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Wang Y, Yuan H, Zhao M, Fang L. Identification of signature of gene expression in biliary atresia using weighted gene co-expression network analysis. Medicine (Baltimore) 2022; 101:e30232. [PMID: 36123893 PMCID: PMC9478247 DOI: 10.1097/md.0000000000030232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Biliary atresia (BA) is the most common cause of obstructive jaundice during the neonatal period. This study aimed to identify gene expression signature in BA. The datasets were obtained from the Gene Expression Omnibus database. Weighted gene co-expression network analysis identified a critical module associated with BA, whereas Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed the functions of the essential modules. The high-connectivity genes in the most relevant module constructed protein-protein interaction networks via the string website and Cytoscape software. Hub genes screened by lasso regression consisted of a disease classification model using the randomforest method. Receiver operating characteristic curves were used to assess models' sensitivity and specificity and the model was verified using the internal and external validation sets. Ten gene modules were constructed by WGCNA, of which the brown module had a strong positive correlation with BA, comprising 443 genes. Functional enrichment analysis revealed that module genes were mainly involved in biological processes, such as extracellular matrix organization, cell adhesion, inflammatory response, and the Notch pathway (P < .001), whereas these genes were involved in the metabolic pathways and cell adhesion molecules (P < .001). Thirty-nine high-connectivity genes in the brown module constructed protein-protein interaction networks. keratin 7 (KRT7) and C-X-C motif chemokine ligand 8 (CXCL8) were used to construct a diagnostic model that had an accuracy of 93.6% and the area under the receiver operating curves for the model was 0.93. The study provided insight into the signature of gene expression and possible pathogenesis of BA; furthermore, it identified that the combination of KRT7 and CXCL8 could be a potential diagnostic model for BA.
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Affiliation(s)
- Yongliang Wang
- Hepatological Surgery Department, The First People’s Hospital of Guiyang City, Guizhou Province, China
| | - Hongtao Yuan
- Hepatological Surgery Department, The First People’s Hospital of Guiyang City, Guizhou Province, China
- *Correspondence: Hongtao Yuan, Hepatological Surgery Department, The NO.1 People’s Hospital of Guiyang City, Guizhou Province, China (e-mail:
| | - Maojun Zhao
- Emergency Department, The First People’s Hospital of Guiyang City, Guizhou Province, China
| | - Li Fang
- Department of Critical Care Medicine, The First People’s Hospital of Guiyang City, Guizhou Province, China
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2
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Ekambaram R, Dharmalingam S. Design and development of biomimetic electrospun sulphonated polyether ether ketone nanofibrous scaffold for bone tissue regeneration applications: in vitro and in vivo study. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2022; 33:947-975. [PMID: 34985405 DOI: 10.1080/09205063.2022.2025637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/30/2021] [Accepted: 01/02/2022] [Indexed: 06/14/2023]
Abstract
Bone defect restoration remains challenging in orthopedic medical practices. In this study an attempt is carried out to probe the use of new biomimetic SPEEK (sulfonated polyether ether ketone) based nanofibrous scaffold to deliver amine functionalized hydroxyapatite nanoparticles loaded resveratrol for its potent functionality in osteogenic differentiation. SPEEK polymer with reactive functional group SO3H was synthesized through process of sulphonation reaction. Amine functionalized nanoparticles with protonated amino groups revamp the molecular interaction by the formation of hydrogen bonds that in turn intensify the bioactivity of the nanofibrous scaffold. Osteoconductive functionalized nanohydroxyapatite enhances the cell proliferation and osteogenicity with improved cell attachment and spreading. The results of FT-IR, XRD, Carbon-Silica NMR and EDX analysis confirmed the amine functionalization of the hydroxyapatite nanoparticles. Surface morphological analysis of the fabricated nanofibers through SEM and AFM analysis shows vastly interconnected porous structure that mimics the bone extracellular matrix, which enhances the cell compatibility. Cell adhesion and live dead assay of the nanoscaffolds express less cytotoxicity. Mineralization and alkaline phosphatase assay establish the osteogenic differentiation of the nanofibrous scaffold. The in vitro biocompatibility studies reveal that the fabricated scaffold was osteo-compatible with MG63 cell lines. Hemocompatibility study further proved that the designed biomimetic nanofibrous scaffold was highly suitable for bone tissue engineering. The results of in vivo analysis in zebrafish model for the fabricated nanofibers demonstrated significant increase in the caudal fin regeneration indicating mineralization of osteoblast. Thus, the commending results obtained instigate the potentiality of the composite nanofibrous scaffold as an effective biomimetic substrate for bone tissue regeneration.
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3
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Kapuria S, Bai H, Fierros J, Huang Y, Ma F, Yoshida T, Aguayo A, Kok F, Wiens KM, Yip JK, McCain ML, Pellegrini M, Nagashima M, Hitchcock PF, Mochizuki N, Lawson ND, Harrison MMR, Lien CL. Heterogeneous pdgfrb+ cells regulate coronary vessel development and revascularization during heart regeneration. Development 2022; 149:274137. [PMID: 35088848 PMCID: PMC8918812 DOI: 10.1242/dev.199752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022]
Abstract
Endothelial cells emerge from the atrioventricular canal to form coronary blood vessels in juvenile zebrafish hearts. We find that pdgfrb is first expressed in the epicardium around the atrioventricular canal and later becomes localized mainly in the mural cells. pdgfrb mutant fish show severe defects in mural cell recruitment and coronary vessel development. Single-cell RNA sequencing analyses identified pdgfrb+ cells as epicardium-derived cells (EPDCs) and mural cells. Mural cells associated with coronary arteries also express cxcl12b and smooth muscle cell markers. Interestingly, these mural cells remain associated with coronary arteries even in the absence of Pdgfrβ, although smooth muscle gene expression is downregulated. We find that pdgfrb expression dynamically changes in EPDCs of regenerating hearts. Differential gene expression analyses of pdgfrb+ EPDCs and mural cells suggest that they express genes that are important for regeneration after heart injuries. mdka was identified as a highly upregulated gene in pdgfrb+ cells during heart regeneration. However, pdgfrb but not mdka mutants show defects in heart regeneration after amputation. Our results demonstrate that heterogeneous pdgfrb+ cells are essential for coronary development and heart regeneration.
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Affiliation(s)
- Subir Kapuria
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA,Authors for correspondence (; ; )
| | - Haipeng Bai
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA,Laboratory of Chemical Genomics, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, People's Republic of China
| | - Juancarlos Fierros
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA,Department of Biology, California State University, San Bernardino, San Bernardino, CA 92407, USA
| | - Ying Huang
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Feiyang Ma
- Department of Molecular, Cell and Developmental Biology, College of Letters and Sciences, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Tyler Yoshida
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA,Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90007, USA
| | - Antonio Aguayo
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Fatma Kok
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Katie M. Wiens
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA,Science Department, Bay Path University, Longmeadow, MA 01106, USA
| | - Joycelyn K. Yip
- Laboratory for Living Systems Engineering, Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Megan L. McCain
- Laboratory for Living Systems Engineering, Department of Biomedical Engineering, USC Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA,Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, College of Letters and Sciences, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Mikiko Nagashima
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
| | - Peter F. Hitchcock
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
| | - Naoki Mochizuki
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Osaka, 564-8565, Japan
| | - Nathan D. Lawson
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Michael M. R. Harrison
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA,Authors for correspondence (; ; )
| | - Ching-Ling Lien
- Department of Surgery, The Saban Research Institute and Heart Institute of Children's Hospital Los Angeles, Los Angeles, CA 90027, USA,Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA,Authors for correspondence (; ; )
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Banu S, Gaur N, Nair S, Ravikrishnan T, Khan S, Mani S, Bharathi S, Mandal K, Kuram NA, Vuppaladadium S, Ravi R, Murthy CLN, Quoseena M, Babu NS, Idris MM. Transcriptomic and proteomic analysis of epimorphic regeneration in zebrafish caudal fin tissue. Genomics 2022; 114:110300. [DOI: 10.1016/j.ygeno.2022.110300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 01/13/2022] [Accepted: 02/01/2022] [Indexed: 11/26/2022]
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Ulhaq ZS, Tse WKF. A Brief Analysis of Proteomic Profile Changes during Zebrafish Regeneration. Biomolecules 2021; 12:biom12010035. [PMID: 35053182 PMCID: PMC8773715 DOI: 10.3390/biom12010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022] Open
Abstract
Unlike mammals, zebrafish are capable to regenerate many of their organs, however, the response of tissue damage varies across tissues. Understanding the molecular mechanism behind the robust regenerative capacity in a model organism may help to identify and develop novel treatment strategies for mammals (including humans). Hence, we systematically analyzed the current literature on the proteome profile collected from different regenerated zebrafish tissues. Our analyses underlining that several proteins and protein families responsible as a component of cytoskeleton and structure, protein synthesis and degradation, cell cycle control, and energy metabolism were frequently identified. Moreover, target proteins responsible for the initiation of the regeneration process, such as inflammation and immune response were less frequently detected. This highlights the limitation of previous proteomic analysis and suggested a more sensitive modern proteomics analysis is needed to unfold the mechanism. This brief report provides a list of target proteins with predicted functions that could be useful for further biological studies.
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Affiliation(s)
- Zulvikar Syambani Ulhaq
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Maulana Malik Ibrahim State Islamic University of Malang, Batu 65144, Indonesia;
- National Research and Innovation Agency, Central Jakarta 10340, Indonesia
| | - William Ka Fai Tse
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
- Correspondence:
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Wang M, Xu W, Zou J, Li S, Song Z, Zheng F, Ji W, Xu Z, Wang Q. The Programming of Antioxidant Capacity, Immunity, and Lipid Metabolism in Dojo Loach ( Misgurnus anguillicaudatus) Larvae Linked to Sodium Chloride and Hydrogen Peroxide Pre-treatment During Egg Hatching. Front Physiol 2021; 12:768907. [PMID: 34777025 PMCID: PMC8581469 DOI: 10.3389/fphys.2021.768907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Non-nutritional stress during early life period has been reported to promote the metabolic programming in fish induced by nutritional stimulus. Sodium chloride (NaCl) and hydrogen peroxide (H2O2) have been widely applied during fish egg hatching, but the influences on health and metabolism of fish in their later life remain unknown. In the present study, H2O2 treatment at 400mg/L but not 200mg/L significantly increased the loach hatchability and decreased the egg mortality, while NaCl treatment at 1,000 and 3,000mg/L showed no significant influences on the loach hatchability nor egg mortality. Further studies indicated that 400mg/L H2O2 pre-treatment significantly enhanced the antioxidant capacity and the mRNA expression of genes involved in immune response of loach larvae, accompanied by the increased expression of genes involved in fish early development. However, the expression of most genes involved in lipid metabolism, including catabolism and anabolism of loach larvae, was significantly upregulated after 200mg/L H2O2 pre-treatment. NaCl pre-treatment also increased the expression of antioxidant enzymes; however, only the expression of C1q within the detected immune-related genes was upregulated in loach larvae. One thousand milligram per liter NaCl pre-treatment significantly increased the expression of LPL and genes involved in fish early development. Thus, our results suggested the programming roles of 400mg/L H2O2 pre-treatment during egg hatching in enhancing antioxidant capacity and immune response of fish larvae via promoting fish early development.
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Affiliation(s)
- Mengya Wang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Wenyu Xu
- Ocean University of China, Qingdao, China
| | - Jiahong Zou
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Shuaitong Li
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zixi Song
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Feifei Zheng
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Wei Ji
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zhen Xu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Qingchao Wang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
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Weng Y, Huang Z, Wu A, Yu Q, Lu H, Lou Z, Lu L, Bao Z, Jin Y. Embryonic toxicity of epoxiconazole exposure to the early life stage of zebrafish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 778:146407. [PMID: 34030390 DOI: 10.1016/j.scitotenv.2021.146407] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/03/2021] [Accepted: 03/06/2021] [Indexed: 06/12/2023]
Abstract
Epoxiconazole (EPX), as a broad-spectrum triazole fungicide, is widely used in agriculture to resist pests and diseases, while it may have potential toxicity to non-target organisms. In the present study, early developmental stage zebrafish were used as the subject organisms to assess the toxicity of EPX, and the possible mechanism of toxicity was also discussed by biochemical and transcriptomic analysis. Through embryo toxicity test, we had made it clear that the 96 h LC50 of embryo was 7.204 mg/L, and acute exposure to EPX effected hatching rate, heartbeats, body length and even morphological defects. Then, by being exposed to EPX for 7 days at concentrations of 175 (1/40 LC50), 350 (1/20 LC50) and 700 (1/10 LC50), biochemical parameters were affected, mainly manifested as increase of the triglyceride (TG) level and decrease of glucose content. Correspondingly, the transcription of genes related of glucose metabolism, lipid metabolism and cholesterol metabolism were also affected significantly in larval zebrafish. Moreover, some pathways, including lipid metabolism, glucose metabolism and amino acid metabolism were affected through transcriptome sequencing analysis in the larval zebrafish. Further data analysis based on the sequencing, EPX exposure also affected the expression of genes related to cell apoptosis. We further conformed that the bright fluorescence on the liver and bright spots near the liver by acridine orange staining. In addition, the mRNA levels of apoptosis related genes were also significantly affected in the EPX exposed larval zebrafish. Taken together, the work could provide an insight into toxic effects of EPX on the zebrafish larvae at embryo toxicity and transcriptional levels, providing some evidences for the toxic effects of triazole fungicides on non-target organisms.
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Affiliation(s)
- You Weng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhuizui Huang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Anyi Wu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Qianxuan Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Huahui Lu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Ze Lou
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Longxi Lu
- Zhejiang Provincial Center for Disease Control and Prevention, Zhejiang 310051, China.
| | - Zhiwei Bao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yuanxiang Jin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China.
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Ohgo S, Sakamoto T, Nakajima W, Matsunaga S, Wada N. Visualization of extracellular vesicles in the regenerating caudal fin blastema of zebrafish using in vivo electroporation. Biochem Biophys Res Commun 2020; 533:1371-1377. [PMID: 33077180 DOI: 10.1016/j.bbrc.2020.10.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 10/10/2020] [Indexed: 01/03/2023]
Abstract
Zebrafish have high regenerative ability in several organs including the fin. Although various mechanisms underlying fin regeneration have been revealed, some mechanisms remain to be elucidated. Recently, extracellular vesicles (EVs) have been the focus of research with regard to their role in cell-to-cell communication. It has been suggested that cells in regenerating tissues communicate using EVs. In this study, we examined the involvement of EVs in the caudal fin regeneration of zebrafish using an in vivo electroporation method. The process of regeneration appeared normal after in vivo electroporation, and the transferred plasmid showed mosaic expression in the blastema. We took advantage of this mosaic expression to observe the distribution of exosomal markers in the blastema. We transferred exosomal markers by in vivo electroporation and identified EVs in the regenerating caudal fin. The results suggest that blastemal cells communicate with other cells via EVs during caudal fin regeneration.
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Affiliation(s)
- Shiro Ohgo
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan.
| | - Takuya Sakamoto
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Wataru Nakajima
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Naoyuki Wada
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
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