center for Stem Cell Biology and Regeneration Medicine, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA
| | - Jun Ooehara
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regeneration Medicine, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Xun Lan
- Department of Genetics, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Chen-Yi Lai
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regeneration Medicine, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Yusuke Nakauchi
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regeneration Medicine, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, CA, USA; Department of Biology, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA; Division of Stem Cell Therapy, Center for Stem Cell Biology and Regeneration Medicine, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan.
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Sun M, Hussain S, Hu Y, Yan J, Min Z, Lan X, Guo Y, Zhao Y, Huang H, Feng M, Han Y, Zhang F, Zhu W, Meng L, Li D, Sun J, Lu S. Maintenance of SOX9 stability and ECM homeostasis by selenium-sensitive PRMT5 in cartilage. Osteoarthritis Cartilage 2019; 27:932-944. [PMID: 30858101 DOI: 10.1016/j.joca.2019.02.797] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 02/10/2019] [Accepted: 02/27/2019] [Indexed: 02/02/2023]
Abstract
OBJECTIVES Selenium (Se) plays pivotal roles in maintaining optimal health. Nevertheless, how Se influences the metabolism of extracellular matrix (ECM) in cartilage remains unclear. The aim of the present study was to observe protein dimethylation by certain Se-sensitive PRMT and to elucidate its effects on the key transcriptional factor in cartilage. METHODS We observed the expression of selenoproteins and markers of ECM metabolism in chondrocytes and articular cartilage of the rats under Se-deficiency by RT-qPCR, immunoblotting and immunohistochemistry. Then, we analyzed the expression of total dimethylated protein by using specific antibody under different Se statuses. After Se sensitive PRMT was identified, we used siRNA or PRMT inhibitor or stably overexpressing vector to intervene in the PRMT expression and identified the key transcriptional factor. Co-immunoprecipitation was applied to verify the interaction between PRMT and the key transcriptional factor. Finally, we measured the half-life time of the key transcriptional factor by immunoblotting after cycloheximide treatment. RESULTS In chondrocytes and cartilage of the rats with Se deficiency, we found an aberrant metabolism manifesting decreased expression of Col2a1 and increased expression of Mmp-3. Then, we identified that PRMT5 was the unique type II PRMT, sensitive to Se status. PRMT5 upregulation led to the increased COL2A1 expression but decreased MMP-3 expression in chondrocytes. Furthermore, we revealed that PRMT5 improved SOX9 stability by dimethylating the protein, which contributed to maintain the matrix metabolic homeostasis of the chondrocytes. CONCLUSIONS Se-sensitive PRMT5 increases the half-life of SOX9 protein via PTM and helps to maintain ECM homeostasis of the articular cartilage.
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Affiliation(s)
- M Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - S Hussain
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - Y Hu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - J Yan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - Z Min
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - X Lan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - Y Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - Y Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - H Huang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - M Feng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - Y Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - F Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - W Zhu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - L Meng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - D Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - J Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China.
| | - S Lu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, PR China; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China.
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Zhang YQ, Lan X, Zhang J, Zhou R, Dai ZY, Wu C, Bao YH, Yang LQ, Zhou FM, Zhao RP, Zeng G. [Association between gestational weight gain and adverse pregnancy outcomes: a prospective study]. Zhonghua Liu Xing Bing Xue Za Zhi 2018; 39:1626-1629. [PMID: 30572390 DOI: 10.3760/cma.j.issn.0254-6450.2018.12.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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 explore the association between gestational weight gain (GWG) and adverse pregnancy outcomes. Methods: A prospective study was conducted among 1 220 healthy singleton pregnant women in the first trimester of pregnancy, from Chengdu city, Sichuan province. Pre-gestational body mass and other basic information were collected through a set of questionnaires. Weight at the last week before delivery was measured and GWG was classified by IOM criteria (2009). Related information on pregnancy outcomes was collected after delivery, through the hospital information system. Multiple non-conditional logistic regression models were used to test the association between GWG and adverse pregnancy outcomes. Results: In total, data on 1 045 pregnant women were analyzed. Compared with adequate GWG, excessive GWG was associated with the increased risks of cord entanglement and large for gestational age (OR=1.641, 95%CI: 1.197-2.252; OR=1.678, 95%CI: 0.132-2.488), respectively. Additionally, when compared with the adequate GWG, insufficient GWG was associated with the increased risk of preterm delivery (OR=3.189, 95%CI: 1.604-6.341). Conclusions: Both excessive and insufficient GWG appeared associated with the pregnancy outcomes. Weight monitoring should be strengthened for pregnant women to reduce related risks on adverse pregnancy outcomes.
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Affiliation(s)
- Y Q Zhang
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health, Sichuan University, Chengdu 610041, China
| | - X Lan
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health, Sichuan University, Chengdu 610041, China
| | - J Zhang
- Department of Nutrition, Maternity and Child Health Care Central Hospital of Sichuan, Chengdu 610045, China
| | - R Zhou
- Department of Obstetrics, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Z Y Dai
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health, Sichuan University, Chengdu 610041, China
| | - C Wu
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health, Sichuan University, Chengdu 610041, China
| | - Y H Bao
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health, Sichuan University, Chengdu 610041, China
| | - L Q Yang
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health, Sichuan University, Chengdu 610041, China
| | - F M Zhou
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health, Sichuan University, Chengdu 610041, China
| | - R P Zhao
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health, Sichuan University, Chengdu 610041, China
| | - G Zeng
- Department of Nutrition, Food Hygiene and Toxicology, West China School of Public Health, Sichuan University, Chengdu 610041, China
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46
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Ma L, Li Z, Cai Y, Xu H, Yang R, Lan X. Genetic variants in fat- and short-tailed sheep from high-throughput RNA-sequencing data. Anim Genet 2018; 49:483-487. [DOI: 10.1111/age.12699] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2018] [Indexed: 12/30/2022]
Affiliation(s)
- L. Ma
- Shaanxi Key Laboratory of Molecular Biology for Agriculture; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - Z. Li
- College of Life Sciences; Northwest A&F University; Yangling Shaanxi 712100 China
| | - Y. Cai
- Science Experimental Center; Northwest University for Nationalities; Lanzhou Gansu 730030 China
- College of Life Science and Engineering; Northwest University for Nationalities; Lanzhou 730030 China
| | - H. Xu
- Science Experimental Center; Northwest University for Nationalities; Lanzhou Gansu 730030 China
- College of Life Science and Engineering; Northwest University for Nationalities; Lanzhou 730030 China
| | - R. Yang
- College of Life Sciences; Northwest A&F University; Yangling Shaanxi 712100 China
| | - X. Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture; College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
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47
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He J, Lan X, Duan HL, Luo H, Zhou XD. CA916798 affects growth and metastasis of androgen-dependent prostate cancer cells. Eur Rev Med Pharmacol Sci 2018; 22:4477-4487. [PMID: 30058677 DOI: 10.26355/eurrev_201807_15499] [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] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Abnormal activation of androgen receptor (AR) signaling pathway is a critical pathogenic mechanism and therapeutic target for prostate cancer (PCa). The CA916798 is a tumor-associated gene and may be regulated by the androgen-AR pathway. This study aims to investigate the function of CA916798 in the growth and metastasis of androgen-dependent PCa cells. MATERIALS AND METHODS CA916798 expression in PCa cell lines was investigated. LNCap cells were divided into 4 groups: LNCap, LNCap+ Dihydrotestosterone (DHT), LNCap+DHT+siCA916798, and LNCap+DHT+siRA group. CA916798 expressions in LNCap cells treated with siCA917698 or siAR were examined. The viability, apoptosis, migration, and invasion of PCa cells were examined. Dual luciferase and ChIP assays were used to examine the interaction between the AR and CA916798. RESULTS Endogenous CA916798 mRNA levels in PC3 cells were significantly higher than those in LNCap cells (p < 0.05). However, CA916798 was androgen-sensitive in LNCap cells, but not in PC-3 cells. Dual luciferase and ChIP assays showed that AR could specifically bind to the promoter regions of the CA916798. Knockdown of CA916798 (LNCap+DHT+siCA916798) and AR (LNCap+DHT+siAR) resulted in decreased cell viability, migration, and invasion, while it induced apoptosis and G1 cell cycle arrest in LNCap cells. CONCLUSIONS DHT could initiate the transcription of CA916798, which further mediates the androgen-AR signaling pathway-dependent cell growth and metastasis of the prostate cancer cell line LNCap.
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Affiliation(s)
- J He
- Department of Respiratory Diseases, Southwest Hospital of the Third Military Medical University (Army Medical University), Chongqing, P.R. China.
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48
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Hankey W, Chen Z, Bergman MJ, Fernandez MO, Hancioglu B, Lan X, Jegga AG, Zhang J, Jin VX, Aronow BJ, Wang Q, Groden J. Chromatin-associated APC regulates gene expression in collaboration with canonical WNT signaling and AP-1. Oncotarget 2018; 9:31214-31230. [PMID: 30131849 PMCID: PMC6101278 DOI: 10.18632/oncotarget.25781] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 02/06/2018] [Accepted: 07/05/2018] [Indexed: 11/25/2022] Open
Abstract
Mutation of the APC gene occurs in a high percentage of colorectal tumors and is a central event driving tumor initiation in the large intestine. The APC protein performs multiple tumor suppressor functions including negative regulation of the canonical WNT signaling pathway by both cytoplasmic and nuclear mechanisms. Published reports that APC interacts with β-catenin in the chromatin fraction to repress WNT-activated targets have raised the possibility that chromatin-associated APC participates more broadly in mechanisms of transcriptional control. This screening study has used chromatin immunoprecipitation and next-generation sequencing to identify APC-associated genomic regions in colon cancer cell lines. Initial target selection was performed by comparison and statistical analysis of 3,985 genomic regions associated with the APC protein to whole transcriptome sequencing data from APC-deficient and APC-wild-type colon cancer cells, and two types of murine colon adenomas characterized by activated Wnt signaling. 289 transcripts altered in expression following APC loss in human cells were linked to APC-associated genomic regions. High-confidence targets additionally validated in mouse adenomas included 16 increased and 9 decreased in expression following APC loss, indicating that chromatin-associated APC may antagonize canonical WNT signaling at both WNT-activated and WNT-repressed targets. Motif analysis and comparison to ChIP-seq datasets for other transcription factors identified a prevalence of binding sites for the TCF7L2 and AP-1 transcription factors in APC-associated genomic regions. Our results indicate that canonical WNT signaling can collaborate with or antagonize the AP-1 transcription factor to fine-tune the expression of shared target genes in the colorectal epithelium. Future therapeutic strategies for APC-deficient colorectal cancers might be expanded to include agents targeting the AP-1 pathway.
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Affiliation(s)
- William Hankey
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Zhong Chen
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Maxwell J Bergman
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Max O Fernandez
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Baris Hancioglu
- Biomedical Informatics Shared Resource, The Ohio State University, Columbus, Ohio, United States of America
| | - Xun Lan
- Department of Basic Medical Sciences, Tsinghua University School of Medicine, Beijing, China
| | - Anil G Jegga
- Division of Bioinformatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Jie Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Bruce J Aronow
- Division of Bioinformatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Qianben Wang
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Joanna Groden
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
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Chen M, Tang TC, Wang Y, Shui J, Xiao XH, Lan X, Yu P, Zhang C, Wang SH, Yao J, Zheng H, Huang DQ. Randomised clinical trial: Tong-Xie-Yao-Fang granules versus placebo for patients with diarrhoea-predominant irritable bowel syndrome. Aliment Pharmacol Ther 2018; 48:160-168. [PMID: 29856472 DOI: 10.1111/apt.14817] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 03/17/2018] [Accepted: 04/30/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Tong-Xie-Yao-Fang (TXYF) is a Chinese herbal formula for treating chronic diarrhoea accompanied by abdominal pain. The results were inconsistent in previous trials examining its effect. AIM To study the efficacy of TXYF granules for treating diarrhoea-predominant irritable bowel syndrome (IBS-D). METHODS We performed a double-blind, placebo-controlled randomised trial and enrolled 160 participants with IBS-D. The participants had VAS scores ≥3 cm in IBS-D global symptoms and ≥2 days in a week with abdominal pain and loose stools (Bristol score 5, 6 or 7). They were randomly assigned to received TXYF or placebo during a treatment period of 4 weeks, and they were followed up for 8 weeks after treatment. The primary outcome was adequate relief of IBS-D global symptoms for at least 2 of 4 weeks during weeks 1-4. Secondary outcomes included mean weekly VAS scores of IBS-D major symptoms, mean weekly stool frequency, mean weekly Bristol score, and adverse events. RESULTS 155 of 160 patients completed the trial. We found a significantly higher rate of adequate relief of global symptoms in TXFY group during weeks 1 to 4 (57.5% vs 37.5%, χ2 = 5.6391, P = 0.017); logistic regression analysis showed a similar result (OR 2.2, 95% CI 1.2-4.4, P = 0.016). Most of the secondary outcomes showed superiority of TXYF over placebo in weekly assessment from week 3 to week 7. The adverse event rate was low in both groups (3.8% vs 3.8%, P = 1.000). CONCLUSION During a 4 week trial, TXFY granules were superior to placebo in controlling symptoms of IBS-D.
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Affiliation(s)
- M Chen
- Clinical Medicine College/Teaching hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - T-C Tang
- Clinical Medicine College/Teaching hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Y Wang
- Colorectal Department, Luzhou People's Hospital, Luzhou, Sichuan, China
| | - J Shui
- Clinical Medicine College/Teaching hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - X-H Xiao
- Clinical Medicine College/Teaching hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - X Lan
- Clinical Medicine College/Teaching hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - P Yu
- Clinical Medicine College/Teaching hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - C Zhang
- Clinical Medicine College/Teaching hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - S-H Wang
- Colorectal Department, Luzhou People's Hospital, Luzhou, Sichuan, China
| | - J Yao
- Colorectal Department, Luzhou People's Hospital, Luzhou, Sichuan, China
| | - H Zheng
- Acupuncture and Tuina School/3rd Teaching Hosptial, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - D-Q Huang
- Clinical Medicine College/Teaching hospital, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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50
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Li X, Abhinandan K, Zhang T, Wei D, Li Y, Lan X, Samuel MA. Temporal regulation of two cytosolic phosphoglucomutases during stigma development in ornamental kale (Brassica oleracea var. acephala). Plant Signal Behav 2018; 13:e1467698. [PMID: 29944433 PMCID: PMC6103284 DOI: 10.1080/15592324.2018.1467698] [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] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/11/2018] [Indexed: 06/08/2023]
Abstract
Phosphoglucomutases (PGM) (5.4.2.2.) belong to the Phosphohexomutases superfamily and are highly specific in catalyzing the interconversion of Glc-1-P to Glc-6-P. In this study, we characterize the expression and activity of two cytosolic PGMs (cPGM2 and cPGM3) stigmas of ornamental kale during flower development. In stigmas, cPGM expression and activity showed a gradual increase during stigma development with the highest activity around the time of anthesis. Blocking of cPGM activity in the stigmas using a known inhibitor, resulted in breakdown of self-incompatibility in immature S3 and S4 stigmas, but had no effect on the fully mature S5 stigmas. It is likely that cPGMs are required for accumulation of factors necessary for SI response in mature stigmas.
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Affiliation(s)
- X. Li
- College of Life Science, Northeast Forestry University, Harbin, Heilongjiang Province, China
| | - K. Abhinandan
- Department of Biological Sciences, University of Calgary, Calgary, AB Canada
| | - T. Zhang
- College of Life Science, Northeast Forestry University, Harbin, Heilongjiang Province, China
| | - D. Wei
- College of Life Science, Northeast Forestry University, Harbin, Heilongjiang Province, China
| | - Y. Li
- College of Life Science, Northeast Forestry University, Harbin, Heilongjiang Province, China
| | - X. Lan
- College of Life Science, Northeast Forestry University, Harbin, Heilongjiang Province, China
- Department of Biological Sciences, University of Calgary, Calgary, AB Canada
| | - M. A. Samuel
- Department of Biological Sciences, University of Calgary, Calgary, AB Canada
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