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Li S, Huang X, Zheng S, Zhang W, Liu F, Cao Q. High expression of SRSF1 facilitates osteosarcoma progression and unveils its potential mechanisms. BMC Cancer 2024; 24:580. [PMID: 38735973 DOI: 10.1186/s12885-024-12346-y] [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: 08/22/2023] [Accepted: 05/06/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND SRSF1, a member of Serine/Arginine-Rich Splicing Factors (SRSFs), has been observed to significantly influence cancer progression. However, the precise role of SRSF1 in osteosarcoma (OS) remains unclear. This study aims to investigate the functions of SRSF1 and its underlying mechanism in OS. METHODS SRSF1 expression level in OS was evaluated on the TCGA dataset, TAGET-OS database. qRT-PCR and Western blotting were employed to assess SRSF1 expression in human OS cell lines as well as the interfered ectopic expression states. The effect of SRSF1 on cell migration, invasion, proliferation, and apoptosis of OS cells were measured by transwell assay and flow cytometry. RNA sequence and bioinformatic analyses were conducted to elucidate the targeted genes, relevant biological pathways, and alternative splicing (AS) events regulated by SRSF1. RESULTS SRSF1 expression was consistently upregulated in both OS samples and OS cell lines. Diminishing SRSF1 resulted in reduced proliferation, migration, and invasion and increased apoptosis in OS cells while overexpressing SRSF1 led to enhanced growth, migration, invasion, and decreased apoptosis. Mechanistically, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and Gene Set Enrichment Analysis (GSEA) revealed that the biological functions of SRSF1 were closely associated with the dysregulation of the protein targeting processes, location of the cytosolic ribosome, extracellular matrix (ECM), and proteinaceous extracellular matrix, along with the PI3K-AKT pathway, Wnt pathway, and HIPPO pathway. Transcriptome analysis identified AS events modulated by SRSF1, especially (Skipped Exon) SE events and (Mutually exclusive Exons) MXE events, revealing potential roles of targeted molecules in mRNA surveillance, RNA degradation, and RNA transport during OS development. qRT-PCR confirmed that SRSF1 knockdown resulted in the occurrence of alternative splicing of SRRM2, DMKN, and SCAT1 in OS. CONCLUSIONS Our results highlight the oncogenic role of high SRSF1 expression in promoting OS progression, and further explore the potential mechanisms of action. The significant involvement of SRSF1 in OS development suggests its potential utility as a therapeutic target in OS.
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Affiliation(s)
- Shuqi Li
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xinyi Huang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Shuang Zheng
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Pathology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, China
| | - Wenhui Zhang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Fang Liu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Department of Liver Tumor Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Qinghua Cao
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
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Zeng X, Zhao R, Wu Z, Ma Z, Cen C, Gao S, Hong W, Yao Y, Wen K, Ding S, Wang J, Lu W, Wang X, Wang T. [ 18 F] -FAPI-42 PET/CT assessment of Progressive right ventricle fibrosis under pressure overload. Respir Res 2023; 24:270. [PMID: 37932744 PMCID: PMC10626814 DOI: 10.1186/s12931-023-02565-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Right heart failure (RHF) is a complication of pulmonary hypertension (PH) and increases the mortality independently of the underlying disease. However, the process of RHF development and progression is not fully understood. We aimed to develop effective approaches for early diagnosis and precise evaluation of RHF. METHODS Right ventricle (RV) pressure overload was performed via pulmonary artery banding (PAB) surgery in Sprague-Dawley (SD) rats to induce RHF. Echocardiography, right heart catheterization, histological staining, fibroblast activation protein (FAP) immunofluorescence and 18 F-labelled FAP inhibitor-42 ([18 F] -FAPI-42) positron emission tomography/computed tomography (PET/CT) were performed at day 3, week 1, 2, 4 and 8 after PAB. RNA sequencing was performed to explore molecular alterations between PAB and sham group at week 2 and week 4 after PAB respectively. RESULTS RV hemodynamic disorders were aggravated, and RV function was declined based on right heart catheterization and echocardiography at week 2, 4 and 8 after PAB. Progressive cardiac hypertrophy, fibrosis and capillary rarefaction could be observed in RV from 2 to 8 weeks after PAB. RNA sequencing indicated 80 upregulated genes and 43 downregulated genes in the RV at both week 2 and week 4 after PAB; Gene Ontology (GO) analysis revealed that fibrosis as the most significant biological process in the RV under pressure overload. Immunofluorescence indicated that FAP was upregulated in the RV from week 2 to week 8 after PAB; and [18 F] -FAPI-42 PET/CT revealed FAPI uptake was significantly higher in RV at week 2 and further increased at week 4 and 8 after PAB. CONCLUSION RV function is progressively declined with fibrosis as the most prominent molecular change after pressure overload, and [18 F] -FAPI-42 PET/CT is as sensitive and accurate as histopathology in RV fibrosis evaluation.
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Affiliation(s)
- Xiaohui Zeng
- State Key Laboratory of Respiratory Diseases, Guangdong Key Laboratory of Vascular Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ruiyue Zhao
- Department of Nuclear Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhixiong Wu
- State Key Laboratory of Respiratory Diseases, Guangdong Key Laboratory of Vascular Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhuoji Ma
- State Key Laboratory of Respiratory Diseases, Guangdong Key Laboratory of Vascular Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Chunxian Cen
- State Key Laboratory of Respiratory Diseases, Guangdong Key Laboratory of Vascular Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shanshan Gao
- State Key Laboratory of Respiratory Diseases, Guangdong Key Laboratory of Vascular Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wanxian Hong
- State Key Laboratory of Respiratory Diseases, Guangdong Key Laboratory of Vascular Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yanrong Yao
- Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Kexin Wen
- Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shangwei Ding
- Department of Ultrasound, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jian Wang
- State Key Laboratory of Respiratory Diseases, Guangdong Key Laboratory of Vascular Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wenju Lu
- State Key Laboratory of Respiratory Diseases, Guangdong Key Laboratory of Vascular Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xinlu Wang
- Department of Nuclear Medicine, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Tao Wang
- State Key Laboratory of Respiratory Diseases, Guangdong Key Laboratory of Vascular Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
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Huang C, Zhang H, Yang Y, Liu H, Chen J, Wang Y, Liang L, Hu H, Liu Y. Synthesis, characterization, molecular docking, RNA-sequence and anticancer efficacy evaluation in vitro of ruthenium(II) complexes on B16 cells. J Inorg Biochem 2023; 247:112329. [PMID: 37478780 DOI: 10.1016/j.jinorgbio.2023.112329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/07/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
In recent years, the studies of the ruthenium(II) complexes on anticancer activity have been paid great attention, many Ru(II) complexes possess high anticancer efficiency. In this paper, three ligands CPIP (2-(4-chlorophenyl)-1H-imidazo[4,5-f][1,10]phenanthroline), DCPIP (2-(3,4-dichlorophenyl)-1H-imidazo[4,5-f][1,10]phenanthroline), TCPIP (2-(2,3,5-trichlorophenyl)-1H-imidazo[4,5-f][1,10]phenanthroline) and their three ruthenium (II) complexes [Ru(dip)2(CPIP)](PF6)2 (1, dip = 4,7-diphenyl-1,10-phenanthroline), [Ru(dip)2(DCPIP)](PF6)2 (2) and [Ru(dip)2(TCPIP)](PF6)2 (3) were synthesized and characterized. 3-(4,5-dimethylthiazole-2-yl)-2,5-biphenyl tetrazolium bromide (MTT) assay was used to investigate in vitro cytotoxicity of complexes against various cancer cells. The results showed that complexes 1-3 exhibited pronounced cytotoxic effect on B16 cells with low IC50 values of 7.2 ± 0.1, 11.7 ± 0.6 and 1.2 ± 0.2 μM, respectively. The 3D model demonstrated that the complexes can validly prevent the cell proliferation. Apoptosis determined using Annexin V-FITC/PI double staining revealed that complexes 1-3 can effectively induce apoptosis in B16 cells. The intracellular localization of 1-3 in the mitochondria, the levels of intracellular reactive oxygen species (ROS), the opening of mitochondrial permeability transition pore as well as the decline of mitochondrial membrane potential were investigated, which demonstrated that the complexes 1-3 led to apoptosis via a ROS-mediated mitochondrial dysfunction pathway. The RNA-sequence indicated that the complexes upregulate the expression of 74 genes and downregulate the expression of 81 genes. The molecular docking showed that the complexes interact with the proteins through hydrogen bond, π-cation and π-π interaction. The results show that ruthenium(II) complexes 1, 2 and 3 can block tumor cell growth and induce cell death through autophagy and ROS-mediated mitochondrial dysfunction pathways.
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Affiliation(s)
- Chunxia Huang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Huiwen Zhang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Yan Yang
- Department of Pharmacy, Guangdong Second Provincial General Hospital, Guangzhou 510317, PR China.
| | - Haimei Liu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Jing Chen
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Yi Wang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Lijuan Liang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Huiyan Hu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Yunjun Liu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topic Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou 510006, PR China.
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Nakamuta S, Sakuma A, Nikaido M, Kato H, Miyazaki M, Yamamoto Y, Nakamuta N. Expression of type 1 vomeronasal receptors in the olfactory organ of the African lungfish, Protopterus dolloi. Acta Histochem 2023; 125:152078. [PMID: 37540956 DOI: 10.1016/j.acthis.2023.152078] [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: 02/28/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 08/06/2023]
Abstract
The vomeronasal organ is an olfactory organ found in amphibians and higher vertebrates. Type 1 vomeronasal receptors, one of the major olfactory receptors in vertebrates, are expressed in the vomeronasal organ in mammals. In amphibians and fish, they are expressed in the olfactory epithelium. The lungfish, which is the species of fish most closely related to amphibians, has a primitive vomeronasal organ: the recess epithelium. Expression of type 1 vomeronasal receptors has been reported in both the olfactory epithelium and the recess epithelium in three species of African lungfish and one species of South American lungfish. However, a previous study suggested that in the African lungfish Protopterus dolloi these receptors are expressed only in the olfactory epithelium. In this study, we identified 21 type 1 vomeronasal receptor genes in P. dolloi and examined the expression sites in the olfactory organ. In P. dolloi, most cells expressing the type 1 vomeronasal receptor were distributed in the olfactory epithelium, but a few were also found in the recess epithelium. This implies that the functions of the olfactory epithelium and the primitive vomeronasal organ are incompletely separated, and that all extant African and South American lungfish share this trait.
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Affiliation(s)
- Shoko Nakamuta
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Atsuhiro Sakuma
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Hideaki Kato
- Faculty of Education, Shizuoka University, 836 Ohya, Shizuoka, 422-8529, Japan
| | - Masao Miyazaki
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Yoshio Yamamoto
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Nobuaki Nakamuta
- Laboratory of Veterinary Anatomy, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan.
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Zheng QM, Zhou ZR, Hou XY, Lv N, Zhang YQ, Cao H. Transcriptome Analysis of the Mouse Medial Prefrontal Cortex in a Chronic Constriction Injury Model. Neuromolecular Med 2023; 25:375-387. [PMID: 36971954 DOI: 10.1007/s12017-023-08742-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 09/27/2022] [Accepted: 03/03/2023] [Indexed: 03/29/2023]
Abstract
The medial prefrontal cortex (mPFC) is critical for both the sensory and emotional/cognitive components of pain. However, the underlying mechanism remains largely unknown. Here, we examined changes in the transcriptomic profiles in the mPFC of mice with chronic pain using RNA sequencing (RNA-seq) technology. A mouse model of peripheral neuropathic pain was established via chronic constriction injury (CCI) of the sciatic nerve. CCI mice developed sustained mechanical allodynia and thermal hyperalgesia, as well as cognitive impairment four weeks after surgery. RNA-seq was conducted 4 weeks after CCI surgery. Compared with contral group, RNA-seq identified a total 309 and 222 differentially expressed genes (DEGs) in the ipsilateral and contralateral mPFC of CCI model mice, respectively. GO analysis indicated that the functions of these genes were mainly enriched in immune- and inflammation-related processes such as interferon-gamma production and cytokine secretion. KEGG analysis further showed the enrichment of genes involved in the neuroactive ligand-receptor interaction signaling pathway and Parkinson disease pathway that have been reported to be importantly involved in chronic neuralgia and cognitive dysfunction. Our study may provide insights into the possible mechanisms underlying neuropathic pain and pain-related comorbidities.
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Affiliation(s)
- Qi-Min Zheng
- Department of Translational Neuroscience, Jing'an District Centre Hospital of Shanghai, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China
| | - Zi-Rui Zhou
- Department of Translational Neuroscience, Jing'an District Centre Hospital of Shanghai, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China
| | - Xin-Yu Hou
- Department of Translational Neuroscience, Jing'an District Centre Hospital of Shanghai, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China
| | - Ning Lv
- Department of Translational Neuroscience, Jing'an District Centre Hospital of Shanghai, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China
| | - Yu-Qiu Zhang
- Department of Translational Neuroscience, Jing'an District Centre Hospital of Shanghai, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China
| | - Hong Cao
- Department of Translational Neuroscience, Jing'an District Centre Hospital of Shanghai, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, 200032, China.
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Chen Q, Li N, Zeng S, Wu S, Luo X, Zhang S, Zhu L, Wu J, Xie T, Bai S, Zhang H, Jiang Z, Lin S, Wu N, Jiang Y, Fang S, Wang X, Shu Y, Luo H. ZIKV infection differentially affects the transcriptional profiles in HTR8 and U251 cells. Virus Res 2023; 334:199166. [PMID: 37390859 PMCID: PMC10410584 DOI: 10.1016/j.virusres.2023.199166] [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: 12/29/2022] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/02/2023]
Abstract
The mechanism by which Zika virus (ZIKV) causes severe birth defects in pregnant women remains unclear. Cell tropisms in placenta and brain play a crucial role in ZIKV pathogenesis, leading to congenital Zika syndrome (CZS). To identify the host factors involved in ZIKV infection, we compared the transcriptional profiles of ZIKV-infected human first-trimester placental trophoblast cells HTR8/SVneo and a human glioblastoma astrocytoma cell line U251. Our results demonstrated that ZIKV exhibited lower rates of mRNA replication and protein expression in HTR8 than in U251 cells, while showing a higher release of infectious viral particles. However, a greater number of differentially expressed genes (DEGs) were found in ZIKV-infected U251 cells than in ZIKV-infected HTR8 cells. Several of these DEGs were enriched in distinct biological processes related to the characteristics of each cell type that may contribute to foetal damage. Both cell types exhibited activation of common interferons, inflammatory cytokines, and chemokine production upon ZIKV infection. Moreover, the neutralization of tumour necrosis factor-alpha (TNF-α) promoted ZIKV infection in both trophoblasts and glioblastoma astrocytoma cells. Overall, we identified multiple DEGs associated with ZIKV pathogenesis.
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Affiliation(s)
- Qiqi Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China
| | - Nina Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China
| | - Shike Zeng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; Huizhou Municipal Central Hospital, Huizhou 516001, PR China
| | - Shu Wu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; Cancer Hospital Chinese Academy of Medical Sciences, Shenzhen Center, Shenzhen 518172, PR China
| | - Xin Luo
- The Emergency Department, Eighth People's Hospital of Nanyang City, Nanyang 473000, PR China
| | - Shengze Zhang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China
| | - Lin Zhu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jiani Wu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; Shaoxing Center for Disease Control and Prevention, Shaoxing 312075, PR China
| | - Ting Xie
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China
| | - Shaohui Bai
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China
| | - Hao Zhang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China
| | - Zhiyuan Jiang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China
| | - Shaoli Lin
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China
| | - Nan Wu
- Shenzhen Nanshan Center for Disease Control and Prevention, Shenzhen 518054, PR China
| | - Ying Jiang
- Shenzhen Nanshan Center for Disease Control and Prevention, Shenzhen 518054, PR China
| | - Shisong Fang
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518073, PR China
| | - Xin Wang
- Shenzhen Center for Disease Control and Prevention, Shenzhen 518073, PR China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100176, PR China; Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, PR China
| | - Huanle Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, PR China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, PR China; Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, PR China.
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Zhou Y, Li X, Zhang X, Li M, Luo N, Zhao Y. Screening of Candidate Housekeeping Genes in Uterus Caruncle by RNA-Sequence and qPCR Analyses in Different Stages of Goat ( Capra hircus). Animals (Basel) 2023; 13:1897. [PMID: 37370406 DOI: 10.3390/ani13121897] [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: 03/04/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
The uterus is a critical pregnancy organ for mammals. The normal growth and development of ruminant uterus caruncles are crucial to maintain gestation and fetal health in goats. Quantitative real-time polymerase chain reaction (qRT-PCR) is a reliable tool to study gene expression profiling for exploring the intrinsic mechanism underlying the conversion process of uterus caruncle tissue. However, the candidate housekeeping genes (HKGs) are required for normalizing the expression of function genes. In our study, 22 HKGs were selected from analyzing transcriptome data at non-pregnancy and pregnancy processes and previous reports about HKGs in goat tissues. We assessed them for expression suitability in 24 samples from uterus tissues at 15 non-pregnant days (Stage 1), early (Stage 2), and medium-later pregnant days (Stage 3). The expression stability of these genes was evaluated by using geNorm, Normfinder, Bestkeeper, and Delta Ct algorithms and, comprehensively, by ReFinder. In addition, the most and least stable HKGs were used to normalize the target genes expression of SPP1, VEGFA, and PAG8. It was found that traditional reference genes, such as ACTB and GAPDH, were not suitable for target gene normalization. In contrast, PPIB selected from RNA sequencing data and EIF3K selected from previous references showed the least variation and were recommended as the best HKGs during the nonpregnant stage and the whole stages of goat uterus caruncle tissue, respectively. It is the first time the HKGs genes in uterus during the non-pregnant day and throughout the total pregnancy have been explored. These findings found suitable HKGs in uterus caruncle tissues at various stages of non-pregnancy and pregnancy; these can be useful for gene expression studies to reveal the molecular mechanisms of uterus development in goats.
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Affiliation(s)
- Yumei Zhou
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing Herbivore Engineering Research Center, Chongqing 400715, China
| | - Xingchun Li
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing Herbivore Engineering Research Center, Chongqing 400715, China
| | - Xinyue Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing Herbivore Engineering Research Center, Chongqing 400715, China
| | - Minghui Li
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing Herbivore Engineering Research Center, Chongqing 400715, China
| | - Nanjian Luo
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing Herbivore Engineering Research Center, Chongqing 400715, China
- School of Preclinical Medicine, Zunyi Medical University, Zunyi 563000, China
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing Herbivore Engineering Research Center, Chongqing 400715, China
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Chen Y, Li W, Yang Y, Zhong R, Hu H, Huang C, Chen J, Liang L, Liu Y. Significant increase of anticancer efficacy in vitro and in vivo of liposome entrapped ruthenium(II) polypyridyl complexes. Eur J Med Chem 2023; 257:115541. [PMID: 37295162 DOI: 10.1016/j.ejmech.2023.115541] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 04/18/2023] [Revised: 05/23/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Two polypyridyl ruthenium(II) complexes [Ru(DIP)2(BIP)](PF6)2 (DIP = 4,7-diphenyl-1,10-phenanthrolie, BIP = 2-(1,1'-biphenyl-4-yl)-1H-imidazo[4,5-f][1,10]phenanthroline, Ru1) and [Ru(DIP)2(CBIP)](PF6)2 (CBIP = 2-(4'-chloro-1,1'-biphenyl-4-yl)-1H-imidazo[4,5-f][1,10]phenanthroline, Ru2) were synthesized. The cytotoxic activities in vitro of Ru1, Ru2 toward B16, A549, HepG2, SGC-7901, HeLa, BEL-7402, non-cancer LO2 were investigated using MTT method (3-(4,5-dimethylthiazole)-2,5-diphenltetraazolium bromide). Unexpectedly, Ru1, Ru2 can't prevent these cancer cells proliferation. To improve the anti-cancer effect, we used liposomes to entrap the complexes Ru1, Ru2 to form Ru1lipo, Ru2lipo. As expectation, Ru1lipo and Ru2lipo exhibit high anti-cancer efficacy, especially, Ru1lipo (IC50 3.4 ± 0.1 μM), Ru2lipo (IC50 3.5 ± 0.1 μM) display strong ability to block the cell proliferation in SGC-7901. The cell colony, wound healing, and cell cycle distribution show that the complexes can validly inhibit the cell growth at G2/M phase. Apoptotic studied with Annex V/PI doubling method showed that Ru1lipo and Ru2lipo can effectively induce apoptosis. Reactive oxygen species (ROS), malondialdehyde, glutathione and GPX4 demonstrate that Ru1lipo and Ru2lipo improve ROS and malondialdehyde levels, inhibit generation of glutathione, and finally result in a ferroptosis. Ru1lipo and Ru2lipo interact on the lysosomes and mitochondria and damage mitochondrial dysfunction. Additionally, Ru1lipo and Ru2lipo increase intracellular Ca2+ concentration and induce autophagy. The RNA-sequence and molecular docking were performed, the expression of Bcl-2 family was investigated by Western blot analysis. Antitumor in vivo experiments confirm that 1.23 mg/kg, 2.46 mg/kg of Ru1lipo possesses a high inhibitory rate of 53.53% and 72.90% to prevent tumor growth, hematoxylin-eosin (H&E) results show that Ru1lipo doesn't cause chronic organ damage and strongly promotes the necrosis of solid tumor. Taken together, we conclude that Ru1lipo and Ru2lipo cause cell death through the following pathways: autophagy, ferroptosis, ROS-regulated mitochondrial dysfunction, and blocking the PI3K/AKT/mTOR.
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Affiliation(s)
- Yichuan Chen
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Wenlong Li
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Yan Yang
- Department of Pharmacy, Guangdong Second Provincial General Hospital, 510317, PR China.
| | - Ruitong Zhong
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Huiyan Hu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Chunxia Huang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Jing Chen
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Lijuan Liang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Yunjun Liu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
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9
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Yuan Y, Zhang Y, Chen J, Huang C, Liu H, Li W, Liang L, Wang Y, Liu Y. Synthesis, biological evaluation of novel iridium(III) complexes targeting mitochondria toward melanoma B16 cells. Eur J Med Chem 2023; 247:115046. [PMID: 36577214 DOI: 10.1016/j.ejmech.2022.115046] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 10/07/2022] [Revised: 12/12/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
A new ligand 2-(1E,3E,5E,7E)-2,6-dimethyl-8-(2,6,6-trimethylcyclohex-1-yl)octa-1,2,5,7-tetraen-1-yl)-1H-imidazo[4,5-f][1,10]phenanthroline (DTOIP) was synthesized and combined with [Ir(ppy)2Cl]2·2H2O (ppy = deprotonated Hppy: 2-phenylpyridine), [Ir(piq)2Cl]2·2H2O (piq = deprotonated Hpiq: 1-phenylisoquinoline) and [Ir(bzq)2Cl]2·2H2O (bzq = deprotonated Hbzq: benzo[h]quinolone) to form [Ir(ppy)2(DTOIP)](PF6) (Ir1), [Ir(piq)2(DTOIP)](PF6) (Ir2), and [Ir(bzq)2(DTOIP)](PF6) (Ir3), respectively. The complexes were characterized by elemental analysis, high-resolution mass spectrometry (HRMS), 1H NMR and 13C NMR. The antiproliferative activity of the complexes toward B16, BEL-7402, Eca-109 and normal LO2 cells was evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method. Complexes Ir1, Ir2 and Ir3 showed high antiproliferative activity against B16 cells with a low IC50 values of 0.4 ± 0.1, 2.0 ± 0.1 and 1.4 ± 0.09 μM, respectively. Three-dimensional (3D) in vitro cell models also demonstrated that the iridium(III) complexes have a remarkable cytotoxicity to B16 cells. The experiments of cellular uptake, mitochondrial localization, and intracellular distribution of the drugs proved that the three iridium(III) complexes can enter the mitochondria, leading to the loss of mitochondrial membrane potential (MMP), decreased glutathione (GSH) levels, causing an increase of intracellular ROS content, and DNA damage, finally inducing apoptosis. RNA-sequence and bioinformatics analyses were used to analyze the differentially expressed genes and enriched biology processes. Antitumor in vivo demonstrated that complex Ir1 (5 mg/kg) exhibits a high efficacy to inhibit the tumor growth with an inhibitory rate of 71.67%. These results show that the complexes may be potent anticancer candidate drugs.
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Affiliation(s)
- Yuhan Yuan
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Yuanyuan Zhang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Jing Chen
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Chunxia Huang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Haimei Liu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Wenlong Li
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Lijuan Liang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Yi Wang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Yunjun Liu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
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10
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Ju HM, Kim BC, Lim I, Byun BH, Woo SK. Estimation of an Image Biomarker for Distant Recurrence Prediction in NSCLC Using Proliferation-Related Genes. Int J Mol Sci 2023; 24:ijms24032794. [PMID: 36769108 PMCID: PMC9917349 DOI: 10.3390/ijms24032794] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/22/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
This study aimed to identify a distant-recurrence image biomarker in NSCLC by investigating correlations between heterogeneity functional gene expression and fluorine-18-2-fluoro-2-deoxy-D-glucose positron emission tomography (18F-FDG PET) image features of NSCLC patients. RNA-sequencing data and 18F-FDG PET images of 53 patients with NSCLC (19 with distant recurrence and 34 without recurrence) from The Cancer Imaging Archive and The Cancer Genome Atlas Program databases were used in a combined analysis. Weighted correlation network analysis was performed to identify gene groups related to distant recurrence. Genes were selected for functions related to distant recurrence. In total, 47 image features were extracted from PET images as radiomics. The relationship between gene expression and image features was estimated using a hypergeometric distribution test with the Pearson correlation method. The distant recurrence prediction model was validated by a random forest (RF) algorithm using image texture features and related gene expression. In total, 37 gene modules were identified by gene-expression pattern with weighted gene co-expression network analysis. The gene modules with the highest significance were selected (p-value < 0.05). Nine genes with high protein-protein interaction and area under the curve (AUC) were identified as hub genes involved in the proliferation function, which plays an important role in distant recurrence of cancer. Four image features (GLRLM_SRHGE, GLRLM_HGRE, SUVmean, and GLZLM_GLNU) and six genes were identified to be correlated (p-value < 0.1). AUCs (accuracy: 0.59, AUC: 0.729) from the 47 image texture features and AUCs (accuracy: 0.767, AUC: 0.808) from hub genes were calculated using the RF algorithm. AUCs (accuracy: 0.783, AUC: 0.912) from the four image texture features and six correlated genes and AUCs (accuracy: 0.738, AUC: 0.779) from only the four image texture features were calculated using the RF algorithm. The four image texture features validated by heterogeneity group gene expression were found to be related to cancer heterogeneity. The identification of these image texture features demonstrated that advanced prediction of NSCLC distant recurrence is possible using the image biomarker.
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Affiliation(s)
- Hye Min Ju
- Radiological and Medico-Oncological Sciences, University of Science and Technology, Daejeon 34113, Republic of Korea
- Division of RI-Convergence Research, Korea Institute of Radiological and Medical Sciences, Seoul 07812, Republic of Korea
| | - Byung-Chul Kim
- Department of Nuclear Medicine, Korea Institute of Radiological and Medical Sciences, Seoul 07812, Republic of Korea
| | - Ilhan Lim
- Department of Nuclear Medicine, Korea Institute of Radiological and Medical Sciences, Seoul 07812, Republic of Korea
| | - Byung Hyun Byun
- Department of Nuclear Medicine, Korea Institute of Radiological and Medical Sciences, Seoul 07812, Republic of Korea
| | - Sang-Keun Woo
- Radiological and Medico-Oncological Sciences, University of Science and Technology, Daejeon 34113, Republic of Korea
- Division of RI-Convergence Research, Korea Institute of Radiological and Medical Sciences, Seoul 07812, Republic of Korea
- Correspondence: ; Tel.: +82-2-970-1659
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11
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Wang G, Zhang Y, Hu N, Liu Q, Ma F, Xie J. Mesenchymal Stem Cells Attenuate Acute Lung Injury in Mice Partly by Suppressing Alveolar Macrophage Activation in a PGE2-Dependent Manner. Inflammation 2022. [PMID: 35699823 DOI: 10.1007/s10753-022-01670-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/26/2022] [Accepted: 04/08/2022] [Indexed: 11/05/2022]
Abstract
Mesenchymal stem cells (MSCs) have been demonstrated to attenuate acute lung injury (ALI). We also found that they can suppress the activation of alveolar macrophages (AMs), which can partly account for their therapeutic effects. MSCs do not inherently own immunosuppressive effects, when co-cultured with inflammatory immune cells, MSCs can be activated by inflammatory cytokines and meanwhile exert immunosuppressive effects. In order to further research, RNA sequencing (RNA-seq) of MSCs cultured before and after co-culturing with activated macrophages was performed. The data suggested a total of 5268 differentially expressed genes (DEGs) along the process. We used the data of 2754 upregulated DEGs to develop a signaling network of genes and the transcription factors targeting them in order to predict the altered functions of MSCs after exposure to inflammatory stimuli. This constructed network revealed some critical target genes and potential roles of MSCs under inflammatory conditions. According to the network, Ptgs2 was assumed to be an important gene participating in the immunosuppressive effects of MSCs. We also identified significant increases in the expression of COX2 protein and the secretion of PGE2 from MSCs. The use of the COX2 inhibitor NS-398 restrained the secretion of PGE2 and reversed the suppression of macrophage activation by MSCs in vitro. In addition, a selective antagonist of PGE2 binding receptor (EP4 receptor), GW627368X, also reversed the inhibitory effects of MSCs on AMs and the protective effects in ALI mouse. In summary, the therapeutic effects of MSCs on ALI partly occur through suppressing AM activation via PGE2 binding to EP4 receptor.
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Cai J, Liang J, Zhang Y, Shen L, Lin H, Hu T, Zhan S, Xie M, Liang S, Xian M, Wang S. Cyclo-(Phe-Tyr) as a novel cyclic dipeptide compound alleviated ischemic stroke reperfusion brain injury via JUNB/JNK/NF-κB and SOX5/PI3K/AKT pathways. Pharmacol Res 2022; 180:106230. [PMID: 35483515 DOI: 10.1016/j.phrs.2022.106230] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 02/15/2022] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 12/20/2022]
Abstract
Ischemic stroke reperfusion (IR) can cause adverse reactions including apoptosis, oxidative stress, and inflammation, but the existing therapeutic strategies have been limited. Moreover, the regulation of microglia plays an important role in brain injury after reperfusion. Hence, it is imperative to find new and effective drugs for modulating microglia to treat IR brain injury. Cyclic peptide compound cyclo-(Phe-Tyr) (Sparganin C, SC) is a compound isolated from Sparganii Rhizoma. However, the protective effects of SC on the central nervous system are rather unclear. In an attempt to elucidate the protective effects and mechanism of SC on cerebral damage induced by the IR, we used a middle cerebral artery occlusion reperfusion (MCAO/R) model in rats and discovered that SC significantly decreased the size of cerebral infarcts, improved neurological scores, and blocked inflammatory and oxidative factor release. Using RNA-Seq and metabolomics association analyses, SC was shown to have a protective impact through the JUNB and SOX5-related pathways. Metabolomic analysis revealed twenty-eight differentially expressed biomarkers. In addition, the detection of SC content in brain tissue using LC/MS revealed that SC had blood-brain barrier penetration. To investigate the mechanism, we established an in vitro BV2 cell oxygen-glucose deprived re-oxygenation (OGD/R) model and used siRNA as well as an inhibitor. The protective effects of SC were dependent on the JUNB and SOX5 to inhibit inflammation and apoptosis in microglia. Our findings revealed for the first that SC against IR injury by reducing inflammation and apoptosis while simultaneously acting as potential therapeutic lead compound for ischemic stroke.
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Key Words
- 1-Deoxy-1-(N6-lysino)-D-fructose (PubChem CID: 433981164)
- 10Z
- 13Z
- 16Z)/16:0) (PubChem CID: 52923621)
- 2-O-(5,8,11,14,17-Eicosapentaenoyl)-1-O-hexadecylglycero-3-phosphocholine (PubChem CID: 10485310)
- Alanyl-Arginine (PubChem CID: 446132), PC (16:0/15:0) (PubChem CID: 24778680)
- Cyclo(Tyr-Phe) (PubChem CID: 44198062)
- Cyclo-(Phe-Tyr)
- Diacetone alcohol (PubChem CID: 31256)
- Homoanserine (PubChem CID: 20849429)
- Ischemic stroke reperfusion
- JUNB
- Methyl jasmonate (PubChem CID: 5281929)
- PC(22:4(7Z
- PC(P-18:1(11Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)) (PubChem CID: 53480781)
- RNA-sequence
- SOX5
- metabolomics
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Affiliation(s)
- Jiale Cai
- Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangzhou 510006, China; Engineering & Technology Research Center for Chinese Materia Medica Quality of the Universities of Guangdong Province, Guangzhou 510006, China
| | - Jiayin Liang
- Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangzhou 510006, China; Engineering & Technology Research Center for Chinese Materia Medica Quality of the Universities of Guangdong Province, Guangzhou 510006, China
| | - Yutong Zhang
- Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Lin Shen
- Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Huiting Lin
- Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangzhou 510006, China
| | - Tao Hu
- Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangzhou 510006, China; Engineering & Technology Research Center for Chinese Materia Medica Quality of the Universities of Guangdong Province, Guangzhou 510006, China
| | - Sikai Zhan
- Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangzhou 510006, China; Engineering & Technology Research Center for Chinese Materia Medica Quality of the Universities of Guangdong Province, Guangzhou 510006, China
| | - Meixia Xie
- Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangzhou 510006, China; Engineering & Technology Research Center for Chinese Materia Medica Quality of the Universities of Guangdong Province, Guangzhou 510006, China
| | - Shengwang Liang
- Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangzhou 510006, China; Engineering & Technology Research Center for Chinese Materia Medica Quality of the Universities of Guangdong Province, Guangzhou 510006, China
| | - Minghua Xian
- Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangzhou 510006, China; Engineering & Technology Research Center for Chinese Materia Medica Quality of the Universities of Guangdong Province, Guangzhou 510006, China.
| | - Shumei Wang
- Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangzhou 510006, China; Engineering & Technology Research Center for Chinese Materia Medica Quality of the Universities of Guangdong Province, Guangzhou 510006, China.
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13
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Zhou H, Gong K, Yang Y, Wu Q, Wang Q, Shen Y, Xie L, Gong Y, Liu H, Liu J. MKI67 as a potential diagnostic biomarker in pulmonary hypertension. Front Pediatr 2022; 10:1016889. [PMID: 36389368 PMCID: PMC9663476 DOI: 10.3389/fped.2022.1016889] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/11/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Right heart failure results from advanced pulmonary hypertension (PH) and has a poor prognosis. There are few available treatments for right heart failure. Pulmonary artery remodeling, including changes in pulmonary artery endothelial cells to endothelial-mesenchymal cells, and aberrant fibroblast and pulmonary artery smooth muscle cell (PASMC) proliferation, are characteristics of the pathophysiological process of PH. As a result, the clinical situation requires novel PH diagnostic and treatment targets. METHODS Monocrotaline was used to create an animal model of PH, and lung tissue was removed for transcriptome sequencing. The targets with the highest differences were chosen for transfection after possible targets were identified using bioinformatic techniques and confirmed by qPCR to examine their function in hypoxic PASMCs. RESULTS After sequencing 781 differentially expressed mRNAs, we compared them with the GEO dataset and found 43 differentially expressed genes. We chose the top three scores for further study and verification and discovered that MKI67, a crucial element of the cell cycle that regulates PASMC proliferation, had the greatest effect. After suppressing MKI67 in PASMCs, both cell proliferation and migration decreased. CONCLUSION Several potential targets were chosen for this study, and MKI67 was found to play a regulatory role in cell migration and proliferation. This implies that PH can be diagnosed and treated using MKI67.
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Affiliation(s)
- Huiling Zhou
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, China
| | - Ke Gong
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, China
| | - Yifeng Yang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, China
| | - Qin Wu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, China
| | - Qiuguo Wang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, China
| | - Yadan Shen
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, China.,Extracorporeal Life Support Center of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, China
| | - Li Xie
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, China
| | - Yibo Gong
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, China
| | - Haidan Liu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, China.,The Clinical Center for Gene Diagnosis and Therapy of the State Key Laboratory of Medical Genetics, the Second Xiangya Hospital of Central South University, Central South University, Changsha, China
| | - Jijia Liu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, China
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Lv D, Chen D, Wang Z, Cui Z, Ma JH, Ji S, Chen J, Tang S. COL10A1 is a novel factor in the development of choroidal neovascularization. Microvasc Res 2022; 139:104239. [PMID: 34520774 DOI: 10.1016/j.mvr.2021.104239] [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: 06/15/2021] [Revised: 08/16/2021] [Accepted: 08/31/2021] [Indexed: 11/29/2022]
Abstract
With the dramatic rise in the aging population, researching age-related macular degeneration (AMD), especially the severe form neovascular AMD (nAMD), has become more important than ever. In this study, we found that collagen type X was increased in retina-choroid tissue of mice with laser-induced choroidal neovascularization (CNV) based on immunohistofluorescence. RNA sequencing and bioinformatic analyses were performed to compare the retina-choroid tissue complex of the CNV mouse model to normal controls. Collagen type X alpha 1 chain (Col10a1) was among the most significantly upregulated genes, and the results were validated with an animal model at the mRNA and protein levels by quantitative real-time polymerase chain reaction (qPCR) and western blotting, respectively. COL10A1 was also upregulated in human retinal microvascular endothelial cells (HRMECs), human umbilical vein endothelial cells (HUVECs), RPE19 cells and RF/6A cells under hypoxic conditions. Next, in vitro and in vivo experiments were performed to study the effect of COL10A1 on neovascularization. siRNA knockdown of COL10A1 suppressed the proliferation and tube formation ability of HRMECs under hypoxic conditions. Snail family transcriptional repressor 1 (SNAIL1) and angiopoietin-2 (ANGPT2) were downregulated in COL10A1 knockdown HRMECs under hypoxic conditions and thus were potential downstream genes. Significant decreases in CNV leakage and CNV lesion area, as assessed by fundus fluorescein angiography (FFA) and immunofluorescence of choroidal flat mounts, respectively, were observed in a mouse model intravitreally injected with anti-collagen X monoclonal antibody (mAb) compared to the controls. In conclusion, COL10A1 promotes CNV formation and may represent a new candidate target for the treatment and diagnosis of nAMD and other neovascular diseases.
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Affiliation(s)
- Da Lv
- Aier School of Ophthalmology, Central South University, Changsha, China; Aier Eye Institute, Changsha, China
| | | | - Zhijie Wang
- Aier School of Ophthalmology, Central South University, Changsha, China; Aier Eye Institute, Changsha, China
| | | | - Jacey Hongjie Ma
- Aier School of Ophthalmology, Central South University, Changsha, China; Aier Eye Institute, Changsha, China
| | | | - Jiansu Chen
- Aier School of Ophthalmology, Central South University, Changsha, China; Aier Eye Institute, Changsha, China; Key Laboratory for Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China; Institute of Ophthalmology, Medical College, Jinan University, Guangzhou, China.
| | - Shibo Tang
- Aier School of Ophthalmology, Central South University, Changsha, China; Aier Eye Institute, Changsha, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
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15
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Sumiyoshi R, Koga T, Furukawa K, Umeda M, Yamamoto K, Mori R, Kawakami A. A case of tocilizumab-refractory idiopathic multicentric Castleman's disease successfully treated with sirolimus. Clin Immunol 2021; 233:108887. [PMID: 34798240 DOI: 10.1016/j.clim.2021.108887] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/18/2022]
Abstract
mTOR signaling may be a new therapeutic target for IL-6 inhibitor refractory iMCD-NOS.
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Affiliation(s)
- Remi Sumiyoshi
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Medical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan; Nagasaki University Hospital, Clinical Research Center, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Tomohiro Koga
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Medical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan; Center for Bioinformatics and Molecular Medicine, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.
| | - Kaori Furukawa
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Medical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Masataka Umeda
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Medical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Kazuko Yamamoto
- Department of Respiratory Medicine, Nagasaki University Hospital, Nagasaki, Japan
| | - Ryoichi Mori
- Department of Pathology, School of Medicine and Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Atsushi Kawakami
- Department of Immunology and Rheumatology, Division of Advanced Preventive Medical Sciences, Nagasaki University Graduate School of Medical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
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Xu L, Sun X, Wan X, Li K, Jian F, Li W, Jiang R, Han R, Li H, Kang X, Wang Y. Dietary supplementation with Clostridium butyricum improves growth performance of broilers by regulating intestinal microbiota and mucosal epithelial cells. ACTA ACUST UNITED AC 2021; 7:1105-1114. [PMID: 34738041 PMCID: PMC8551407 DOI: 10.1016/j.aninu.2021.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/11/2021] [Accepted: 01/17/2021] [Indexed: 12/14/2022]
Abstract
Clostridium butyricum has been widely considered an antibiotic substitute in recent years. It can promote growth performance, improve the immune response and enhance the intestinal barrier function of the host. In the present study, 1-d-old Arbor Acres (AA) broilers were fed C. butyricum (1 × 109 cfu/kg) for 28 d. The transcriptomic characteristics of epithelial cells of the cecal mucosa were determined by RNA-sequence, and the cecal microbiota composition was explored by 16S ribosomal RNA gene sequencing. The changes in the intestinal mucosa of broilers were then analyzed by tissue staining. Gene Ontology (GO) annotations identified substance transport and processes and pathways that might participate in intestinal development and cell viability. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the differentially expressed genes are involved in numerous pathways related to amino acid and vitamin metabolism and antioxidant and defensive functions, among others. The relative expression of some genes associated with intestinal barrier function (claudins 2, 15, 19, and 23, tight junction proteins 1, 2, and 3 and mucin 1) was significantly increased in the treatment group (P < 0.05 or P < 0.01). Moreover, the proportion of Firmicutes was higher in the C. butyricum-treated group, whereas the proportion of Proteobacteria was higher in the control group. At the genus level, the relative abundances of Butyricicoccus and Lactobacillus, among other bacteria, were increased after C. butyricum supplementation. The tissue staining analysis showed that the cecal mucosa of broilers was significantly ameliorated after the addition of C. butyricum (P < 0.05 or P < 0.01). These results showed that dietary supplementation with C. butyricum can enhance the antioxidant capacity, mucosal barrier function, and stabilize the cecal microbiota, resulting in improving the growth performance.
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Affiliation(s)
- Laipeng Xu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiangli Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xianhua Wan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Keke Li
- Henan Jinbaihe Biotechnology Co., Ltd, Anyang, 455000, China
| | - Fuchun Jian
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Wenting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450046, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450046, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450046, China
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450046, China
| | - Yanbin Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450046, China
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Abstract
Circular RNAs (circRNAs) are a new and large group of non-coding RNA molecules that are abundantly expressed in the central nervous system. However, very little is known about their roles in traumatic brain injury. In this study, we firstly screened differentially expressed circRNAs in normal and injured brain tissues of mice after traumatic brain injury. We found that the expression of circLphn3 was substantially decreased in mouse models of traumatic brain injury and in hemin-treated bEnd.3 (mouse brain cell line) cells. After overexpressing circLphn3 in bEnd.3 cells, the expression of the tight junction proteins, ZO-1, ZO-2, and occludin, was upregulated, and the expression of miR-185-5p was decreased. In bEnd.3 cells transfected with miR-185-5p mimics, the expression of ZO-1 was decreased. Dual-luciferase reporter assays showed that circLphn3 bound to miR-185-5p, and that miR-185-5p bound to ZO-1. Additionally, circLphn3 overexpression attenuated the hemin-induced high permeability of the in vitro bEnd.3 cell model of the blood-brain barrier, while miR-185-5p transfection increased the permeability. These findings suggest that circLphn3, as a molecular sponge of miR-185-5p, regulates tight junction proteins' expression after traumatic brain injury, and it thereby improves the permeability of the blood-brain barrier. This study was approved by the Animal Care and Use Committee of Chongqing Medical University of China (approval No. 2021-177) on March 22, 2021.
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Affiliation(s)
- Yu-Qi Cheng
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chen-Rui Wu
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Meng-Ran Du
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qiang Zhou
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Bi-Ying Wu
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jia-Yuan-Yuan Fu
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ehab Balawi
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wei-Lin Tan
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zheng-Bu Liao
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Zhai M, Yang S, Lin S, Zhu H, Xu L, Liao H, Song XJ. Distinct Gene Expression Patterns of Ion Channels and Cytokines in Rat Primary Sensory Neurons During Development of Bone Cancer and Cancer Pain. Front Mol Neurosci 2021; 14:665085. [PMID: 34025351 PMCID: PMC8134751 DOI: 10.3389/fnmol.2021.665085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/09/2021] [Indexed: 12/25/2022] Open
Abstract
Cancer and cancer pain processes a major clinical challenge and the underlined mechanisms of pathogenesis remain elusive. We examined the specific changes in the transcriptomic profiles in the dorsal root ganglion (DRG) neurons of rats with bone cancer and bone cancer pain (BCP) using RNA sequencing technology. The bone cancer and BCP was induced by tumor cells implantation (TCI) into the tibia bone cavity in adult female rats. One week after treatment, TCI caused up- and down-regulation of thousands of genes in DRG. These genes were mainly involved in the immune process, inflammatory response, and intracellular signaling transduction of carbohydrate and cytokine. The cAMP and calcium signaling pathways were the major processes in the initial responses. Differentially expressed gene (DEG) analysis further showed that the genes for ion channels increased during day 1-7, while the genes for cytokine signaling pathways sustainedly increased during day 7-14 after TCI. The time courses of gene expression for ion channels and cytokines support their distinct roles in the early induction and late maintenance of BCP development. In addition, among the top 500 up- and down-regulated genes, 80-90% were unique for bone cancer pain as well as neuropathic and inflammatory pain, while less than 2% were shared among the three different forms of pain. This study reveals the uniqueness of mechanisms underlying bone cancer with pain, which is, to a large extent, differently from pain after acute inflammatory and nerve injury and provides novel potential targets of DEGs for bone cancer with pain.
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Affiliation(s)
- Mingzhu Zhai
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education of China), Peking University Cancer Hospital and Institute, Beijing, China.,SUSTech Center for Pain Medicine, School of Medicine, Southern University of Science and Technology, Shenzhen, China.,Department of Perioperative Medicine, SUSTech Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Shaomin Yang
- Department of Pain Medicine, Shenzhen Nanshan Hospital, Huazhong University of Science and Technology, Shenzhen, China
| | - Simin Lin
- Department of Laboratory Animal Center, Southern University of Science and Technology, Shenzhen, China
| | - Hanxu Zhu
- SUSTech Center for Pain Medicine, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Lihong Xu
- SUSTech Center for Pain Medicine, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Huabao Liao
- SUSTech Center for Pain Medicine, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Xue-Jun Song
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education of China), Peking University Cancer Hospital and Institute, Beijing, China.,SUSTech Center for Pain Medicine, School of Medicine, Southern University of Science and Technology, Shenzhen, China.,Department of Perioperative Medicine, SUSTech Hospital, Southern University of Science and Technology, Shenzhen, China
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19
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Wang Y, Wang X, Xu W, Wang Y, Huang L, Yue J, An Q, Li S. Transcriptome analysis of mild hypothermia protection against radiation -induced rat lung injury based on RNA -seq. Zhong Nan Da Xue Xue Bao Yi Xue Ban 2021; 46:345-350. [PMID: 33967079 PMCID: PMC10930314 DOI: 10.11817/j.issn.1672-7347.2021.190727] [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] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Indexed: 11/03/2022]
Abstract
OBJECTIVES To analyze the differentially expressed genes (DEGs) with radiation-induced rat lung injury, and to reveal the protective mechanism for mild hypothermia in the radiation-induced lung injury in rats at the transcriptome level. METHODS A total of 10 male SD rats aged 6-8 weeks were randomly divided into 2 groups to establish a rat model of radiation-induced lung injury, and one group was treated with mild hypothermia. RNA was extracted from left lung tissue of each group, and sequenced by BGISEQ-500 platform. Significance analysis of DEGs was carried out by edgeR software. Gene ontology (GO) function enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were used to analyze the gene function. Then 5 key DEGs were verified by real-time reverse transcription PCR (real-time RT-PCR). RESULTS There were 2 790 DEGs (false discovery rate<0.001, |log2(fold change)|>1) in the mild hypothermia group compared with the model group, in which 2 257 genes were up-regulated and 533 genes were down-regulated. When real-time RT-PCR was used to validate the 5 key genes, the result was consistent with the RNA-seq. GO functional enrichment analysis showed that these DEGs were related to cell binding, metabolic process and cell membrane structure, etc. KEGG pathway enrichment analysis showed that these genes were involved in important biological pathways such as cell adhesion molecules, mammalian target of rapamycin, tight junction, and NF-κB. CONCLUSIONS The DEGs and pathways related to mild hypothermia protection against radiation-induced lung injury in rats are obtained, which provides an experimental basis for the protection of mild hypothermia against radiation-induced lung injury.
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Affiliation(s)
- Yuanfei Wang
- Drug Safety Evaluation Center of China Institute for Radiation Protection; Shanxi Key Laboratory of Drug Toxicology and Drug for Radiation Injury; Key Laboratory on Radiotoxicology and Radiopharmaceutical Preclinical Evaluation, China National Nuclear Corporation, Taiyuan 030006, China.
| | - Xingang Wang
- Drug Safety Evaluation Center of China Institute for Radiation Protection; Shanxi Key Laboratory of Drug Toxicology and Drug for Radiation Injury; Key Laboratory on Radiotoxicology and Radiopharmaceutical Preclinical Evaluation, China National Nuclear Corporation, Taiyuan 030006, China
| | - Wenli Xu
- Drug Safety Evaluation Center of China Institute for Radiation Protection; Shanxi Key Laboratory of Drug Toxicology and Drug for Radiation Injury; Key Laboratory on Radiotoxicology and Radiopharmaceutical Preclinical Evaluation, China National Nuclear Corporation, Taiyuan 030006, China
| | - Yongli Wang
- Drug Safety Evaluation Center of China Institute for Radiation Protection; Shanxi Key Laboratory of Drug Toxicology and Drug for Radiation Injury; Key Laboratory on Radiotoxicology and Radiopharmaceutical Preclinical Evaluation, China National Nuclear Corporation, Taiyuan 030006, China
| | - Liqun Huang
- Drug Safety Evaluation Center of China Institute for Radiation Protection; Shanxi Key Laboratory of Drug Toxicology and Drug for Radiation Injury; Key Laboratory on Radiotoxicology and Radiopharmaceutical Preclinical Evaluation, China National Nuclear Corporation, Taiyuan 030006, China
| | - Juan Yue
- Drug Safety Evaluation Center of China Institute for Radiation Protection; Shanxi Key Laboratory of Drug Toxicology and Drug for Radiation Injury; Key Laboratory on Radiotoxicology and Radiopharmaceutical Preclinical Evaluation, China National Nuclear Corporation, Taiyuan 030006, China
| | - Quan An
- Drug Safety Evaluation Center of China Institute for Radiation Protection; Shanxi Key Laboratory of Drug Toxicology and Drug for Radiation Injury; Key Laboratory on Radiotoxicology and Radiopharmaceutical Preclinical Evaluation, China National Nuclear Corporation, Taiyuan 030006, China
| | - Shufang Li
- Drug Safety Evaluation Center of China Institute for Radiation Protection; Shanxi Key Laboratory of Drug Toxicology and Drug for Radiation Injury; Key Laboratory on Radiotoxicology and Radiopharmaceutical Preclinical Evaluation, China National Nuclear Corporation, Taiyuan 030006, China.
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20
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Zhou J, Chen S, Shi W, David-Schwartz R, Li S, Yang F, Lin Z. Transcriptome profiling reveals the effects of drought tolerance in Giant Juncao. BMC Plant Biol 2021; 21:2. [PMID: 33390157 PMCID: PMC7780708 DOI: 10.1186/s12870-020-02785-7] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 12/06/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Giant Juncao is often used as feed for livestock because of its huge biomass. However, drought stress reduces forage production by affecting the normal growth and development of plants. Therefore, investigating the molecular mechanisms of drought tolerance will provide important information for the improvement of drought tolerance in this grass. RESULTS A total of 144.96 Gb of clean data was generated and assembled into 144,806 transcripts and 93,907 unigenes. After 7 and 14 days of drought stress, a total of 16,726 and 46,492 differentially expressed genes (DEGs) were observed, respectively. Compared with normal irrigation, 16,247, 23,503, and 11,598 DEGs were observed in 1, 5, and 9 days following rehydration, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed abiotic stress-responsive genes and pathways related to catalytic activity, methyltransferase activity, transferase activity, and superoxide metabolic process. We also identified transcription factors belonging to several families, including basic helix-loop-helix (bHLH), WRKY, NAM (no apical meristem), ATAF1/2 and CUC2 (cup-shaped cotyledon) (NAC), fatty acyl-CoA reductase (FAR1), B3, myeloblastosis (MYB)-related, and basic leucine zipper (bZIP) families, which are important drought-rehydration-responsive proteins. Weighted gene co-expression network analysis was also used to analyze the RNA-seq data to predict the interrelationship between genes. Twenty modules were obtained, and four of these modules may be involved in photosynthesis and plant hormone signal transduction that respond to drought and rehydration conditions. CONCLUSIONS Our research is the first to provide a more comprehensive understanding of DEGs involved in drought stress at the transcriptome level in Giant Juncao with different drought and recovery conditions. These results may reveal insights into the molecular mechanisms of drought tolerance in Giant Juncao and provide diverse genetic resources involved in drought tolerance research.
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Affiliation(s)
- Jing Zhou
- National Engineering Research Center of Juncao, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Siqi Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenjiao Shi
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rakefet David-Schwartz
- Institute of Plant Sciences, Volcani Center, Agriculture Research Organization, 50250, Bet Dagan, Israel
| | - Sutao Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Fulin Yang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhanxi Lin
- National Engineering Research Center of Juncao, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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21
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He C, Liu X, Teixeira da Silva JA, Liu N, Zhang M, Duan J. Transcriptome sequencing and metabolite profiling analyses provide comprehensive insight into molecular mechanisms of flower development in Dendrobium officinale (Orchidaceae). Plant Mol Biol 2020; 104:529-548. [PMID: 32876816 DOI: 10.1007/s11103-020-01058-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 04/30/2020] [Accepted: 08/18/2020] [Indexed: 05/21/2023]
Abstract
This research provides comprehensive insight into the molecular networks and molecular mechanisms underlying D. officinale flower development. Flowers are complex reproductive organs and play a crucial role in plant propagation, while also providing sustenance for insects and natural bioactive metabolites for humans. However, knowledge about gene regulation and floral metabolomes in flowers is limited. In this study, we used an important orchid species (Dendrobium officinale), whose flowers can be used to make herbal tea, to perform transcriptome sequencing and metabolic profiling of early- and medium-stage flower buds, as well as opened flowers, to provide comprehensive insight into the molecular mechanisms underlying flower development. A total of 8019 differentially expressed genes (DEGs) and 239 differentiated metabolites were found. The transcription factors that were identified and analyzed belong exclusively to the MIKC-type MADS-box proteins and auxin responsive factors that are known to be involved in flower development. The expression of genes involved in chlorophyll and carotenoid biosynthesis strongly matched the metabolite accumulation patterns. The genes related to flavonoid and polysaccharide biosynthesis were active during flower development. Interestingly, indole-3-acetic acid and abscisic acid, whose trend of accumulation was inverse during flower development, may play an important role in this process. Collectively, the identification of DEGs and differentiated metabolites could help to illustrate the regulatory networks and molecular mechanisms important for flower development in this orchid.
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Affiliation(s)
- Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xuncheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | | | - Nan Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Mingze Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
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22
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Ge Z, Zhou B, Zheng X, Yang M, Lü J, Deng H, Tang K, Chen W. [Circular RNA expression pattern and competing endogenous RNA network involved in rotator cuff tendinopathy]. Zhongguo Xiu Fu Chong Jian Wai Ke Za Zhi 2020; 34:608-614. [PMID: 32410429 DOI: 10.7507/1002-1892.201911094] [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] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Objective To detect the differentially expressed circular RNA (circRNA) in rotator cuff tendinopathy and analyze the potential molecular mechanism of these parental genes. Methods Ten supraspinatus tendons donated from patients who underwent tendon repair surgery between June 2018 and June 2019 were used for RNA-sequence. All rotator cuff tendinopathy and normal tendon samples were confirmed by MRI, histological staining, and observation by arthroscopy. All pathological tendons were matched with tendon samples for patients' age, gender, body mass index, and Bonar score. The bioinformatic analysis was performed based on the differentially expressed circRNA and their parental genes, including gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and competing endogenous RNA (ceRNA) network construction. Results There were 94 differentially expressed circRNAs, including 31 up-regulated and 63 down-regulated, detected between the rotator cuff tendinopathy and normal tendon samples with |log2 fold change (FC)| >2, P<0.05. GO analysis showed that the genes were mostly enriched in response to cyclic adenosine monophosphate (cAMP). KEGG pathway analysis showed that the most genes were enriched in extracellular matrix-receptor interaction, protein digestion and absorption, cell cycle, and nuclear factor κB signaling pathway. ceRNA networks showed the interactions among circRNAs, mRNAs, and miRNAs. And circRNA.8951-has-miR-6089-DNMT3B was the most sum max energy. Conclusion This bioinformatic study reveals several potential therapeutic targets for rotator cuff tendinopathy, which paves the way to better treatment and prevention of this disorder.
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Affiliation(s)
- Zilu Ge
- Department of Orthopeadics/Sports Medicine Center, the First Affiliated Hospital of the Army Medical University, Chongqing, 400038, P.R.China
| | - Binghua Zhou
- Department of Orthopeadics/Sports Medicine Center, the First Affiliated Hospital of the Army Medical University, Chongqing, 400038, P.R.China
| | - Xiaolong Zheng
- Department of Orthopeadics/Sports Medicine Center, the First Affiliated Hospital of the Army Medical University, Chongqing, 400038, P.R.China
| | - Mingyu Yang
- Department of Orthopeadics/Sports Medicine Center, the First Affiliated Hospital of the Army Medical University, Chongqing, 400038, P.R.China
| | - Jingtong Lü
- Department of Orthopeadics/Sports Medicine Center, the First Affiliated Hospital of the Army Medical University, Chongqing, 400038, P.R.China
| | - Honghao Deng
- Department of Orthopeadics/Sports Medicine Center, the First Affiliated Hospital of the Army Medical University, Chongqing, 400038, P.R.China
| | - Kanglai Tang
- Department of Orthopeadics/Sports Medicine Center, the First Affiliated Hospital of the Army Medical University, Chongqing, 400038, P.R.China
| | - Wan Chen
- Department of Orthopeadics/Sports Medicine Center, the First Affiliated Hospital of the Army Medical University, Chongqing, 400038, P.R.China
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Zhu M, Yu J, Zhao M, Wang M, Yang G. Transcriptome analysis of metabolisms related to fruit cracking during ripening of a cracking-susceptible grape berry cv. Xiangfei (Vitis vinifera L.). Genes Genomics 2020; 42:639-50. [PMID: 32274647 DOI: 10.1007/s13258-020-00930-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/28/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Grape is an economically valuable fruit around the world. However, some cultivars are prone to fruit cracking during ripening, leading to severe losses. OBJECTIVE We aimed to find important metabolisms related to fruit cracking during ripening process. METHODS RNA-Sequence and analysis was applied to the pericarp of cracking-susceptible 'Xiang Fei' at 1 (W1), 2 (W2) and 3 weeks (W3) after veraison on Illumina HiSeq xten; RESULTS: Compared with W1, the berry cracking rate increased significantly in W2 and W3. Through transcriptomic analysis, a total of 22,609 genes were expressed in the grape pericarp, among which 805 and 2758 genes were significantly differentially regulated in W1-vs.-W2 and W1-vs.-W3 comparison, respectively. Besides, 304 and 354 genes were up- and down-regulated in both comparisons. The significantly enriched GO terms of both W1-W2 and W1-W3 are related to cell wall and wax biosynthesis. And lipid metabolism, which are involved in the top 20 enriched KEGG pathways of both comparisons, was related to wax biosynthesis. Further, GO enrichment analysis of differentially expressed genes (DEGs) with same regulatory changes also indicated that the continuously up-regulated DEGs are significantly enriched in cell wall component biosynthesis and hydrolase. CONCLUSION These findings suggested that genes related to cell wall metabolism and cuticle biosynthesis may play important roles in regulating grape berry cracking. Our results provide a reference for further studies on the molecular mechanism underlying fruit cracking.
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Li Y, Wu Z, Li R, Miao Y, Weng P, Wang L. Integrated transcriptomic and proteomic analysis of the acetic acid stress in Issatchenkia orientalis. J Food Biochem 2020; 44:e13203. [PMID: 32232868 DOI: 10.1111/jfbc.13203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 07/11/2019] [Revised: 02/22/2020] [Accepted: 02/25/2020] [Indexed: 11/30/2022]
Abstract
Issatchenkia orientalis known as a multi-tolerant non-Saccharomyces yeast, which tolerant environmental stresses, exhibits potential in wine making and bioethanol production. It is essential for the growth of I. orientalis to tolerant acetic acid in the mixed cultures with Saccharomyces cerevisiae. In this work, RNA-sequence and TMT (Tandem Mass Tag) were used to examine the comprehensive transcriptomic and proteomic profiles of I. orientalis in response to acetic acid. The results showed that 876 genes were identified differentially transcribed in I. orientalis genome and 399 proteins expressed in proteome after 4 hr acetic acid (90 mM, pH 4.5). The comprehensive analysis showed a series of determinants of acetic acid tolerance: Glycolysis and TCA cycle provide enough nicotinamide adenine dinucleotide to effectively convert acetic acid. Genes associated with potassium, iron, zinc, and glutathione synthesis were upregulated. The same changes of differentially expressed genes and proteins were mainly concentrated in chaperones, coenzyme, energy production, and transformation. PRACTICAL APPLICATIONS: In addition to the main fermentation products, wine yeast also produces metabolite acetic acid in the fermentation process, and yeast cells are exposed to acetic acid stress, which restrains cell proliferation. Issatchenkia orientalis exhibits great potential in winemaking and bioethanol production. The yeast is known as a multi-tolerant non-Saccharomyces yeast that can tolerate a variety of environmental stresses. In this study, RNA-Seq and TMT were conducted to investigate the changes in transcriptional and proteomic profile of I. orientalis under acetic acid stress. The knowledge of the transcription and expression changes of the I. orientalis is expected to understand the tolerance mechanisms in I. orientalis and to guide traditional fermentation processes by Saccharomyces cerevisiae improving its high resistance to acetic acid stress.
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Affiliation(s)
- Yingdi Li
- Department of Food Science and Engineering, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China
| | - Zufang Wu
- Department of Food Science and Engineering, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China.,Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang Province, Ningbo University, Ningbo, P.R. China
| | - Ruoyun Li
- Department of Food Science and Engineering, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China
| | - Yingjie Miao
- Department of Food Science and Engineering, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China
| | - Peifang Weng
- Department of Food Science and Engineering, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China
| | - Liping Wang
- School of Food Science and Technology, Shanghai Ocean University, Shanghai, China
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Taguchi K, Chen L, Usawachintachit M, Hamamoto S, Kang M, Sugino T, Unno R, Tzou DT, Sherer BA, Okada A, Yasui T, Ho SP, Stoller ML, Chi T. Fatty acid-binding protein 4 downregulation drives calcification in the development of kidney stone disease. Kidney Int 2020; 97:1042-1056. [PMID: 32247632 DOI: 10.1016/j.kint.2020.01.042] [Citation(s) in RCA: 17] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 12/30/2022]
Abstract
Nephrolithiasis is a significant source of morbidity, and its incidence has increased significantly over the last decades. This rise has been attributed to concurrent increasing rates of obesity, associated with a 3-time risk of developing NL. To date, the mechanism by which obesity is linked to stone formation has not been elucidated. We aimed to utilize a transcriptomics approach to discover the missing link between these two epidemic diseases. We investigated gene expression profiling of nephrolithiasis patients by two RNA-sequencing approaches: comparison between renal papilla tissue with and without the presence of calcified Randall's plaques (RP), and comparison between the papilla, medulla, and cortex regions from within a single recurrent stone forming kidney. Results were overlaid between differently expressed genes found in the patient cohort and in the severely lithogenic kidney to identify common genes. Overlay of these two RNA-sequencing datasets demonstrated there is impairment of lipid metabolism in renal papilla tissue containing RP linked to downregulation of fatty acid binding protein (FABP) 4. Immunohistochemistry of human kidney specimens and microarray analysis of renal tissue from a nephrolithiasis mouse model confirmed that FABP4 downregulation is associated with renal stone formation. In a FABP4 knockout mouse model, FABP4 deficiency resulted in development of both renal and urinary crystals. Our study revealed that FABP4 plays an important, previously unrecognized role in kidney stone formation, providing a feasible mechanism to explain the link between nephrolithiasis and metabolic syndrome.
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Affiliation(s)
- Kazumi Taguchi
- Department of Urology, University of California, San Francisco, California, USA; Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Ling Chen
- Division of Biomaterials and Bioengineering, Department of Preventive and Restorative Dental Sciences, University of California San Francisco, San Francisco, California, USA
| | - Manint Usawachintachit
- Department of Urology, University of California, San Francisco, California, USA; Division of Urology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Shuzo Hamamoto
- Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Misun Kang
- Division of Biomaterials and Bioengineering, Department of Preventive and Restorative Dental Sciences, University of California San Francisco, San Francisco, California, USA
| | - Teruaki Sugino
- Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Rei Unno
- Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - David T Tzou
- Department of Urology, University of California, San Francisco, California, USA
| | - Benjamin A Sherer
- Department of Urology, University of California, San Francisco, California, USA
| | - Atsushi Okada
- Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Takahiro Yasui
- Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Sunita P Ho
- Division of Biomaterials and Bioengineering, Department of Preventive and Restorative Dental Sciences, University of California San Francisco, San Francisco, California, USA
| | - Marshall L Stoller
- Department of Urology, University of California, San Francisco, California, USA
| | - Thomas Chi
- Department of Urology, University of California, San Francisco, California, USA.
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Iqbal A, Dong Q, Wang X, Gui H, Zhang H, Zhang X, Song M. Transcriptome Analysis Reveals Differences in Key Genes and Pathways Regulating Carbon and Nitrogen Metabolism in Cotton Genotypes under N Starvation and Resupply. Int J Mol Sci 2020; 21:E1500. [PMID: 32098345 DOI: 10.3390/ijms21041500] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/12/2020] [Accepted: 02/20/2020] [Indexed: 01/03/2023] Open
Abstract
Nitrogen (N) is the most important limiting factor for cotton production worldwide. Genotype-dependent ability to cope with N shortage has been only partially explored in cotton, and in this context, the comparison of molecular responses of cotton genotypes with different nitrogen use efficiency (NUE) is of particular interest to dissect the key molecular mechanisms underlying NUE. In this study, we employed Illumina RNA-Sequencing to determine the genotypic difference in transcriptome profile using two cotton genotypes differing in NUE (CCRI-69, N-efficient, and XLZ-30, N-inefficient) under N starvation and resupply treatments. The results showed that a large genetic variation existed in differentially expressed genes (DEGs) related to amino acid, carbon, and nitrogen metabolism between CCRI-69 and XLZ-30. Further analysis of metabolic changes in cotton genotypes under N resupply showed that nitrogen metabolism and aromatic amino acid metabolism pathways were mainly enriched in CCRI-69 by regulating carbon metabolism pathways such as starch and sucrose metabolism, glycolysis/gluconeogenesis, and pentose phosphate pathway. Additionally, we performed an expression network analysis of genes related to amino acid, carbon, and nitrogen metabolism. In total, 75 and 33 genes were identified as hub genes in shoots and roots of cotton genotypes, respectively. In summary, the identified hub genes may provide new insights into coordinating carbon and nitrogen metabolism and improving NUE in cotton.
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Zhou A, Cao Y, Zhou D, Hu S, Tan W, Xiao X, Yu Y, Li X. Global transcriptomic analysis of Cronobacter sakazakii CICC 21544 by RNA-seq under inorganic acid and organic acid stresses. Food Res Int 2019; 130:108963. [PMID: 32156398 DOI: 10.1016/j.foodres.2019.108963] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 08/13/2019] [Revised: 12/23/2019] [Accepted: 12/25/2019] [Indexed: 01/07/2023]
Abstract
Cronobacter sakazakii is a common foodborne pathogen that can tolerate various stress conditions. Acidic environment is a common stress condition encountered by bacteria in food processing and gastrointestinal digestion, including both inorganic and organic acids. In order to elucidate the Acid Tolerance Response (ATR) of C. sakazakii, we performed high-throughput RNA-seq to compare gene expression under hydrochloric acid and citric acid stresses. In this study, 107 differentially expressed genes (DEGs) were identified in both acids, of which 85 DEGs were functionally related to the regulation of acid tolerance. Multiple layers of mechanisms may be applied by C. sakazakii in response to acid stress: Firstly, in order to reduce excessive intracellular protons, C. sakazakii pumps them out through trans-membrane proteins or consumes them through metabolic reactions. Secondly, under acidic conditions, a large amount of reactive oxygen species and hydroxyl radicals accumulate in the cells, resulting in oxidative damage. C. sakazakii protects cells by up-regulating the antioxidant stress genes such as soxS and madB. Thirdly, C. sakazakii chooses energy efficient metabolic pathways to reduce energy consumption and maintain necessary processes. Finally, genes involved in chemotaxis and motility were differentially expressed to respond to different acidic conditions. This study systematically analyzed the acid-resistant mechanism of C. sakazakii under the stress of organic and inorganic acids, and provided a theoretical basis for better control of its contamination in food.
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Affiliation(s)
- Ailian Zhou
- School of Food Sciences and Engineering, South China University of Technology, Guangzhou City, Guangdong Province 510640, China
| | - Yifang Cao
- School of Food Sciences and Engineering, South China University of Technology, Guangzhou City, Guangdong Province 510640, China
| | - Donggen Zhou
- Ningbo International Travel Healthcare Center. No. 336 Liuting Street, Haishu District, Ningbo City, Zhejiang Province 315012, China
| | - Shuangfang Hu
- Key Laboratory of Molecular Epidemiology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen City, Guangdong Province 518055, China
| | - Wanjing Tan
- School of Food Sciences and Engineering, South China University of Technology, Guangzhou City, Guangdong Province 510640, China
| | - Xinglong Xiao
- School of Food Sciences and Engineering, South China University of Technology, Guangzhou City, Guangdong Province 510640, China.
| | - Yigang Yu
- School of Food Sciences and Engineering, South China University of Technology, Guangzhou City, Guangdong Province 510640, China
| | - Xiaofeng Li
- State Key Laboratory of Pulp and Paper Engineering, College of Light Industry and Food Sciences, South China University of Technology, 381 Wusan Road, Tianhe District, Guangzhou City 510640, Guangdong Province, China.
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28
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Qu J, Xu S, Tian X, Li T, Wang L, Zhong Y, Xue J, Guo D. Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents. PeerJ 2019; 7:e7528. [PMID: 31523504 PMCID: PMC6717500 DOI: 10.7717/peerj.7528] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 03/08/2019] [Accepted: 07/22/2019] [Indexed: 01/06/2023] Open
Abstract
In seeds, the endosperm is a crucial organ that plays vital roles in supporting embryo development and determining seed weight and quality. Starch is the predominant storage carbohydrate of the endosperm and accounts for ∼70% of the mature maize kernel weight. Nonetheless, because starch biosynthesis is a complex process that is orchestrated by multiple enzymes, the gene regulatory networks of starch biosynthesis, particularly amylose and amylopectin biosynthesis, have not been fully elucidated. Here, through high-throughput RNA sequencing, we developed a temporal transcriptome atlas of the endosperms of high-amylose maize and common maize at 5-, 10-, 15- and 20-day after pollination and found that 21,986 genes are involved in the programming of the high-amylose and common maize endosperm. A coexpression analysis identified multiple sequentially expressed gene sets that are closely correlated with cellular and metabolic programmes and provided valuable insight into the dynamic reprogramming of the transcriptome in common and high-amylose maize. In addition, a number of genes and transcription factors were found to be strongly linked to starch synthesis, which might help elucidate the key mechanisms and regulatory networks underlying amylose and amylopectin biosynthesis. This study will aid the understanding of the spatiotemporal patterns and genetic regulation of endosperm development in different types of maize and provide valuable genetic information for the breeding of starch varieties with different contents.
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Affiliation(s)
- Jianzhou Qu
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.,Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, China
| | - Shutu Xu
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.,Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, China
| | - Xiaokang Tian
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.,Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, China
| | - Ting Li
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.,Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, China
| | - Licheng Wang
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.,Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, China
| | - Yuyue Zhong
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.,Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, China
| | - Jiquan Xue
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.,Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, China
| | - Dongwei Guo
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.,Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, China
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29
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Sun Z, Li J, Lin M, Zhang S, Luo J, Tang Y. An RNA-seq-Based Expression Profiling of Radiation-Induced Esophageal Injury in a Rat Model. Dose Response 2019; 17:1559325819843373. [PMID: 31105479 PMCID: PMC6505253 DOI: 10.1177/1559325819843373] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 11/16/2022] Open
Abstract
Radiation-induced acute injury is the main reason for the suspension of radiotherapy and unsuccessful treatment of cancer. It is of great importance to understand the molecular mechanism of radiation-induced esophageal injury. We used RNA-seq data from normal esophageal tissue and irradiated esophageal tissues and applied computational approaches to identify and characterize differentially expressed genes and detected 40 059 messenger RNAs (mRNAs) previously annotated and 717 novel long noncoding RNAs (lncRNAs). There were 14 upregulated and 32 downregulated lncRNAs among the differentially expressed lncRNA group. Their target genes were involved in the mRNA surveillance pathway, pathological immune responses, and cellular homeostasis. Additionally, we found 853 differentially expressed mRNAs, and there were 384 upregulated and 469 downregulated mRNAs. Notably, we found that the differentially expressed mRNAs were enriched for steroid biosynthesis, the tumor necrosis factor signaling pathway, focal adhesion, pathways in cancer, extracellular matrix-receptor interaction, and so on. The response of normal esophageal tissues to ionizing radiation is multifarious. The radiation-induced cell damage response by multiple pathways followed by pathological immune responses activated. Studies on the dynamic network of molecules involved in radiation-induced esophageal injury are under way to clarify the regulatory mechanisms and identify the candidate targets.
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Affiliation(s)
- Zhiqiang Sun
- Department of Oncology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Jinhui Li
- Department of Gastroenterology, South Campus, Ren Ji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Min Lin
- Department of Gastroenterology, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Shuyu Zhang
- School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Judong Luo
- Department of Oncology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Yiting Tang
- Department of Radiotherapy, Changzhou Tumor Hospital, Soochow University, Changzhou, China
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30
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Kim J, Shin MY, Park SJ. RNA-sequencing Profiles of Cell Cycle-Related Genes Upregulated during the G2-Phase in Giardia lamblia. Korean J Parasitol 2019; 57:185-189. [PMID: 31104412 PMCID: PMC6526219 DOI: 10.3347/kjp.2019.57.2.185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/27/2019] [Indexed: 01/13/2023]
Abstract
To identify the component(s) involved in cell cycle control in the protozoan Giardia lamblia, cells arrested at the G1/S- or G2-phase by treatment with nocodazole and aphidicolin were prepared from the synchronized cell cultures. RNA-sequencing analysis of the 2 stages of Giardia cell cycle identified several cell cycle genes that were up-regulated at the G2-phase. Transcriptome analysis of cells in 2 distinct cell cycle stages of G. lamblia confirmed previously reported components of cell cycle (PcnA, cyclin B, and CDK) and identified additional cell cycle components (NEKs, Mad2, spindle pole protein, and CDC14A). This result indicates that the cell cycle machinery operates in this protozoan, one of the earliest diverging eukaryotic lineages.
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Affiliation(s)
- Juri Kim
- Department of Environmental Medical Biology and Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Mee Young Shin
- Department of Environmental Medical Biology and Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Soon-Jung Park
- Department of Environmental Medical Biology and Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
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Wang R, Xu S, Jiang C, Sun H, Feng S, Zhou S, Zhuang G, Bai Z, Zhuang X. Transcriptomic Sequencing and Co-Expression Network Analysis on Key Genes and Pathways Regulating Nitrogen Use Efficiency in Myriophyllum aquaticum. Int J Mol Sci 2019; 20:ijms20071587. [PMID: 30934901 PMCID: PMC6480359 DOI: 10.3390/ijms20071587] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 02/13/2019] [Revised: 03/19/2019] [Accepted: 03/27/2019] [Indexed: 11/16/2022] Open
Abstract
Massively input and accumulated ammonium is one of the main causes of eutrophication in aquatic ecosystems, which severely deteriorates water quality. Previous studies showed that one of the commonly used macrophytes, Myriophyllum aquaticum, was capable of not only withstanding ammonium of high concentration, but also efficiently assimilating extracellular ammonium to constitutive amino acids and proteins. However, the genetic mechanism regulating such efficient nitrogen metabolism in M. aquaticum is still poorly understood. Therefore, RNA-based analysis was performed in this study to understand the ammonium regulatory mechanism in M. aquaticum in response to various concentrations of ammonium. A total of 7721 genes were differentially expressed, of which those related to nitrogen-transport, assimilation, and remobilization were highly-regulated in response to various concentrations of ammonium. We have also identified transcription factors and protein kinases that were rapidly induced in response to ammonium, which suggests their involvement in ammonium-mediated signalling. Meanwhile, secondary metabolism including phenolics and anthocyanins biosynthesis was also activated in response to various concentrations of ammonium, especially at high ammonium concentrations. These results proposed a complex physiological and genetic regulation network related to nitrogen, carbohydrate, transcription factors, and secondary metabolism for nitrogen use efficiency in M. aquaticum.
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Affiliation(s)
- Rui Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shengjun Xu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Cancan Jiang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Haishu Sun
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shugeng Feng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Sining Zhou
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guoqiang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhihui Bai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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Chappell S, Patel T, Guetta-Baranes T, Sang F, Francis PT, Morgan K, Brookes KJ. Observations of extensive gene expression differences in the cerebellum and potential relevance to Alzheimer's disease. BMC Res Notes 2018; 11:646. [PMID: 30180886 PMCID: PMC6123947 DOI: 10.1186/s13104-018-3732-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/24/2018] [Indexed: 12/15/2022] Open
Abstract
Objectives In order to determine how gene expression is altered in disease it is of fundamental importance that the global distribution of gene expression levels across the disease-free brain are understood and how differences between tissue types might inform tissue choice for investigation of altered expression in disease state. The aim of this pilot project was to use RNA-sequencing to investigate gene expression differences between five general areas of post-mortem human brain (frontal, temporal, occipital, parietal and cerebellum), and in particular changes in gene expression in the cerebellum compared to cortex regions for genes relevant to Alzheimer’s disease, as the cerebellum is largely preserved from disease pathology and could be an area of interest for neuroprotective pathways. Results General gene expression profiles were found to be similar between cortical regions of the brain, however the cerebellum presented a distinct expression profile. Focused exploration of gene expression for genes associated with Alzheimer’s disease suggest that those involved in the immunity pathway show little expression in the brain. Furthermore some Alzheimer’s disease associated genes display significantly different expression in the cerebellum compared with other brain regions, which might indicate potential neuroprotective measures.
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Affiliation(s)
- Sally Chappell
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Tulsi Patel
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Tamar Guetta-Baranes
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Fei Sang
- DeepSeq Facility, University of Nottingham, Nottingham, UK
| | - Paul T Francis
- Wolfson Centre for Age Related Diseases, King's College London, London, UK
| | - Kevin Morgan
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Keeley J Brookes
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK.
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Qureshi AA, Khan DA, Mushtaq S, Ye SQ, Xiong M, Qureshi N. δ-Tocotrienol feeding modulates gene expression of EIF2, mTOR, protein ubiquitination through multiple-signaling pathways in chronic hepatitis C patients. Lipids Health Dis 2018; 17:167. [PMID: 30031388 PMCID: PMC6054847 DOI: 10.1186/s12944-018-0804-7] [Citation(s) in RCA: 3] [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: 04/17/2018] [Accepted: 06/26/2018] [Indexed: 12/12/2022] Open
Abstract
Background δ-Tocotrienol is a naturally occurring proteasome inhibitor, which has the capacity to inhibit proliferation and induce apoptosis in several cancer cells obtained from several organs of humans, and other cancer cell lines. Moreover, results of plasma total mRNAs after δ-tocotrienol feeding to hepatitis C patients revealed significant inhibition in the expression of pro-inflammatory cytokines (TNF-α, VCAM1, proteasome subunits) and induction in the expression of ICAM1 and IFN-γ after post-treatment. This down-regulation of proteasome subunits leads to autophagy, apoptosis of immune cells and several genes. The present study describes RNA-sequence analysis of plasma total mRNAs obtained from δ-tocotrienol treatment of hepatitis C patients on gene expression regulated by proteasome. Methods Pooled specimens of plasma total mRNAs of pre-dose versus post-dose of δ-tocotrienol treatment of hepatitis C patients were submitted to RNA-sequence analyses. The data based on > 1 and 8-fold expression changes of 2136 genes were uploaded into “Ingenuity Pathway Analyses (IPA)” for core analysis, which describes possible canonical pathways, upstream regulators, diseases and functional metabolic networks. Results The IPA of “molecules” indicated fold change in gene expression of 953 molecules, which covered several categories of biological biomarkers. Out of these, gene expression of 220 related to present study, 12 were up-regulated, and 208 down-regulated after δ-tocotrienol treatment. The gene expression of transcription regulators (ceramide synthase 3 and Mohawk homeobox) were up-regulated, and gene expression of 208 molecules were down-regulated, involved in several biological functions (HSP90AB1, PSMC3, CYB5R4, NDUFB1, CYP2R1, TNFRF1B, VEGFA, GPR65, PIAS1, SFPQ, GPS2, EIF3F, GTPBP8, EIF4A1, HSPA14, TLR8, TUSSC2). IPA of “causal network” indicated gene regulators (676), in which 76 down-regulated (26 s proteasomes, interleukin cytokines, and PPAR-ligand-PPA-Retinoic acid-RXRα, PPARγ-ligand-PPARγ-Retinoic acid-RARα, IL-21, IL-23) with significant P-values. The IPA of “diseases and functions” regulators (85) were involved with cAMP, STAT2, 26S proteasome, CSF1, IFNγ, LDL, TGFA, and microRNA-155-5p, miR-223, miR-21-5p. The IPA of “upstream analysis” (934) showed 57 up-regulated (mainly 38 microRNAs) and 64 gene regulators were down-regulated (IL-2, IL-5, IL-6, IL-12, IL-13, IL-15, IL-17, IL-18, IL-21, IL-24, IL-27, IL-32), interferon β-1a, interferon γ, TNF-α, STAT2, NOX1, prostaglandin J2, NF-κB, 1κB, TCF3, and also miRNA-15, miRNA-124, miRNA-218-5P with significant activation of Z-Score (P < 0.05). Conclusions This is first report describing RNA-sequence analysis of δ-tocotrienol treated plasma total mRNAs obtained from chronic hepatitis C patients, that acts via multiple-signaling pathways without any side-effects. These studies may lead to development of novel classes of drugs for treatment of chronic hepatitis C patients. Electronic supplementary material The online version of this article (10.1186/s12944-018-0804-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Asaf A Qureshi
- Department of Biomedical Science, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA.
| | - Dilshad A Khan
- Department of Chemical Pathology and Endocrinology, Armed Forces Institute of Pathology (AFIP), National University of Medical Sciences, Rawalpindi, 64000, Pakistan
| | - Shahida Mushtaq
- Department of Chemical Pathology and Endocrinology, Armed Forces Institute of Pathology (AFIP), National University of Medical Sciences, Rawalpindi, 64000, Pakistan
| | - Shui Qing Ye
- Department of Biomedical Science, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA.,Division of Experimental and Translational Genetics, Department of Pediatrics, Childern's Mercy Hospital, 2401 Gillham Road, Kansas City, MO, 64108, USA.,Department of Biomedical and Health Informatics, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA
| | - Min Xiong
- Department of Biomedical Science, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA.,Division of Experimental and Translational Genetics, Department of Pediatrics, Childern's Mercy Hospital, 2401 Gillham Road, Kansas City, MO, 64108, USA
| | - Nilofer Qureshi
- Department of Biomedical Science, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA.,Pharmacology/Toxicology, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO, 64108, USA
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Hook SE, Kroon FJ, Metcalfe S, Greenfield PA, Moncuquet P, McGrath A, Smith R, Warne MSJ, Turner RD, McKeown A, Westcott DA. Global transcriptomic profiling in barramundi (Lates calcarifer) from rivers impacted by differing agricultural land uses. Environ Toxicol Chem 2017; 36:103-112. [PMID: 27219023 DOI: 10.1002/etc.3505] [Citation(s) in RCA: 5] [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: 08/11/2015] [Revised: 11/23/2015] [Accepted: 05/22/2016] [Indexed: 06/05/2023]
Abstract
Most catchments discharging into the Great Barrier Reef lagoon have elevated loads of suspended sediment, nutrients, and pesticides, including photosystem II inhibiting herbicides, associated with upstream agricultural land use. To investigate potential impacts of declining water quality on fish physiology, RNA sequencing (RNASeq) was used to characterize and compare the hepatic transcriptomes of barramundi (Lates calcarifer) captured from 2 of these tropical river catchments in Queensland, Australia. The Daintree and Tully Rivers differ in upstream land uses, as well as sediment, nutrient, and pesticide loads, with the area of agricultural land use and contaminant loads lower in the Daintree. In fish collected from the Tully River, transcripts involved in fatty acid metabolism, amino acid metabolism, and citrate cycling were also more abundant, suggesting elevated circulating cortisol concentrations, whereas transcripts involved in immune responses were less abundant. Fish from the Tully also had an increased abundance of transcripts associated with xenobiotic metabolism. Previous laboratory-based studies observed similar patterns in fish and amphibians exposed to the agricultural herbicide atrazine. If these transcriptomic patterns are manifested at the whole organism level, the differences in water quality between the 2 rivers may alter fish growth and fitness. Environ Toxicol Chem 2017;36:103-112. © 2016 SETAC.
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Affiliation(s)
- Sharon E Hook
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Kirrawee, New South Wales, Australia
| | - Frederieke J Kroon
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Suzanne Metcalfe
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Dutton Park, Queensland, Australia
| | - Paul A Greenfield
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, New South Wales, Australia
| | - Philippe Moncuquet
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Acton, Australian Capital Territory, Australia
| | - Annette McGrath
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Acton, Australian Capital Territory, Australia
| | - Rachael Smith
- Queensland Department of Science, Information Technology, and Innovation, Brisbane, Queensland, Australia
| | - Michael St J Warne
- Queensland Department of Science, Information Technology, and Innovation, Brisbane, Queensland, Australia
| | - Ryan D Turner
- Queensland Department of Science, Information Technology, and Innovation, Brisbane, Queensland, Australia
| | - Adam McKeown
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Smithfield, Queensland, Australia
| | - David A Westcott
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Atherton, Queensland, Australia
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Yang S, Cai Q, Bard J, Jamison J, Wang J, Yang W, Hu BH. Variation analysis of transcriptome changes reveals cochlear genes and their associated functions in cochlear susceptibility to acoustic overstimulation. Hear Res 2015; 330:78-89. [PMID: 26024952 DOI: 10.1016/j.heares.2015.04.010] [Citation(s) in RCA: 14] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 04/04/2015] [Accepted: 04/10/2015] [Indexed: 10/23/2022]
Abstract
Individual variation in the susceptibility of the auditory system to acoustic overstimulation has been well-documented at both the functional and structural levels. However, the molecular mechanism responsible for this variation is unclear. The current investigation was designed to examine the variation patterns of cochlear gene expression using RNA-seq data and to identify the genes with expression variation that increased following acoustic trauma. This study revealed that the constitutive expressions of cochlear genes displayed diverse levels of gene-specific variation. These variation patterns were altered by acoustic trauma; approximately one-third of the examined genes displayed marked increases in their expression variation. Bioinformatics analyses revealed that the genes that exhibited increased variation were functionally related to cell death, biomolecule metabolism, and membrane function. In contrast, the stable genes were primarily related to basic cellular processes, including protein and macromolecular syntheses and transport. There was no functional overlap between the stable and variable genes. Importantly, we demonstrated that glutamate metabolism is related to the variation in the functional response of the cochlea to acoustic overstimulation. Taken together, the results indicate that our analyses of the individual variations in transcriptome changes of cochlear genes provide important information for the identification of genes that potentially contribute to the generation of individual variation in cochlear responses to acoustic overstimulation.
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Affiliation(s)
- Shuzhi Yang
- Center for Hearing and Deafness, University at Buffalo, NY, 14214, USA.
| | - Qunfeng Cai
- Center for Hearing and Deafness, University at Buffalo, NY, 14214, USA.
| | - Jonathan Bard
- Next-Generation Sequencing and Expression Analysis Core, New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, 14263, USA.
| | - Jennifer Jamison
- Next-Generation Sequencing and Expression Analysis Core, New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, 14263, USA.
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY, 14263, USA.
| | - Weiping Yang
- Center for Hearing and Deafness, University at Buffalo, NY, 14214, USA.
| | - Bo Hua Hu
- Center for Hearing and Deafness, University at Buffalo, NY, 14214, USA.
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