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Yu PC, Hou D, Chang B, Liu N, Xu CH, Chen X, Hu CL, Liu T, Wang X, Zhang Q, Liu P, Jiang Y, Fei MY, Zong LJ, Zhang JY, Liu H, Chen BY, Chen SB, Wang Y, Li ZJ, Li X, Deng CH, Ren YY, Zhao M, Jiang S, Wang R, Jin J, Yang S, Xue K, Shi J, Chang CK, Shen S, Wang Z, He PC, Chen Z, Chen SJ, Sun XJ, Wang L. SMARCA5 reprograms AKR1B1-mediated fructose metabolism to control leukemogenesis. Dev Cell 2024; 59:1954-1971.e7. [PMID: 38776924 DOI: 10.1016/j.devcel.2024.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/13/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
A significant variation in chromatin accessibility is an epigenetic feature of leukemia. The cause of this variation in leukemia, however, remains elusive. Here, we identify SMARCA5, a core ATPase of the imitation switch (ISWI) chromatin remodeling complex, as being responsible for aberrant chromatin accessibility in leukemia cells. We find that SMARCA5 is required to maintain aberrant chromatin accessibility for leukemogenesis and then promotes transcriptional activation of AKR1B1, an aldo/keto reductase, by recruiting transcription co-activator DDX5 and transcription factor SP1. Higher levels of AKR1B1 are associated with a poor prognosis in leukemia patients and promote leukemogenesis by reprogramming fructose metabolism. Moreover, pharmacological inhibition of AKR1B1 has been shown to have significant therapeutic effects in leukemia mice and leukemia patient cells. Thus, our findings link the aberrant chromatin state mediated by SMARCA5 to AKR1B1-mediated endogenous fructose metabolism reprogramming and shed light on the essential role of AKR1B1 in leukemogenesis, which may provide therapeutic strategies for leukemia.
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Affiliation(s)
- Peng-Cheng Yu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Dan Hou
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Binhe Chang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Na Liu
- Department of Hematology, Institute of Hematology, Shanghai Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Chun-Hui Xu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinchi Chen
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Cheng-Long Hu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ting Liu
- Key Laboratory of Pediatric Hematology & Oncology of the Ministry of Health of China, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiaoning Wang
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Qunling Zhang
- Department of Medical Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ping Liu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yilun Jiang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ming-Yue Fei
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li-Juan Zong
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jia-Ying Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Liu
- Key Laboratory of Pediatric Hematology & Oncology of the Ministry of Health of China, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Bing-Yi Chen
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shu-Bei Chen
- School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zi-Juan Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiya Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chu-Han Deng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi-Yi Ren
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Muying Zhao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shiyu Jiang
- Department of Medical Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Roujia Wang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Jiacheng Jin
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Shaoxin Yang
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Kai Xue
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jun Shi
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Chun-Kang Chang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Shuhong Shen
- Key Laboratory of Pediatric Hematology & Oncology of the Ministry of Health of China, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhikai Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei 230027, China
| | - Peng-Cheng He
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiao-Jian Sun
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lan Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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Liu L, Du RY, Jia RL, Wang JX, Chen CZ, Li P, Kong LM, Li ZH. Micro(nano)plastics in marine medaka: Entry pathways and cardiotoxicity with triphenyltin. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 342:123079. [PMID: 38061435 DOI: 10.1016/j.envpol.2023.123079] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/21/2023] [Accepted: 11/30/2023] [Indexed: 01/26/2024]
Abstract
The simultaneous presence of micro(nano)plastics (MNPs) and pollutants represents a prevalent environmental challenge that necessitates understanding their combined impact on toxicity. This study examined the distribution of 5 μm (PS-MP5) and 50 nm (PS-NP50) polystyrene plastic particles during the early developmental stages of marine medaka (Oryzias melastigma) and assessed their combined toxicity with triphenyltin (TPT). Results showed that 2 mg/L PS-MP5 and PS-NP50 could adhere to the embryo surface. PS-NP50 can passively enter the larvae and accumulate predominantly in the intestine and head, while PS-MP5 cannot. Nonetheless, both types can be actively ingested by the larvae and distributed in the intestine. 2 mg/L PS-MNPs enhance the acute toxicity of TPT. Interestingly, high concentrations of PS-NP50 (20 mg/L) diminish the acute toxicity of TPT due to their sedimentation properties and interactions with TPT. 200 μg/L PS-MNPs and 200 ng/L TPT affect complement and coagulation cascade pathways and cardiac development of medaka larvae. PS-MNPs exacerbate TPT-induced cardiotoxicity, with PS-NP50 exhibiting stronger effects than PS-MP5, which may be related to the higher adsorption capacity of NPs to TPT and their ability to enter the embryos before hatching. This study elucidates the distribution of MNPs during the early developmental stages of marine medaka and their effects on TPT toxicity, offering a theoretical foundation for the ecological risk assessment of MNPs.
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Affiliation(s)
- Ling Liu
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Ren-Yan Du
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Ruo-Lan Jia
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Jin-Xin Wang
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Cheng-Zhuang Chen
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Ping Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Ling-Ming Kong
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China.
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Li Y, Feng L, Xie D, Luo Y, Lin M, Gao J, Zhang Y, He Z, Zhu YZ, Gong Q. Icariside II mitigates myocardial infarction by balancing mitochondrial dynamics and reducing oxidative stress through the activation of Nrf2/SIRT3 signaling pathway. Eur J Pharmacol 2023; 956:175987. [PMID: 37572941 DOI: 10.1016/j.ejphar.2023.175987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/14/2023]
Abstract
Nuclear factor erythroid 2-related factor 2 (Nrf2)/silent mating type information regulation 2 homolog 3 (SIRT3) signaling pathway plays a pivotal role in regulating mitochondrial dynamics and oxidative stress, which are considered to be the principal pathogenesis of myocardial infarction (MI). Our previous study proved that pretreatment with icariside II (ICS II), a major active ingredient of Herbal Epimedii, exerts cardioprotective effect on MI, however, whether post-treatment with ICS II can alleviate MI and its underlying mechanism are still uncertain. Therefore, the present study was designed to investigate the therapeutic effect and the possible mechanism of ICS II on MI both in vivo and in vitro. The results revealed that post-treatment with ICS II markedly ameliorated myocardial injury in MI-induced mice and mitigated oxygen and glucose deprivation (OGD)-elicited cardiomyocyte injury. Further researches showed that ICS II promoted mitochondrial fusion, and suppressed mitochondrial fission and oxidative stress, which were achieved by facilitating the nuclear translocation of Nrf2 and activation of SIRT3. In summary, our findings indicate that ICS II mitigates MI-induced mitochondrial dynamics disorder and oxidative stress via activating the Nrf2/SIRT3 signaling pathway.
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Affiliation(s)
- Yeli Li
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR, China; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Linying Feng
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR, China
| | - Dianyou Xie
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR, China
| | - Yunmei Luo
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR, China; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Mu Lin
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR, China
| | - Jianmei Gao
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR, China; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China; Department of Clinical Pharmacotherapeutics, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Yuandong Zhang
- Department of Clinical Pharmacotherapeutics, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Zhixu He
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, China
| | - Yi Zhun Zhu
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR, China.
| | - Qihai Gong
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR, China; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China.
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4
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Bomber ML, Wang J, Liu Q, Barnett KR, Layden HM, Hodges E, Stengel KR, Hiebert SW. Human SMARCA5 is continuously required to maintain nucleosome spacing. Mol Cell 2023; 83:507-522.e6. [PMID: 36630954 PMCID: PMC9974918 DOI: 10.1016/j.molcel.2022.12.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023]
Abstract
Genetic models suggested that SMARCA5 was required for DNA-templated events including transcription, DNA replication, and DNA repair. We engineered a degron tag into the endogenous alleles of SMARCA5, a catalytic component of the imitation switch complexes in three different human cell lines to define the effects of rapid degradation of this key regulator. Degradation of SMARCA5 was associated with a rapid increase in global nucleosome repeat length, which may allow greater chromatin compaction. However, there were few changes in nascent transcription within the first 6 h of degradation. Nevertheless, we demonstrated a requirement for SMARCA5 to control nucleosome repeat length at G1/S and during the S phase. SMARCA5 co-localized with CTCF and H2A.Z, and we found a rapid loss of CTCF DNA binding and disruption of nucleosomal phasing around CTCF binding sites. This spatiotemporal analysis indicates that SMARCA5 is continuously required for maintaining nucleosomal spacing.
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Affiliation(s)
- Monica L Bomber
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kelly R Barnett
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Hillary M Layden
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Emily Hodges
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kristy R Stengel
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA.
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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5
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Gao J, Ma C, Xia D, Chen N, Zhang J, Xu F, Li F, He Y, Gong Q. Icariside II preconditioning evokes robust neuroprotection against ischaemic stroke, by targeting Nrf2 and the OXPHOS/NF-κB/ferroptosis pathway. Br J Pharmacol 2023; 180:308-329. [PMID: 36166825 DOI: 10.1111/bph.15961] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND AND PURPOSE Astrocytic nuclear factor erythroid-derived 2-related factor 2 (Nrf2) is a potential therapeutic target of ischaemic preconditioning (IPC). Icariside II (ICS II) is a naturally occurring flavonoid derived from Herba Epimedii with Nrf2 induction potency. This study was designed to clarify if exposure to ICS II mimicks IPC neuroprotection and if Nrf2 from astrocytes contributes to ICS II preconditioning against ischaemic stroke. EXPERIMENTAL APPROACH Mice with transient middle cerebral artery occlusion (MCAO)-induced focal cerebral ischaemia and primary astrocytes challenged with oxygen-glucose deprivation (OGD) were used to explore the neuroprotective effect of ICS II preconditioning. Additionally, Nrf2-deficient mice were pretreated with ICS II to determine whether ICS II exerts its neuroprotection by activating Nrf2. KEY RESULTS ICS II pretreatment mitigated cerebral injury in the mouse model of ischaemic stroke along with improving long-term recovery. Furthermore, proteomics screening identified Nrf2 as a crucial gene evoked by ICS II treatment and required for the anti-oxidative effect and anti-inflammatory effect of ICS II. Also, ICS II directly bound to Nrf2 and reinforced the transcriptional activity of Nrf2 after MCAO. Moreover, ICS II pretreatment exerted cytoprotective effects on astrocyte cultures following lethal OGD exposure, by promoting Nrf2 nuclear translocation and activating the OXPHOS/NF-κB/ferroptosis axis, while neuroprotection was decreased in Nrf2-deficient mice and Nrf2 siRNA blocked effects of ICS II. CONCLUSION AND IMPLICATIONS ICS II preconditioning provides robust neuroprotection against ischaemic stroke via the astrocytic Nrf2-mediated OXPHOS/NF-κB/ferroptosis axis. Thus, ICS II could be a promising Nrf2 activator to treat ischaemic stroke.
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Affiliation(s)
- Jianmei Gao
- School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China.,Department of Pharmacology, Key Laboratory of Basic Pharmacology of Guizhou Province, Zunyi Medical University, Zunyi, China
| | - Congjian Ma
- School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China.,Department of Pharmacology, Key Laboratory of Basic Pharmacology of Guizhou Province, Zunyi Medical University, Zunyi, China
| | - Dianya Xia
- School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China.,Department of Pharmacology, Key Laboratory of Basic Pharmacology of Guizhou Province, Zunyi Medical University, Zunyi, China
| | - Nana Chen
- School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China.,Department of Pharmacology, Key Laboratory of Basic Pharmacology of Guizhou Province, Zunyi Medical University, Zunyi, China
| | - Jianyong Zhang
- School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China.,Department of Pharmacology, Key Laboratory of Basic Pharmacology of Guizhou Province, Zunyi Medical University, Zunyi, China
| | - Fan Xu
- Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Fei Li
- School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China.,Department of Pharmacology, Key Laboratory of Basic Pharmacology of Guizhou Province, Zunyi Medical University, Zunyi, China
| | - Yuqi He
- School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China.,Department of Pharmacology, Key Laboratory of Basic Pharmacology of Guizhou Province, Zunyi Medical University, Zunyi, China
| | - Qihai Gong
- School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China.,Department of Pharmacology, Key Laboratory of Basic Pharmacology of Guizhou Province, Zunyi Medical University, Zunyi, China
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6
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Ding Y, Liu F. Protocol for isolation and ATAC-seq library construction of zebrafish red blood cells. STAR Protoc 2022; 3:101889. [PMID: 36595911 PMCID: PMC9700001 DOI: 10.1016/j.xpro.2022.101889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/19/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022] Open
Abstract
Understanding chromatin dynamics in red blood cells (RBCs) is critical for exploring the differentiation process and homeostasis maintenance during erythropoiesis. Here, we describe a protocol for isolation of zebrafish erythrocytes labelled with gata1:dsRed by fluorescence-activated cell sorting. We detail steps for ATAC-seq library construction from the isolated RBCs and describe how to analyze the quality of the library. The library can then be used to assay genome-wide chromatin accessibility in these RBCs. For complete details on the use and execution of this protocol, please refer to Ding et al. (2021).1.
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Affiliation(s)
- Yanyan Ding
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Institute for Stem Cell and Regeneration, University of Chinese Academy of Sciences, Beijing, China,School of Life Sciences, Shandong University, Qingdao, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Institute for Stem Cell and Regeneration, University of Chinese Academy of Sciences, Beijing, China,School of Life Sciences, Shandong University, Qingdao, China,Corresponding author
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7
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Shen X, Zhong J, He J, Han J, Chen N. Identification of m6A modification patterns and development of m6A-hypoxia prognostic signature to characterize tumor microenvironment in triple-negative breast cancer. Front Immunol 2022; 13:978092. [PMID: 36105819 PMCID: PMC9465332 DOI: 10.3389/fimmu.2022.978092] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/10/2022] [Indexed: 11/20/2022] Open
Abstract
Background N6-methylation (m6A) modification of RNA has been found to have essential effects on aspects of the tumor microenvironment (TME) including hypoxia status and mobilization of immune cells. However, there are no studies to explore the combined effect of m6A modification and hypoxia on molecular heterogeneity and TME of triple-negative breast cancer (TNBC). Methods We collected The Cancer Genome Atlas (TCGA-TNBC, N=139), the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC-TNBC, N=297), the GSE103091, GSE21653, and GSE135565 series from the Gene Expression Omnibus (GEO-TNBC, N=247), and FUSCCTNBC (N=245) for our study. The non-negative matrix factorization algorithm was used to cluster TNBC samples. Immune cell infiltration was analyzed by the CIBERSORT algorithm. The enrichment scores were calculated by single-sample gene set enrichment analysis(ssGSEA) to characterize TME in TNBC samples. Immunohistochemistry (IHC) and qRT-PCR were performed to detect the gene expression. Results Based on the expression of m6A-related genes, we identified three distinct m6A clusters (denoted A, B, and C) in TNBC samples. Comparing the TME characteristics among the three clusters, we observed that cluster C was strongly related to hypoxia status and immune suppression, whereas clusters A and B displayed more immune cell infiltration. Therefore, we combine m6A and hypoxia related genes to classify two m6A-hypoxia clusters of TNBC and screened six prognostic genes by LASSO-Cox regression to construct a m6A-hypoxia signature(MHPS), which divided TNBC samples into high- and low-risk groups. We identified different TME features, immune cell infiltration between the two groups, and a better immunotherapy response was observed in the low-risk group. A nomogram was constructed with tumor size, lymph node, and risk score to improve clinical application of MHPS. Conclusion We identified distinct TME characteristics of TNBC based on three different m6A modification patterns. Then, we constructed a specific m6A-hypoxia signature for TNBC to evaluate risk and predict immunotherapy response of patients, to enable more accurate treatment in the future.
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Affiliation(s)
- Xi Shen
- Department of Head and Neck Oncology and Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jianxin Zhong
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Jinlan He
- Department of Head and Neck Oncology and Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jiaqi Han
- Department of Head and Neck Oncology and Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Nianyong Chen
- Department of Head and Neck Oncology and Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
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