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Yamaguchi N, Sawano T, Nakatani J, Nakano-Doi A, Nakagomi T, Matsuyama T, Tanaka H. Voluntary running exercise modifies astrocytic population and features in the peri-infarct cortex. IBRO Neurosci Rep 2023; 14:253-263. [PMID: 36880055 PMCID: PMC9984846 DOI: 10.1016/j.ibneur.2023.02.004] [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: 10/07/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Rehabilitative exercise following a brain stroke has beneficial effects on the morphological plasticity of neurons. Particularly, voluntary running exercise after focal cerebral ischemia promotes functional recovery and ameliorates ischemia-induced dendritic spine loss in the peri-infarct motor cortex layer 5. Moreover, neuronal morphology is affected by changes in the perineuronal environment. Glial cells, whose phenotypes may be altered by exercise, are known to play a pivotal role in the formation of this perineuronal environment. Herein, we investigated the effects of voluntary running exercise on glial cells after middle cerebral artery occlusion. Voluntary running exercise increased the population of glial fibrillary acidic protein-positive astrocytes born between post-operative days (POD) 0 and 3 on POD15 in the peri-infarct cortex. After exercise, transcriptomic analysis of post-ischemic astrocytes revealed 10 upregulated and 70 downregulated genes. Furthermore, gene ontology analysis showed that the 70 downregulated genes were significantly associated with neuronal morphology. In addition, exercise reduced the number of astrocytes expressing lipocalin 2, a regulator of dendritic spine density, on POD15. Our results suggest that exercise modifies the composition of astrocytic population and their phenotype.
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Key Words
- ACSA-2, astrocyte cell surface antigen-2
- Astrocytes
- BrdU, 5-bromo-2′-deoxyuridine
- Cerebral ischemia
- DEG, differentially expressed gene
- EDTA, ethylenediaminetetraacetic acid
- FBS, fetal bovine serum
- GFAP, glial fibrillary acidic protein
- GO, gene ontology
- GST-π, glutathione S-transferase-π
- Gstp1, glutathione S-transferase, pi 1
- Gstp2, glutathione S-transferase, pi 2
- Iba1, ionized calcium-binding adapter molecule 1
- Ig, immunoglobulin
- Lcn2, lipocalin 2
- MCAO, middle cerebral artery occlusion
- PBS, phosphate-buffered saline
- PFA, 4% paraformaldehyde
- POD, post-operative day
- Proliferation
- TUNEL, terminal deoxynucleotidyl transferase-mediated dUTP nick 3’-end labeling
- Transcriptome
- Vegfa, vascular endothelial growth factor A
- Voluntary running exercise
- Vtn, vitronectin
- qPCR, quantitative polymerase chain reaction
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Affiliation(s)
- Natsumi Yamaguchi
- Pharmacology Laboratory, Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan.,Ritsumeikan Advanced Research Academy, 1 Nishinokyo-Suzaku-cho, Nakagyo-ku, Kyoto 604-8520, Japan
| | - Toshinori Sawano
- Pharmacology Laboratory, Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
| | - Jin Nakatani
- Pharmacology Laboratory, Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
| | - Akiko Nakano-Doi
- Institute for Advanced Medical Sciences, Hyogo College of Medicine, 1-1 Mukogawacho, Nishinomiya 663-8501, Japan.,Department of Therapeutic Progress in Brain Diseases, Hyogo College of Medicine, 1-1 Mukogawacho, Nishinomiya 663-8501, Japan
| | - Takayuki Nakagomi
- Institute for Advanced Medical Sciences, Hyogo College of Medicine, 1-1 Mukogawacho, Nishinomiya 663-8501, Japan.,Department of Therapeutic Progress in Brain Diseases, Hyogo College of Medicine, 1-1 Mukogawacho, Nishinomiya 663-8501, Japan
| | - Tomohiro Matsuyama
- Department of Therapeutic Progress in Brain Diseases, Hyogo College of Medicine, 1-1 Mukogawacho, Nishinomiya 663-8501, Japan
| | - Hidekazu Tanaka
- Pharmacology Laboratory, Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577, Japan
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Nousbeck J, McAleer MA, Irvine AD. Peripheral Blood Gene Expression Profile of Infants with Atopic Dermatitis. JID Innov 2023; 3:100165. [PMID: 36699197 PMCID: PMC9868882 DOI: 10.1016/j.xjidi.2022.100165] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/06/2022] Open
Abstract
To enhance the understanding of molecular mechanisms and mine previously unidentified biomarkers of pediatric atopic dermatitis, PBMC gene expression profiles were generated by RNA sequencing in infants with atopic dermatitis and age-matched controls. A total of 178 significantly differentially expressed genes (DEGs) (115 upregulations and 63 downregulations) were seen, compared with those in healthy controls. The DEGs identified included IL1β, TNF, TREM1, IL18R1, and IL18RAP. DEGs were validated by real-time RT- qPCR in a larger number of samples from PBMCs of infants with atopic dermatitis aged <12 months. Using the DAVID (Database for Annotation, Visualization and Integrated Discovery) database, functional and pathway enrichment analyses of DEGs were performed. Gene ontology enrichment analysis showed that DEGs were associated with immune responses, inflammatory responses, regulation of immune responses, and platelet activation. Pathway analysis indicated that DEGs were enriched in cytokine‒cytokine receptor interaction, immunoregulatory interactions between lymphoid and nonlymphoid cells, hematopoietic cell lineage, phosphoinositide 3-kinase‒protein kinase B signaling pathway, NK cell‒mediated cytotoxicity, and platelet activation. Furthermore, the protein‒protein interaction network was predicted using the STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) database and visualized with Cytoscape software. Finally, on the basis of the protein‒protein interaction network, 18 hub genes were selected, and two significant modules were obtained. In conclusion, this study sheds light on the molecular mechanisms of pediatric atopic dermatitis and may provide diagnostic biomarkers and therapeutic targets.
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Affiliation(s)
- Janna Nousbeck
- National Children's Research Centre, Dublin, Ireland.,Clinical Medicine, School of Medicine, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Maeve A McAleer
- National Children's Research Centre, Dublin, Ireland.,Department of Paediatric Dermatology, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Alan D Irvine
- National Children's Research Centre, Dublin, Ireland.,Clinical Medicine, School of Medicine, Trinity College Dublin, The University of Dublin, Dublin, Ireland.,Department of Paediatric Dermatology, Children's Health Ireland at Crumlin, Dublin, Ireland
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Li J, Wu T, Song K, Zhu L, Wang Y, Chen T, Wang X. Integrative network analysis reveals subtype-specific long non-coding RNA regulatory mechanisms in head and neck squamous cell carcinoma. Comput Struct Biotechnol J 2023; 21:535-49. [PMID: 36659932 DOI: 10.1016/j.csbj.2022.12.030] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSC) is one of most common malignancies with high mortality worldwide. Importantly, the molecular heterogeneity of HNSC complicates the clinical diagnosis and treatment, leading to poor overall survival outcomes. To dissect the complex heterogeneity, recent studies have reported multiple molecular subtyping systems. For instance, HNSC can be subdivided to four distinct molecular subtypes: atypical, basal, classical, and mesenchymal, of which the mesenchymal subtype is characterized by upregulated epithelial-mesenchymal transition (EMT) and associated with poorer survival outcomes. Despite a wealth of studies into the complex molecular heterogeneity, the regulatory mechanism specific to this aggressive subtype remain largely unclear. Herein, we developed a network-based bioinformatics framework that integrates lncRNA and mRNA expression profiles to elucidate the subtype-specific regulatory mechanisms. Applying the framework to HNSC, we identified a clinically relevant lncRNA LNCOG as a key master regulator mediating EMT underlying the mesenchymal subtype. Five genes with strong prognostic values, namely ANXA5, ITGA5, CCBE1, P4HA2, and EPHX3, were predicted to be the putative targets of LNCOG and subsequently validated in other independent datasets. By integrative analysis of the miRNA expression profiles, we found that LNCOG may act as a ceRNA to sponge miR-148a-3p thereby upregulating ITGA5 to promote HNSC progression. Furthermore, our drug sensitivity analysis demonstrated that the five putative targets of LNCOG were also predictive of the sensitivities of multiple FDA-approved drugs. In summary, our bioinformatics framework facilitates the dissection of cancer subtype-specific lncRNA regulatory mechanisms, providing potential novel biomarkers for more optimized treatment of HNSC.
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Key Words
- AUC, area under the curve
- BH, Benjamini-Hochberg
- CI, confidence interval
- CTRP, The Cancer Therapeutics Response Portal
- Competitive endogenous RNA
- DEG, differentially expressed gene
- DEX, dexamethasone
- DFS, disease-free survival
- EMT, epithelial-mesenchymal transition
- FPKM, fragments per kilobase million
- GEO, Gene Expression Omnibus
- GO, Gene Ontology
- GSEA, gene set enrichment analysis
- HNSC, head and neck squamous cell carcinoma
- HR, hazard ratio
- Head and neck cancer
- ICGC, The International Cancer Genome Consortium
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- LASSO, least absolute shrinkage and selection operator
- Long non-coding RNAs
- Network inference
- OS, overall survival
- ROC, receiver operating characteristic curve
- Subtype-specific
- TCGA, The Cancer Genome Atlas
- TPM, transcripts per million
- UCSC, the University of California Santa Cruz
- ceRNA, the competitive endogenous RNA
- lncRNA, long non-coding RNA
- miRNA, microRNA
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Kong L, Huang Y, Zeng X, Ye C, Wu Z, Guo Y, Pan D. Effects of galactosyltransferase on EPS biosynthesis and freeze-drying resistance of Lactobacillus acidophilus NCFM. Food Chem (Oxf) 2022; 5:100145. [PMID: 36573108 PMCID: PMC9789326 DOI: 10.1016/j.fochms.2022.100145] [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] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/01/2022] [Accepted: 11/12/2022] [Indexed: 11/16/2022]
Abstract
Galactosyltransferase (GalT) is an important enzyme in synthesizing exopolysaccharide (EPS), the major polymer of biofilms protecting cells from severe conditions. However, the contribution to, and regulatory mechanism of GalT, in stressor resistance are still unclear. Herein, we successfully overexpressed GalT in Lactobacillus acidophilus NCFM by genetic engineering. The GalT activity and freeze-drying survival rate of the recombinant strain were significantly enhanced. The EPS yield also increased by 17.8%, indicating a positive relationship between freeze-drying resistance and EPS. RNA-Seq revealed that GalT could regulate the flux of the membrane transport system, pivotal sugar-related metabolic pathways, and promote quorum sensing to facilitate EPS biosynthesis, which enhanced freeze-drying resistance. The findings concretely prove that the mechanism of GalT regulating EPS biosynthesis plays an important role in protecting lactic acid bacteria from freeze-drying stress.
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Key Words
- BP, biological process
- CC, cellular component
- DEG, differentially expressed gene
- ELISA, enzyme linked immunosorbent assay
- EPS, exopolysaccharideS
- Exopolysaccharide
- FT-IR, Fourier transform infrared spectroscopy
- Freeze-drying
- GO, gene ontology
- GalT, galactosyltransferase
- Galactosyltransferase
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- LAB, lactic acid bacteria
- LB, Luria-Bertani
- MF, molecular function
- MRS, de Man, Rogosa and Sharpe
- NCBI, National Center for Biotechnology Information GenBank
- Overexpression
- PCR, polymerase chain reaction
- PEP, phosphoenolpyruvate
- PTS, phosphotransferase system
- QS, quorum sensing
- RT-qPCR, real-time quantitative polymerase chain reaction
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Affiliation(s)
- Lingyu Kong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo 315211, China,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Yuze Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo 315211, China,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Xiaoqun Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo 315211, China,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China,Corresponding author at: State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo 315211, China.
| | - Congyan Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo 315211, China,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Zhen Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo 315211, China,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Yuxing Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo 315211, China,School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210097, China
| | - Daodong Pan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo 315211, China,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
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Yan Z, Feng C, Jin X, Wang F, Liu C, Li N, Qiao Y, Bai Y, Wu F, Giesy JP. Organophosphate esters cause thyroid dysfunction via multiple signaling pathways in zebrafish brain. Environ Sci Ecotechnol 2022; 12:100198. [PMID: 36157343 PMCID: PMC9500371 DOI: 10.1016/j.ese.2022.100198] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 05/04/2023]
Abstract
Organophosphate esters (OPEs) are widespread in various environmental media, and can disrupt thyroid endocrine signaling pathways. Mechanisms by which OPEs disrupt thyroid hormone (TH) signal transduction are not fully understood. Here, we present in vivo-in vitro-in silico evidence establishing OPEs as environmental THs competitively entering the brain to inhibit growth of zebrafish via multiple signaling pathways. OPEs can bind to transthyretin (TTR) and thyroxine-binding globulin, thereby affecting the transport of TH in the blood, and to the brain by TTR through the blood-brain barrier. When GH3 cells were exposed to OPEs, cell proliferation was significantly inhibited given that OPEs are competitive inhibitors of TH. Cresyl diphenyl phosphate was shown to be an effective antagonist of TH. Chronic exposure to OPEs significantly inhibited the growth of zebrafish by interfering with thyroperoxidase and thyroglobulin to inhibit TH synthesis. Based on comparisons of modulations of gene expression with the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases, signaling pathways related to thyroid endocrine functions, such as receptor-ligand binding and regulation of hormone levels, were identified as being affected by exposure to OPEs. Effects were also associated with the biosynthesis and metabolism of lipids, and neuroactive ligand-receptor interactions. These findings provide a comprehensive understanding of the mechanisms by which OPEs disrupt thyroid pathways in zebrafish.
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Key Words
- AChE, acetylcholinesterase
- ANOVA, analysis of variance
- BCF, bioconcentration factor
- BFR, brominated flame retardant
- CD-FBS, charcoal-dextran-treated fetal bovine serum
- CDP, cresyl diphenyl phosphate
- Competitive inhibition assay
- DEG, differentially expressed gene
- DKA, β-diketone antibiotic
- DMSO, dimethyl sulfoxide
- EAS, estrogen
- FBS, fetal bovine serum
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- GO, Gene Ontology
- HPLC-MS/MS, high-performance liquid chromatograph interfaced with a mass spectrometer
- HPT, hypothalamic–pituitary–thyroid
- HS, horse serum
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MAPK, mitogen-activated protein kinase
- Molecular docking simulation
- NIS, Na+/I− symporter
- OD490, optical density
- OPE, organophosphate ester
- OPFR, organophosphate flame retardant
- Organophosphate ester
- P/S, penicillin–streptomycin
- PBDE, polybrominated diphenyl ether
- PBS, phosphate-buffered saline
- RIC20/50, concentration inhibiting 20%/50%
- T4, thyroxin
- TBG, thyroxine-binding globulin
- TCIPP, tris(2-chloroisopropyl) phosphate
- TDCIPP, tris(1,3-dichloro-2-propyl) phosphate (TDCIPP)
- TDCIPP-d15, tris(1,3-dichloroisopropyl) phosphate-D15
- TG, thyroglobulin
- TH, thyroid hormone
- THR, thyroid hormone receptor
- TIPP, tris(isopropyl) phosphate
- TPHP, triphenyl phosphate
- TPO, thyroperoxidase
- TRβ, thyroid hormone receptor β
- TTR, transthyretin
- Thyroid endocrine function
- Transcriptome sequencing
- androgen, and steroidogenesis
- cga, glycoprotein hormone
- qRT-PCR, quantitative real-time PCR
- tshβa, thyroid-stimulating hormone beta subunit a
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Affiliation(s)
- Zhenfei Yan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
- College of Environment, Hohai University, Nanjing, 210098, China
| | - Chenglian Feng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
- Corresponding author.
| | - Xiaowei Jin
- China National Environmental Monitoring Centre, Beijing, 100012, China
- Corresponding author.
| | - Fangkun Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China
| | - Cong Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, 271018, China
| | - Na Li
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yu Qiao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yingchen Bai
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
- College of Environment, Hohai University, Nanjing, 210098, China
| | - John P. Giesy
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, Canada
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Environmental Sciences, Baylor University, Waco, TX, USA
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6
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Albogami S. Comprehensive analysis of gene expression profiles to identify differential prognostic factors of primary and metastatic breast cancer. Saudi J Biol Sci 2022; 29:103318. [PMID: 35677896 PMCID: PMC9168623 DOI: 10.1016/j.sjbs.2022.103318] [Citation(s) in RCA: 2] [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: 02/07/2022] [Revised: 04/17/2022] [Accepted: 05/19/2022] [Indexed: 12/21/2022] Open
Abstract
Breast cancer accounts for nearly half of all cancer-related deaths in women worldwide. However, the molecular mechanisms that lead to tumour development and progression remain poorly understood and there is a need to identify candidate genes associated with primary and metastatic breast cancer progression and prognosis. In this study, candidate genes associated with prognosis of primary and metastatic breast cancer were explored through a novel bioinformatics approach. Primary and metastatic breast cancer tissues and adjacent normal breast tissues were evaluated to identify biomarkers characteristic of primary and metastatic breast cancer. The Cancer Genome Atlas-breast invasive carcinoma (TCGA-BRCA) dataset (ID: HS-01619) was downloaded using the mRNASeq platform. Genevestigator 8.3.2 was used to analyse TCGA-BRCA gene expression profiles between the sample groups and identify the differentially-expressed genes (DEGs) in each group. For each group, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were used to determine the function of DEGs. Networks of protein-protein interactions were constructed to identify the top hub genes with the highest degree of interaction. Additionally, the top hub genes were validated based on overall survival and immunohistochemistry using The Human Protein Atlas. Of the top 20 hub genes identified, four (KRT14, KIT, RAD51, and TTK) were considered as prognostic risk factors based on overall survival. KRT14 and KIT expression levels were upregulated while those of RAD51 and TTK were downregulated in patients with breast cancer. The four proposed candidate hub genes might aid in further understanding the molecular changes that distinguish primary breast tumours from metastatic tumours as well as help in developing novel therapeutics. Furthermore, they may serve as effective prognostic risk markers based on the strong correlation between their expression and patient overall survival.
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Key Words
- BC, breast cancer
- BP, biological process
- Breast cancer
- CC, cellular component
- CI, confidence interval
- DEG, differentially expressed gene
- Differentially expressed genes
- FDR, false discovery rate
- GEPIA, gene expression profiling interactive analysis
- GO, gene ontology
- HR, hazard ratio
- IDC, infiltrating ductal carcinoma
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MCODE, molecular complex detection
- MF, molecular function
- Metastasis
- OS, overall survival
- Overall survival
- PPI, protein-protein interaction
- Prognostic marker
- Protein-protein interaction
- RNA-Seq, RNA sequencing
- STRING, search tool for the retrieval of interacting genes
- TCGA-BRCA, The Cancer Genome Atlas-breast invasive carcinoma
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Affiliation(s)
- Sarah Albogami
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
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7
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van Buuren N, Ramirez R, Turner S, Chen D, Suri V, Aggarwal A, Moon C, Kim S, Kornyeyev D, Bui N, Bhardwaj N, Chan HL, Marcellin P, Buti M, Wallin J, Gaggar A, Fletcher SP, Diehl L, Li L, Mo H, Feierbach B. Characterization of the liver immune microenvironment in liver biopsies from patients with chronic HBV infection. JHEP Rep 2021; 4:100388. [PMID: 34950863 PMCID: PMC8671126 DOI: 10.1016/j.jhepr.2021.100388] [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] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/10/2021] [Accepted: 10/07/2021] [Indexed: 01/05/2023]
Abstract
Background & Aims We aim to describe the liver immune microenvironment by analyzing liver biopsies from patients with chronic HBV infection (CHB). Host immune cell signatures and their corresponding localization were characterized by analyzing the intrahepatic transcriptome in combination with a custom multiplex immunofluorescence panel. Method Matching FFPE and fresh frozen liver biopsies were collected from immune active patients within the open-label phase IV study GS-US-174-0149. RNA-Seq was conducted on 53 CHB liver biopsies from 46 patients. Twenty-eight of the 53 samples had matched FFPE biopsies and were stained with a 12-plex panel including cell segmentation, immune and viral biomarkers. Corresponding serum samples were screened using the MSD Human V-plex Screen Service to identify peripheral correlates for the immune microenvironment. Results Using unsupervised clustering of the transcriptome, we reveal two unique liver immune signatures classified as immune high and immune low based on the quantification of the liver infiltrate gene signatures. Multiplex immunofluorescence analysis demonstrated large periportal lymphoid aggregates in immune high samples consisting of CD4 and CD8 T cells, B cells and macrophages. Differentiation of the high and low immune microenvironments was independent of HBeAg status and peripheral viral antigen levels. In addition, longitudinal analysis indicates that treatment and normalization of ALT correlates with a decrease in liver immune infiltrate and inflammation. Finally, we screened a panel of peripheral biomarkers and identified ICAM-1 and CXCL10 as biomarkers that strongly correlate with these unique immune microenvironments. Conclusion These data provide a description of immune phenotypes in patients with CHB and show that immune responses are downregulated in the liver following nucleotide analogue treatment. This may have important implications for both the safety and efficacy of immune modulator programs aimed at HBV cure. Lay summary Liver biopsies from patients with chronic hepatitis B were submitted to RNA-Seq and multiplex immunofluorescence and identified two different liver immune microenvironments: immune high and immune low. Immune high patients showed elevated immune pathways, including interferon signaling pathways, and increase presence of immune cells. Longitudinal analysis of biopsies from treatment experienced patients showed that treatment correlates with a marked decrease in inflammation and these findings may have important implications for both safety and efficacy of immune modulator programs for HBV cure.
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Key Words
- ALT, alanine aminotransferase
- BCR, B-cell receptor
- CHB, chronic HBV infection
- Chronic HBV
- DEG, differentially expressed gene
- FFPE, formalin-fixed paraffin-embedded
- Hepatitis B
- IHC, immunohistochemistry
- Immune Microenvironment
- Intrahepatic transcriptome
- PEG-IFNα, pegylated-interferon-α
- TCR, T-cell receptor
- TDF, tenofovir disoproxil fumarate
- TLS, tertiary lymphoid structures
- mIF, multiplex immunofluorescence
- multiplex immunofluorescence
- ssGSEA, single sample gene set enrichment analysis
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Affiliation(s)
- Nicholas van Buuren
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States
| | - Ricardo Ramirez
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States
| | - Scott Turner
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States
| | - Diana Chen
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States
| | - Vithika Suri
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States
| | - Abhishek Aggarwal
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States
| | - Christina Moon
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States
| | - Sam Kim
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States
| | - Dmytro Kornyeyev
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States
| | - Nam Bui
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States
| | - Neeru Bhardwaj
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States.,Current address: Foundation Medicine, Cambridge, MA, 02141, United States
| | | | | | - Maria Buti
- Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Jeffrey Wallin
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States
| | - Anuj Gaggar
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States
| | - Simon P Fletcher
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States
| | - Lauri Diehl
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States
| | - Li Li
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States
| | - Hongmei Mo
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States
| | - Becket Feierbach
- Gilead Sciences Inc. 324 Lakeside Dr., Foster City, CA, 94404, United States
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Bojanowski K, Ibeji CU, Singh P, Swindell WR, Chaudhuri RK. A Sensitization-Free Dimethyl Fumarate Prodrug, Isosorbide Di-(Methyl Fumarate), Provides a Topical Treatment Candidate for Psoriasis. JID Innov 2021; 1:100040. [PMID: 34909741 PMCID: PMC8659395 DOI: 10.1016/j.xjidi.2021.100040] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/28/2021] [Accepted: 06/07/2021] [Indexed: 12/27/2022] Open
Abstract
Dimethyl fumarate (DMF) is an effective oral treatment for psoriasis administered in Europe for nearly 60 years. However, its potential has been limited by contact dermatitis that prohibits topical application. This paper characterizes a DMF derivative, isosorbide DMF (IDMF), which was designed to have antipsoriatic effects without skin-sensitizing properties. We show that IDMF exhibits neither genotoxicity nor radiation sensitivity in skin fibroblasts and is nonirritating and nonsensitizing in animal models (rat, rabbit, guinea pig). Microarray analysis of cytokine-stimulated keratinocytes showed that IDMF represses the expression of genes specifically upregulated in psoriatic skin lesions but not those of other skin diseases. IDMF also downregulated genes induced by IL-17A and TNF in keratinocytes as well as predicted targets of NF-κB and the antidifferentiation noncoding RNA (i.e., ANCR). IDMF further stimulated the transcription of oxidative stress response genes (NQO1, GPX2, GSR) with stronger NRF2/ARE activation compared to DMF. Finally, IDMF reduced erythema and scaling while repressing the expression of immune response genes in psoriasiform lesions elicited by topical application of imiquimod in mice. These data show that IDMF exhibits antipsoriatic activity that is similar or improved compared with that exhibited by DMF, without the harsh skin-sensitizing effects that have prevented topical delivery of the parent molecule.
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Key Words
- ARE, antioxidant response element
- CES2, carboxylesterase 2
- CPD, cyclobutane pyrimidine dimer
- CTRL, control
- DEG, differentially expressed gene
- DMF, dimethyl fumarate
- FC, fold change
- FDR, false discovery rate
- GSH, glutathione
- IDMF, isosorbide di-(methyl fumarate)
- IMQ, imiquimod
- KC, keratinocyte
- MMF, monomethyl fumarate
- PN, uninvolved skin from psoriasis patient
- PP, lesional skin from psoriasis patient
- RNA-seq, RNA sequencing
- VEH, vehicle
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Affiliation(s)
- Krzysztof Bojanowski
- Sunny BioDiscovery, Inc, Santa Paula, California, USA.,Symbionyx Pharmaceuticals Inc, Boonton, New Jersey, USA
| | - Collins U Ibeji
- Department of Pure and Industrial Chemistry, Faculty of Physical Sciences, University of Nigeria, Nsukka, Nigeria
| | - Parvesh Singh
- School of Chemistry & Physics, University of KwaZulu-Natal, Durban, South Africa
| | - William R Swindell
- Department of Internal Medicine, The Jewish Hospital, Cincinnati, Ohio, USA
| | - Ratan K Chaudhuri
- Symbionyx Pharmaceuticals Inc, Boonton, New Jersey, USA.,Sytheon Ltd, Boonton, New Jersey, USA
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Schilz JR, Dashner-Titus EJ, Luo L, Simmons KA, MacKenzie DA, Hudson LG. Co-exposure of sodium arsenite and uranyl acetate differentially alters gene expression in CD3/CD28 activated CD4+ T-cells. Toxicol Rep 2021; 8:1917-1929. [PMID: 34926170 PMCID: PMC8649082 DOI: 10.1016/j.toxrep.2021.11.019] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/19/2021] [Accepted: 11/25/2021] [Indexed: 11/25/2022] Open
Abstract
Communities in the western region of the United States experience environmental exposure to metal mixtures from living in proximity to numerous unremediated abandoned uranium mines. Metals including arsenic and uranium co-occur in and around these sites at levels higher than the United States Environmental Protection Agency maximum contaminant levels. To address the potential effect of these metals on the activation of CD4+ T-cells, we used RNA sequencing methods to determine the effect of exposure to sodium arsenite (1 μM and 10 μM), uranyl acetate (3 μM and 30 μM) or a mixture of sodium arsenite and uranyl acetate (1 μM sodium arsenite + 3 μM uranyl acetate). Sodium arsenite induced a dose dependent effect on activation associated gene expression; targeting immune response genes at the lower dose. Increases in oxidative stress gene expression were observed with both sodium arsenite doses. While uranyl acetate alone did not significantly alter activation associated gene expression, the mixture of uranyl acetate with sodium arsenite demonstrated a combined effect relative to sodium arsenite alone. The results demonstrate the need to investigate metal and metalloid mixtures at environmentally relevant concentrations to better understand the toxicological impact of these mixtures on T-cell activation, function and immune dysregulation.
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Key Words
- APC, antigen presenting cell
- AUM, abandoned uranium mine
- Arsenic
- DEG, differentially expressed gene
- GCLM, glutamate-cysteine ligase
- HMOX1, heme oxygenase 1
- IFNγ, interferon gamma
- IL-2, interleukin 2
- MHC, major histone compatibility complex
- Mixture toxicology
- NQO1, NAD(P)H quinone dehydrogenase
- PCA, principal component analysis
- SOD1, super oxide dismutase 1
- T-lymphocytes
- TCR, T-cell receptor
- Th, T-helper
- Uranium
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Affiliation(s)
- Jodi R. Schilz
- Division of Physical Therapy, School of Medicine, University of New Mexico, Albuquerque, NM, United States
| | - Erica J. Dashner-Titus
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States
| | - Li Luo
- Division of Epidemiology, Biostatistics and Preventive Medicine, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, United States
| | - Karen A. Simmons
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States
| | - Debra A. MacKenzie
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States
| | - Laurie G. Hudson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States
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Xu L, Yin L, Qi Y, Tan X, Gao M, Peng J. 3D disorganization and rearrangement of genome provide insights into pathogenesis of NAFLD by integrated Hi-C, Nanopore, and RNA sequencing. Acta Pharm Sin B 2021; 11:3150-3164. [PMID: 34729306 PMCID: PMC8546856 DOI: 10.1016/j.apsb.2021.03.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 12/20/2020] [Revised: 01/30/2021] [Accepted: 02/07/2021] [Indexed: 12/12/2022] Open
Abstract
The three-dimensional (3D) conformation of chromatin is integral to the precise regulation of gene expression. The 3D genome and genomic variations in non-alcoholic fatty liver disease (NAFLD) are largely unknown, despite their key roles in cellular function and physiological processes. High-throughput chromosome conformation capture (Hi-C), Nanopore sequencing, and RNA-sequencing (RNA-seq) assays were performed on the liver of normal and NAFLD mice. A high-resolution 3D chromatin interaction map was generated to examine different 3D genome hierarchies including A/B compartments, topologically associated domains (TADs), and chromatin loops by Hi-C, and whole genome sequencing identifying structural variations (SVs) and copy number variations (CNVs) by Nanopore sequencing. We identified variations in thousands of regions across the genome with respect to 3D chromatin organization and genomic rearrangements, between normal and NAFLD mice, and revealed gene dysregulation frequently accompanied by these variations. Candidate target genes were identified in NAFLD, impacted by genetic rearrangements and spatial organization disruption. Our data provide a high-resolution 3D genome interaction resource for NAFLD investigations, revealed the relationship among genetic rearrangements, spatial organization disruption, and gene regulation, and identified candidate genes associated with these variations implicated in the pathogenesis of NAFLD. The newly findings offer insights into novel mechanisms of NAFLD pathogenesis and can provide a new conceptual framework for NAFLD therapy.
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Key Words
- 3C, chromosome conformation capture
- 3D genome
- 3D, three-dimensional
- ALT, alanine aminotransferase
- AST, aspartate aminotransferase
- Abcg5, ATP-binding cassette sub-family G member 5
- BWA, Burrows-Wheeler Aligner
- CNV, copy number variation
- Camk1d, calcium/calmodulin-dependent protein kinase type 1D
- Chr, chromosome
- Chromatin looping
- DEG, differentially expressed gene
- DEL, deletion
- DI, directionality index
- DUP, duplication
- Elovl6, elongation of very long chain fatty acids protein 6
- FDR, false discovery rate
- FFA, free fatty acid
- Fgfr2, fibroblast growth factor receptor 2
- GCKR, glucokinase regulator
- GO, gene ontology
- GSH, glutathione
- Gadd45g, growth arrest and DNA damage-inducible protein GADD45 gamma
- Grm8, metabotropic glutamate receptor 8
- Gsta1, glutathione S-transferase A1
- H&E, hematoxylin-eosin
- HFD, high-fat diet
- HSD17B13, hydroxysteroid 17-beta dehydrogenase 13
- Hi-C, high-throughput chromosome conformation capture
- IDE, interaction decay exponent
- INS, insertion
- INV, inversion
- IR, inclusion ratio
- IRGM, immunity related GTPase M
- IRS4, insulin receptor substrate 4
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- Kcnma1, calcium-activated potassium channel subunit alpha-1
- LPIN1, lipin 1
- MBOAT7, membrane bound O-acyltransferase domain containing 7
- MDA, malondialdehyde
- NAFLD, non-alcoholic fatty liver disease
- NF1, neurofibromin 1
- NGS, next-generation sequencing
- NOTCH1, notch receptor 1
- ONT, Oxford Nanopore Technologies
- PCA, principal component analysis
- PNPLA3, patatin like phospholipase domain containing 3
- PPP1R3B, protein phosphatase 1 regulatory subunit 3B
- PTEN, phosphatase and tensin homolog
- Pde4b, phosphodiesterase 4B
- Plce1, 1-phosphat-idylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
- Plxnb1, Plexin-B1
- RB1, RB transcriptional corepressor 1
- RNA-seq, RNA-sequencing
- SD, standard deviation
- SOD, superoxide dismutase
- SV, structural variation
- Scd1, acyl-CoA desaturase 1
- Sugct, succinate-hydroxymethylglutarate CoA-transferase
- TAD, topologically associated domain
- TC, total cholesterol
- TG, triglyceride
- TM6SF2, transmembrane 6 superfamily member 2
- TP53, tumor protein p53
- TRA, translocation
- Topologically associated domain
- Transcriptome
- WGS, whole-genome sequencing
- Whole-genome sequencing
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Tsukada T, Sakata-Haga H, Shimada H, Shoji H, Hatta T. Mid-pregnancy maternal immune activation increases Pax6-positive and Tbr2-positive neural progenitor cells and causes integrated stress response in the fetal brain in a mouse model of maternal viral infection. IBRO Neurosci Rep 2021; 11:73-80. [PMID: 34409402 PMCID: PMC8363822 DOI: 10.1016/j.ibneur.2021.07.003] [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: 03/08/2021] [Accepted: 07/31/2021] [Indexed: 12/26/2022] Open
Abstract
Maternal immune activation (MIA) in midpregnancy is a risk factor for neurodevelopmental disorders. Improper brain development may cause malformations of the brain; maldevelopment induced by MIA may lead to a pathology-related phenotype. In this study, a single intraperitoneal injection of 20 mg/kg polyriboinosinic–polyribocytidylic acid [poly(I:C)] was administered to C57BL/6J mice on embryonic day (E) 12.5 to mimic maternal viral infection. Histopathological analysis of neurogenesis was performed using markers for Pax6, Tbr2, and Tbr1. In these fetuses, significant increases were observed in the proportion of Pax6-positive neural progenitor cells and Pax6/Tbr2 double-positive cells 24 h after poly(I:C) injection. There were no differences in the proportion of Tbr1-positive postmitotic neurons 48 h after poly(I:C) injection. At E18.5, there were more Pax6-positive and Tbr2-positive neural progenitor cells in the poly(I:C)-injected group than in the saline-injected group. Gene ontology enrichment analysis of poly(I:C)-induced differentially expressed genes in the fetal brain at E12.5 demonstrated that these genes were enriched in terms including response to cytokine, response to decreased oxygen levels in the category of biological process. At E13.5, activating transcription factor 4 (Atf4), which is an effector of integrated stress response, was significantly upregulated in the fetal brain. Our results show that poly(I:C)-induced MIA at E12.5 leads to dysregulated neurogenesis and upregulates Atf4 in the fetal brain. These findings provide a new insight in the mechanism of MIA causing improper brain development and subsequent neurodevelopmental disorders. MIA increases Pax6-positive and Tbr2-positive neural progenitor cells. MIA impaired the process of neurogenesis from as early as the acute stage. MIA upregulated Atf4, an effector of integrated stress response, in the fetal brain.
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Key Words
- ASD, autism spectrum disorders
- Activating transcription factor 4
- Atf4, activating transcription factor 4
- CP, cortical plate
- DEG, differentially expressed gene
- ISR, integrated stress response
- Integrated stress response
- MIA, Maternal immune activation
- Maternal immune activation
- NPCs, neural progenitor cells
- Neurogenesis
- Polyriboinosinic–polyribocytidylic acid
- SVZ, subventricular zone
- UPR, unfolded protein response
- Unfolded protein response
- VZ, ventricular zone
- [polyI:C], polyriboinosinic–polyribocytidylic acid
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Affiliation(s)
- Tsuyoshi Tsukada
- Department of Anatomy, Kanazawa Medical University, Uchinada, Ishikawa 920-0293, Japan
- Department of Neurosurgery, Kanazawa Medical University, Uchinada, Ishikawa 920-0293, Japan
- Corresponding author at: Department of Anatomy, Kanazawa Medical University, Uchinada, Ishikawa 920-0293, Japan.
| | - Hiromi Sakata-Haga
- Department of Anatomy, Kanazawa Medical University, Uchinada, Ishikawa 920-0293, Japan
| | - Hiroki Shimada
- Department of Medical Science, Kanazawa Medical University, Uchinada, Ishikawa 920-0293, Japan
| | - Hiroki Shoji
- Department of Biology, Kanazawa Medical University, Uchinada, Ishikawa 920-0293, Japan
| | - Toshihisa Hatta
- Department of Anatomy, Kanazawa Medical University, Uchinada, Ishikawa 920-0293, Japan
- Corresponding author.
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12
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Bissig-Choisat B, Alves-Bezerra M, Zorman B, Ochsner SA, Barzi M, Legras X, Yang D, Borowiak M, Dean AM, York RB, Galvan NTN, Goss J, Lagor WR, Moore DD, Cohen DE, McKenna NJ, Sumazin P, Bissig KD. A human liver chimeric mouse model for non-alcoholic fatty liver disease. JHEP Rep 2021; 3:100281. [PMID: 34036256 PMCID: PMC8138774 DOI: 10.1016/j.jhepr.2021.100281] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 12/11/2022] Open
Abstract
Background & Aims The accumulation of neutral lipids within hepatocytes underlies non-alcoholic fatty liver disease (NAFLD), which affects a quarter of the world's population and is associated with hepatitis, cirrhosis, and hepatocellular carcinoma. Despite insights gained from both human and animal studies, our understanding of NAFLD pathogenesis remains limited. To better study the molecular changes driving the condition we aimed to generate a humanised NAFLD mouse model. Methods We generated TIRF (transgene-free Il2rg -/-/Rag2 -/-/Fah -/-) mice, populated their livers with human hepatocytes, and fed them a Western-type diet for 12 weeks. Results Within the same chimeric liver, human hepatocytes developed pronounced steatosis whereas murine hepatocytes remained normal. Unbiased metabolomics and lipidomics revealed signatures of clinical NAFLD. Transcriptomic analyses showed that molecular responses diverged sharply between murine and human hepatocytes, demonstrating stark species differences in liver function. Regulatory network analysis indicated close agreement between our model and clinical NAFLD with respect to transcriptional control of cholesterol biosynthesis. Conclusions These NAFLD xenograft mice reveal an unexpected degree of evolutionary divergence in food metabolism and offer a physiologically relevant, experimentally tractable model for studying the pathogenic changes invoked by steatosis. Lay summary Fatty liver disease is an emerging health problem, and as there are no good experimental animal models, our understanding of the condition is poor. We here describe a novel humanised mouse system and compare it with clinical data. The results reveal that the human cells in the mouse liver develop fatty liver disease upon a Western-style fatty diet, whereas the mouse cells appear normal. The molecular signature (expression profiles) of the human cells are distinct from the mouse cells and metabolic analysis of the humanised livers mimic the ones observed in humans with fatty liver. This novel humanised mouse system can be used to study human fatty liver disease.
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Key Words
- ALP, alkaline phosphatase
- ALT, alanine aminotransferase
- AST, aspartate aminotransferase
- CBPEGs, cholesterol biosynthesis pathway enzyme genes
- CE, cholesteryl ester
- CER, ceramide
- CHHs, chimeric human hepatocytes
- CMHs, chimeric mouse hepatocytes
- CT, confidence transcript
- DAG, diacylglycerol
- DCER, dihydroceramide
- DEG, differentially expressed gene
- FA, fatty acid
- FAH, fumarylacetoacetate hydrolase
- FFA, free fatty acid
- GGT, gamma-glutamyl transpeptidase
- HCC, hepatocellular carcinoma
- HCER, hexosylceramide
- HCT, high confidence transcriptional target
- Human disease modelling
- Humanised mice
- LCER, lactosylceramide
- LPC, lysophosphatidylcholine
- LPE, lysophosphatidylethanolamine
- Lipid metabolism
- MAG, monoacylglycerol
- MUFA, monounsaturated fatty acid
- NAFLD, non-alcoholic fatty liver disease
- NASH, non-alcoholic steatohepatitis
- NC, normal chow
- NTBC, nitisinone
- Non-alcoholic fatty liver disease
- PC, phosphatidylcholine
- PE, phosphatidylethanolamine
- PI, phosphatidylinositol
- PNPLA3, patatin-like-phospholipase domain-containing protein 3
- PUFA, polyunsaturated free FA
- SM, sphingomyelin
- SREBP, sterol regulatory element-binding protein
- Steatosis
- TAG, triacylglycerol
- TIRF, transgene-free Il2rg-/-/Rag2-/-/Fah-/-
- WD, Western-type diet
- hALB, human albumin
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Affiliation(s)
| | - Michele Alves-Bezerra
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Barry Zorman
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Scott A. Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Mercedes Barzi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC, USA
| | - Xavier Legras
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC, USA
| | - Diane Yang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Malgorzata Borowiak
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Institute for Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz Universtiy, Poznan, Poland
| | - Adam M. Dean
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Robert B. York
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | | | - John Goss
- Department of Surgery, Texas Children’s Hospital, Houston, TX, USA
| | - William R. Lagor
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - David D. Moore
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - David E. Cohen
- Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Neil J. McKenna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Pavel Sumazin
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Karl-Dimiter Bissig
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC, USA
- Y.T. and Alice Chen Pediatric Genetics and Genomics Research Center, Duke University, Durham, NC, USA
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
- Duke Cancer Institute, Duke University, Durham, NC, USA
- Corresponding author. Address: Duke University, Division of Medical Genetics, 905 South LaSalle street, Durham, NC-27708, USA. Tel.: +1 919 660 0761; fax: +1 919 660 0762.
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Payen VL, Lavergne A, Alevra Sarika N, Colonval M, Karim L, Deckers M, Najimi M, Coppieters W, Charloteaux B, Sokal EM, El Taghdouini A. Single-cell RNA sequencing of human liver reveals hepatic stellate cell heterogeneity. JHEP Rep 2021; 3:100278. [PMID: 34027339 PMCID: PMC8121977 DOI: 10.1016/j.jhepr.2021.100278] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 02/11/2021] [Accepted: 02/28/2021] [Indexed: 02/07/2023] Open
Abstract
Background & Aims The multiple vital functions of the human liver are performed by highly specialised parenchymal and non-parenchymal cells organised in complex collaborative sinusoidal units. Although crucial for homeostasis, the cellular make-up of the human liver remains to be fully elucidated. Here, single-cell RNA-sequencing was used to unravel the heterogeneity of human liver cells, in particular of hepatocytes (HEPs) and hepatic stellate cells (HSCs). Method The transcriptome of ~25,000 freshly isolated human liver cells was profiled using droplet-based RNA-sequencing. Recently published data sets and RNA in situ hybridisation were integrated to validate and locate newly identified cell populations. Results In total, 22 cell populations were annotated that reflected the heterogeneity of human parenchymal and non-parenchymal liver cells. More than 20,000 HEPs were ordered along the portocentral axis to confirm known, and reveal previously undescribed, zonated liver functions. The existence of 2 subpopulations of human HSCs with unique gene expression signatures and distinct intralobular localisation was revealed (i.e. portal and central vein-concentrated GPC3+ HSCs and perisinusoidally located DBH+ HSCs). In particular, these data suggest that, although both subpopulations collaborate in the production and organisation of extracellular matrix, GPC3+ HSCs specifically express genes involved in the metabolism of glycosaminoglycans, whereas DBH+ HSCs display a gene signature that is reminiscent of antigen-presenting cells. Conclusions This study highlights metabolic zonation as a key determinant of HEP transcriptomic heterogeneity and, for the first time, outlines the existence of heterogeneous HSC subpopulations in the human liver. These findings call for further research on the functional implications of liver cell heterogeneity in health and disease. Lay summary This study resolves the cellular landscape of the human liver in an unbiased manner and at high resolution to provide new insights into human liver cell biology. The results highlight the physiological heterogeneity of human hepatic stellate cells. A cell atlas from the near-native transcriptome of >25,000 human liver cells is presented. Hepatocytes were ordered along the portocentral axis to reveal previously undescribed gene expression patterns and zonated liver functions. Two subpopulations of human hepatic stellate cells (HSCs) are reported, characterised by different spatial distribution in the native tissue. Characteristic gene signatures of HSC subpopulations are suggestive of far-reaching functional differences.
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Key Words
- BSA, bovine serum albumin
- CC, cholangiocyte
- CV, central vein
- DEG, differentially expressed gene
- EC, endothelial cell
- ECM, extracellular matrix
- Extracellular matrix
- FFPE, formaldehyde-fixed paraffin embedded
- GAG, glycosaminoglycan
- GEO, Gene Expression Omnibus
- GO, gene ontology
- HEP, hepatocyte
- HLA, human leukocyte antigen
- HRP, horseradish peroxidase
- HSC, hepatic stellate cell
- Hepatocyte
- ISH, in situ hybridisation
- KLR, killer lectin-like receptor
- LP, lymphoid cell
- Liver cell atlas
- MP, macrophage
- MZ, midzonal
- PC, pericentral
- PP, periportal
- PV, portal vein
- TBS, Tris buffered saline
- TSA, tyramide signal amplification
- UMAP, uniform manifold approximation and projection
- UMI, unique molecular identifier
- VIM, vimentin
- Zonation
- scRNA-seq, single-cell RNA-sequencing
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Affiliation(s)
- Valéry L. Payen
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
- Laboratory of Advanced Drug Delivery and Biomaterials (ADDB), LDRI Institute, Université catholique de Louvain, Brussels, Belgium
| | - Arnaud Lavergne
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | - Niki Alevra Sarika
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
- Laboratory of Advanced Drug Delivery and Biomaterials (ADDB), LDRI Institute, Université catholique de Louvain, Brussels, Belgium
| | - Megan Colonval
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | - Latifa Karim
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | - Manon Deckers
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | - Mustapha Najimi
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
| | - Wouter Coppieters
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | | | - Etienne M. Sokal
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
- Corresponding authors. Address: Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Avenue Mounier 52 Box B1.52.03, 1200 Brussels, Belgium.
| | - Adil El Taghdouini
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
- Corresponding authors. Address: Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Avenue Mounier 52 Box B1.52.03, 1200 Brussels, Belgium.
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Gwag T, Reddy Mooli RG, Li D, Lee S, Lee EY, Wang S. Macrophage-derived thrombospondin 1 promotes obesity-associated non-alcoholic fatty liver disease. JHEP Rep 2020; 3:100193. [PMID: 33294831 PMCID: PMC7689554 DOI: 10.1016/j.jhepr.2020.100193] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 12/12/2022] Open
Abstract
Background & Aims Thrombospondin 1 (TSP1) is a multifunctional matricellular protein. We previously showed that TSP1 has an important role in obesity-associated metabolic complications, including inflammation, insulin resistance, cardiovascular, and renal disease. However, its contribution to obesity-associated non-alcoholic fatty liver disease/non-alcoholic steatohepatitis (NAFLD or NASH) remains largely unknown; thus, we aimed to determine its role. Methods High-fat diet or AMLN (amylin liver NASH) diet-induced obese and insulin-resistant NAFLD/NASH mouse models were utilised, in addition to tissue-specific Tsp1-knockout mice, to determine the contribution of different cellular sources of obesity-induced TSP1 to NAFLD/NASH development. Results Liver TSP1 levels were increased in experimental obese and insulin-resistant NAFLD/NASH mouse models as well as in obese patients with NASH. Moreover, TSP1 deletion in adipocytes did not protect mice from diet-induced NAFLD/NASH. However, myeloid/macrophage-specific TSP1 deletion protected mice against obesity-associated liver injury, accompanied by reduced liver inflammation and fibrosis. Importantly, this protection was independent of the levels of obesity and hepatic steatosis. Mechanistically, through an autocrine effect, macrophage-derived TSP1 suppressed Smpdl3b expression in liver, which amplified liver proinflammatory signalling (Toll-like receptor 4 signal pathway) and promoted NAFLD progression. Conclusions Macrophage-derived TSP1 is a significant contributor to obesity-associated NAFLD/NASH development and progression and could serve as a therapeutic target for this disease. Lay summary Obesity-associated non-alcoholic fatty liver disease is a most common chronic liver disease in the Western world and can progress to liver cirrhosis and cancer. No treatment is currently available for this disease. The present study reveals an important factor (macrophage-derived TSP1) that drives macrophage activation and non-alcoholic fatty liver disease development and progression and that could serve as a therapeutic target for non-alcoholic fatty liver disease/steatohepatitis.
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Key Words
- ALT, alanine aminotransferase
- AMLN, amylin liver NASH
- ASMase, acid sphingomyelinase
- AST, aspartate aminotransferase
- BMDM, bone marrow-derived macrophage
- DEG, differentially expressed gene
- EC, endothelial cell
- ECM, extracellular matrix
- GPI, glycosylphosphatidylinositol
- HFD, high-fat diet
- HSC, hepatic stellate cell
- IL-, interleukin-
- KC, Kupffer cell
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- LFD, low-fat diet
- LPS, lipopolysaccharide
- MDM, monocyte-derived macrophage
- MP, mononuclear phagocyte
- Macrophage
- NAFLD
- NAFLD, non-alcoholic fatty liver disease
- NAS, NAFLD activity score
- NASH
- NASH, non-alcoholic steatohepatitis
- NF-κB, nuclear factor-κB
- Obesity
- SMPDL3B
- SMPDL3B, sphingomyelin phosphodiesterase acid-like 3B
- SREBP1c, sterol regulatory element-binding protein-1 c
- TGF, transforming growth factor
- TLR, Toll-like receptor
- TNF, tumour necrosis factor
- TSP1
- TSP1, thrombospondin 1
- Th, T helper type
- Tsp1fl/fl, TSP1 floxed mice
- Tsp1Δadipo, adipocyte-specific TSP1-knockout mice
- Tsp1Δmɸ, macrophage-specific TSP1-knockout mice
- qPCR, quantitative PCR
- scRNA-seq, single-cell RNA sequencing
- α-SMA, smooth muscle actin
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Affiliation(s)
- Taesik Gwag
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Raja Gopal Reddy Mooli
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Dong Li
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Sangderk Lee
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Eun Y Lee
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Shuxia Wang
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536, USA
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Wang Z, Miu KK, Zhang X, Wan AT, Lu G, Cheung HH, Lee HM, Kong AP, Chan JC, Chan WY. Hepatic miR-192-3p reactivation alleviates steatosis by targeting glucocorticoid receptor. JHEP Rep 2020; 2:100179. [PMID: 33134908 DOI: 10.1016/j.jhepr.2020.100179] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/28/2020] [Accepted: 08/18/2020] [Indexed: 01/08/2023] Open
Abstract
Background & Aims The paradox of hepatic insulin resistance describes the inability for liver to respond to bioenergetics hormones in suppressing gluconeogenesis whilst maintaining lipid synthesis. Here, we report the deficiency of miR-192-3p in the livers of mice with diabetes and its role in alleviating hepatic steatosis. Methods As conventional pre-microRNA (miRNA) stem-loop overexpression only boosts guiding strand (i.e. miR-192-5p) expression, we adopted an artificial AAV(DJ)-directed, RNA Pol III promoter-driven miRNA hairpin construct for star-strand-specific overexpression in the liver. Liver steatosis and insulin resistance markers were evaluated in primary hepatocytes, mice with diabetes, and mice with excessive carbohydrate consumption. Results Functional loss of miR-192-3p in liver exacerbated hepatic micro-vesicular steatosis and insulin resistance in either mice with diabetes or wild-type mice with excessive fructose consumption. Liver-specific overexpression of miR-192-3p effectively halted hepatic steatosis and ameliorated insulin resistance in these mice models. Likewise, hepatocytes overexpressing miR-192-3p exhibited improved lipid accumulation, accompanied with decreases in lipogenesis and lipid-accumulation-related transcripts. Mechanistically, glucocorticoid receptor (GCR, also known as nuclear receptor subfamily 3, group C, member 1 [NR3C1]) was demonstrated to be negatively regulated by miR-192-3p. The effect of miR-192-3p on mitigating micro-vesicular steatosis was ablated by the reactivation of NR3C1. Conclusions The star strand miR-192-3p was an undermined glycerolipid regulator involved in controlling fat accumulation and insulin sensitivity in liver through blockade of hepatic GCR signalling; this miRNA may serve as a potential therapeutic option for the common co-mobility of diabetic mellitus and fatty liver disease. Lay summary The potential regulatory activity of star strand microRNA (miRNA) species has been substantially underestimated. In this study, we investigate the role and mechanism of an overlooked star strand miRNA (miR-192-3p) in regulating hepatic steatosis and insulin signalling in the livers of mice with diabetes and mice under excessive carbohydrate consumption. Liver-specific knockdown of miR-192-3p recapitulated functional loss of the miRNA as in mice with diabetes. This knockdown was characterised by pronounced hepatic micro-vesicular steatosis coupled to insulin resistance. In vivo overexpression of miR-192-3p alleviated hepatic steatosis in mice with diabetes and wild-type mice with excessive fructose consumption. Glucocorticoid receptor (also known as NR3C1) was discovered as the immediate target of miR-192-3p in regulating hepatic lipid turnover and storage.
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Key Words
- 3′-UTR, 3′-untranslated region
- AAV, adeno-associated virus
- CPT, carnitine palmitoyl transferase
- DEG, differentially expressed gene
- DEX, dexamethasone
- DM, diabetes mellitus
- DNL, de novo lipogenesis
- Diabetes mellitus
- FA, fatty acid
- FAO, fatty acid oxidation
- FASN, fatty acid synthase
- GCR, glucocorticoid receptor
- Glucocorticoid receptor
- HFD, high-fat diet
- HFrD, high-fructose drink
- HOMA-IR, homeostatic model assessment of insulin resistance
- Hepatic steatosis
- High carbohydrate consumption
- MicroRNA
- NAFLD, non-alcoholic fatty liver disease
- NR3C1, nuclear receptor subfamily 3, group C, member 1
- NT, non-targeting
- OA, oleic acid
- OGTT, oral glucose tolerance test
- SCD1, stearoyl-CoA desaturase-1
- T2DM, type 2 diabetes mellitus
- TAG, triacylglyceride/triglyceride
- Transcription repressor
- VAT, visceral adipose tissue
- miRNA, microRNA
- shRNA, short hairpin RNA
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Ho PT, Rhee H, Kim J, Seo C, Park JK, Young CR, Won YJ. Impacts of Salt Stress on Locomotor and Transcriptomic Responses in the Intertidal Gastropod Batillaria attramentaria. Biol Bull 2019; 236:224-241. [PMID: 31167089 DOI: 10.1086/703186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Salinity is one of the most crucial environmental factors that structures biogeographic boundaries of aquatic organisms, affecting distribution, abundance, and behavior. However, the association between behavior and gene regulation underlying acclimation to changes in salinity remains poorly understood. In this study, we investigated the effects of salinity stress on behavior (movement distance) and patterns of gene expression (using RNA sequencing) of the intertidal gastropod Batillaria attramentaria. We examined responses to short-term (1-hour) and long-term (30-day) acclimation to a range of salinities (43, 33 [control], 23, 13, and 3 psu). We found that the intertidal B. attramentaria is able to tolerate a broad range of salinity from 13 to 43 psu but not the acute low salinity of 3 psu. Behavioral experiments showed that salt stress significantly influenced snails' movement, with lower salinity resulting in shorter movement distance. Transcriptomic analyses revealed critical metabolic pathways and genes potentially involved in acclimation to salinity stress, including ionic and osmotic regulation, signal and hormonal transduction pathways, water exchange, cell protection, and gene regulation or epigenetic modification. In general, our study presents a robust, integrative laboratory-based approach to investigate the effects of salt stress on a nonmodel gastropod facing detrimental consequences of environmental change. The current genetic results provide a wealth of reference data for further research on mechanisms of ionic and osmotic regulation and adaptive evolution of this coastal gastropod.
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Key Words
- AICC, corrected Akaike Information Criterion
- ATP, adenosine triphosphate
- DEG, differentially expressed gene
- FAA, free amino acid
- FDR, false discovery rate
- GABA, gamma-aminobutyric acid
- Hsp, heat shock protein
- LMM, linear mixed-effects model
- MDS, multidimensional scaling
- RNA-Seq, RNA sequencing.
- fc, fold change
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Yuan L, Chen L, Qian K, Qian G, Wu CL, Wang X, Xiao Y. Co-expression network analysis identified six hub genes in association with progression and prognosis in human clear cell renal cell carcinoma (ccRCC). Genom Data 2017; 14:132-140. [PMID: 29159069 PMCID: PMC5683669 DOI: 10.1016/j.gdata.2017.10.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [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: 07/10/2017] [Revised: 10/12/2017] [Accepted: 10/25/2017] [Indexed: 12/21/2022]
Abstract
Human clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignant adult kidney tumors. We constructed a weighted gene co-expression network to identify gene modules associated with clinical features of ccRCC (n = 97). Six hub genes (CCNB2, CDC20, CEP55, KIF20A, TOP2A and UBE2C) were identified in both co-expression and protein-protein interaction (PPI) networks, which were highly correlated with pathologic stage. The significance of expression of the hub genes in ccRCC was ranked top 4 among all cancers and correlated with poor prognosis. Functional analysis revealed that the hub genes were significantly enriched in cell cycle regulation and cell division. Gene set enrichment analysis suggested that the samples with highly expressed hub gene were correlated with cell cycle and p53 signaling pathway. Taken together, six hub genes were identified to be associated with progression and prognosis of ccRCC, and they might lead to poor prognosis by regulating p53 signaling pathway.
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Key Words
- Clear cell renal cell carcinoma (ccRCC)
- Co-expression network analysis
- DAVID, Database for Annotation, Visualization and Integrated Discovery
- DEG, differentially expressed gene
- DEGs, differentially expressed genes
- GS, gene significance
- GSEA, enrichment analysis and gene set enrichment
- HPA, human protein atlas
- Hub genes
- MEs, module eigengenes
- MS, module significance
- PPI, protein-protein interaction
- Prognosis
- Progression
- SAM, significance analysis of microarrays
- STRING, search tool for the retrieval of interacting genes
- TCGA, the cancer genome atlas
- TOM, topological overlap matrix
- WGCNA, weighted gene co-expression network analysis
- ccRCC, clear cell renal cell carcinoma
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Affiliation(s)
- Lushun Yuan
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Liang Chen
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, The Fifth Hospital of Wuhan, Wuhan, China
| | - Guofeng Qian
- Department of Endocrinology, The First Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Chin-Lee Wu
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xinghuan Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Corresponding author.
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Correspondence to: Y. Xiao, Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.Department of Biological RepositoriesZhongnan Hospital of Wuhan UniversityWuhanChina
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Lindholm ME, Marabita F, Gomez-Cabrero D, Rundqvist H, Ekström TJ, Tegnér J, Sundberg CJ. An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training. Epigenetics 2015; 9:1557-69. [PMID: 25484259 PMCID: PMC4622000 DOI: 10.4161/15592294.2014.982445] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [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] [Indexed: 11/19/2022] Open
Abstract
Regular endurance exercise training induces beneficial functional and health effects in human skeletal muscle. The putative contribution to the training response of the epigenome as a mediator between genes and environment has not been clarified. Here we investigated the contribution of DNA methylation and associated transcriptomic changes in a well-controlled human intervention study. Training effects were mirrored by significant alterations in DNA methylation and gene expression in regions with a homogeneous muscle energetics and remodeling ontology. Moreover, a signature of DNA methylation and gene expression separated the samples based on training and gender. Differential DNA methylation was predominantly observed in enhancers, gene bodies and intergenic regions and less in CpG islands or promoters. We identified transcriptional regulator binding motifs of MRF, MEF2 and ETS proteins in the proximity of the changing sites. A transcriptional network analysis revealed modules harboring distinct ontologies and, interestingly, the overall direction of the changes of methylation within each module was inversely correlated to expression changes. In conclusion, we show that highly consistent and associated modifications in methylation and expression, concordant with observed health-enhancing phenotypic adaptations, are induced by a physiological stimulus.
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Key Words
- 450k arrays
- CS, citrate synthase
- CpG, cytosine-guanine dinucleotide
- DEG, differentially expressed gene
- DMP, differentially methylated position
- DNA methylation
- FDR, false discovery rate
- LUMA, luminometric methylation assay
- MDS, multidimensional scaling
- MEF, myocyte enhancer factor
- MRF, myogenic regulatory factor
- PCA, principal component analysis
- environment
- epigenomics
- exercise
- integrative analysis
- lifestyle
- transcriptional network
- β-HAD, 3-hydroxyacyl-CoA dehydrogenase
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Affiliation(s)
- Maléne E Lindholm
- a Molecular Exercise Physiology; Department of Physiology and Pharmacology; Karolinska Institutet ; Stockholm , Sweden
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Gao X, Yourick JJ, Topping VD, Black T, Olejnik N, Keltner Z, Sprando RL. Toxicogenomic study in rat thymus of F1 generation offspring following maternal exposure to silver ion. Toxicol Rep 2014; 2:341-350. [PMID: 28962367 PMCID: PMC5598402 DOI: 10.1016/j.toxrep.2014.12.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 12/11/2014] [Indexed: 11/23/2022] Open
Abstract
Male and female rats (26-day-old) were exposed to 0.0, 0.4, 4 or 40 mg/kg body weight silver acetate (AgAc) in drinking water for 10 weeks prior to and during mating. Sperm-positive females remained within their dose groups and were exposed to silver acetate during gestation and lactation. At postnatal day 26, the effect of silver ions on the developing F1 generation rat thymus was evaluated at the transcriptional level using whole-genome microarrays. Gene expression profiling analyses identified a dozen differentially expressed genes (DEGs) in each dose group using a loose criterion of fold change (FC) >1.5 and unadjusted p < 0.05, regardless of whether the analysis was conducted within each gender group or with both gender groups combined. No dose-dependent effect was observed on the number of DEGs. In addition, none of these genes had a false discovery rate (FDR) <0.05 after correction for multiple testing. These results in combination with the observation that thymus-to-body-weight ratios were not affected and no histopathological abnormalities were identified indicate that in utero exposure to silver ions up to 26.0 mg/kg (equivalent to 40.0 mg/kg silver acetate) did not have an adverse effect on the developing thymus.
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Key Words
- AGCC, Affymetrix GeneChip Command Console
- AgAc, silver acetate
- AgNP, silver nanoparticle
- DEG, differentially expressed gene
- Developmental toxicity
- FC, fold change
- FDR, false discovery rate
- HCA, hierarchical cluster analysis
- Maternal exposure
- Microarray
- NK, natural killer
- NOEL, no observed effect level
- PCA, principal components analysis
- RMA, robust multi-array average
- Rodent model
- SV, source of variance
- Silver acetate
- Silver ion
- Thymus
- Toxicogenomics
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Affiliation(s)
- Xiugong Gao
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
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