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Del Duca E, Dahabreh D, Kim M, Bar J, Da Rosa JC, Rabinowitz G, Facheris P, Gómez-Arias PJ, Chang A, Utti V, Chowdhury A, Liu Y, Estrada YD, Laculiceanu A, Agache I, Guttman-Yassky E. Transcriptomic evaluation of skin tape-strips in children with allergic asthma uncovers epidermal barrier dysfunction and asthma-associated biomarkers abnormalities. Allergy 2024; 79:1516-1530. [PMID: 38375886 PMCID: PMC11247382 DOI: 10.1111/all.16060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/08/2024] [Accepted: 02/01/2024] [Indexed: 02/21/2024]
Abstract
INTRODUCTION Tape-strips, a minimally invasive method validated for the evaluation of several skin diseases, may help identify asthma-specific biomarkers in the skin of children with allergic asthma. METHODS Skin tape-strips were obtained and analyzed with RNA-Seq from children with moderate allergic asthma (MAA) (n = 11, mean age 7.00; SD = 1.67), severe allergic asthma (SAA) (n = 9, mean age 9.11; SD = 2.37), and healthy controls (HCs) (n = 12, mean age 7.36; SD = 2.03). Differentially expressed genes (DEGs) were identified by fold change ≥2 with a false discovery rate <0.05. Transcriptomic biomarkers were analyzed for their accuracy in distinguishing asthma from HCs, their relationships with asthma-related outcomes (exacerbation rate, lung function-FEV1, IOS-R5-20, and lung inflammation-FeNO), and their links to skin (barrier and immune response) and lung (remodeling, metabolism, aging) pathogenetic pathways. RESULTS RNA-Seq captured 1113 in MAA and 2117 DEGs in SAA. Epidermal transcriptomic biomarkers for terminal differentiation (FLG/filaggrin), cell adhesion (CDH19, JAM2), lipid biosynthesis/metabolism (ACOT2, LOXL2) were significantly downregulated. Gene set variation analysis revealed enrichment of Th1/IFNγ pathways (p < .01). MAA and SAA shared downregulation of G-protein-coupled receptor (OR4A16, TAS1R3), upregulation of TGF-β/ErbB signaling-related (ACVR1B, EGFR, ID1/2), and upregulation of mitochondrial-related (HIGD2A, VDAC3, NDUFB9) genes. Skin transcriptomic biomarkers correlated with the annualized exacerbation rate and with lung function parameters. A two-gene classifier (TSSC4-FAM212B) was able to differentiate asthma from HCs with 100% accuracy. CONCLUSION Tape-strips detected epithelial barrier and asthma-associated signatures in normal-appearing skin from children with allergic asthma and may serve as an alternative to invasive approaches for evaluating asthma endotypes.
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Affiliation(s)
- Ester Del Duca
- Department of Dermatology, Icahn School of Medicine at the Mount Sinai, New York, New York, USA
- Dermatology Clinic, Department of Clinical Internal, Anesthesiological and Cardiovascular Sciences, Sapienza University of Rome, Rome, Italy
| | - Dante Dahabreh
- Department of Dermatology, Icahn School of Medicine at the Mount Sinai, New York, New York, USA
| | - Madeline Kim
- Department of Dermatology, Icahn School of Medicine at the Mount Sinai, New York, New York, USA
| | - Jonathan Bar
- Department of Dermatology, Icahn School of Medicine at the Mount Sinai, New York, New York, USA
| | - Joel Correa Da Rosa
- Department of Dermatology, Icahn School of Medicine at the Mount Sinai, New York, New York, USA
| | - Grace Rabinowitz
- Department of Dermatology, Icahn School of Medicine at the Mount Sinai, New York, New York, USA
| | - Paola Facheris
- Department of Dermatology, Icahn School of Medicine at the Mount Sinai, New York, New York, USA
- Department of Dermatology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Pedro Jesús Gómez-Arias
- Department of Dermatology, Icahn School of Medicine at the Mount Sinai, New York, New York, USA
- Department of Dermatology, Reina Sofía University Hospital, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Cordoba, Spain
| | - Annie Chang
- Department of Dermatology, Icahn School of Medicine at the Mount Sinai, New York, New York, USA
| | - Vivian Utti
- Department of Dermatology, Icahn School of Medicine at the Mount Sinai, New York, New York, USA
| | - Amira Chowdhury
- Department of Dermatology, Icahn School of Medicine at the Mount Sinai, New York, New York, USA
| | - Ying Liu
- Department of Dermatology, Icahn School of Medicine at the Mount Sinai, New York, New York, USA
| | - Yeriel D Estrada
- Department of Dermatology, Icahn School of Medicine at the Mount Sinai, New York, New York, USA
| | - Alexandru Laculiceanu
- Department of Allergy and Clinical Immunology, Transylvania University, Brasov, Romania
| | - Ioana Agache
- Department of Allergy and Clinical Immunology, Transylvania University, Brasov, Romania
| | - Emma Guttman-Yassky
- Department of Dermatology, Icahn School of Medicine at the Mount Sinai, New York, New York, USA
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Mitochondrial Ribosome Dysfunction in Human Alveolar Type II Cells in Emphysema. Biomedicines 2022; 10:biomedicines10071497. [PMID: 35884802 PMCID: PMC9313339 DOI: 10.3390/biomedicines10071497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/17/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
Pulmonary emphysema is characterized by airspace enlargement and the destruction of alveoli. Alveolar type II (ATII) cells are very abundant in mitochondria. OXPHOS complexes are composed of proteins encoded by the mitochondrial and nuclear genomes. Mitochondrial 12S and 16S rRNAs are required to assemble the small and large subunits of the mitoribosome, respectively. We aimed to determine the mechanism of mitoribosome dysfunction in ATII cells in emphysema. ATII cells were isolated from control nonsmokers and smokers, and emphysema patients. Mitochondrial transcription and translation were analyzed. We also determined the miRNA expression. Decreases in ND1 and UQCRC2 expression levels were found in ATII cells in emphysema. Moreover, nuclear NDUFS1 and SDHB levels increased, and mitochondrial transcribed ND1 protein expression decreased. These results suggest an impairment of the nuclear and mitochondrial stoichiometry in this disease. We also detected low levels of the mitoribosome structural protein MRPL48 in ATII cells in emphysema. Decreased 16S rRNA expression and increased 12S rRNA levels were observed. Moreover, we analyzed miR4485-3p levels in this disease. Our results suggest a negative feedback loop between miR-4485-3p and 16S rRNA. The obtained results provide molecular mechanisms of mitoribosome dysfunction in ATII cells in emphysema.
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Cahill KM, Gartia MR, Sahu S, Bergeron SR, Heffernan LM, Paulsen DB, Penn AL, Noël A. In utero exposure to electronic-cigarette aerosols decreases lung fibrillar collagen content, increases Newtonian resistance and induces sex-specific molecular signatures in neonatal mice. Toxicol Res 2022; 38:205-224. [PMID: 35415078 PMCID: PMC8960495 DOI: 10.1007/s43188-021-00103-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/04/2021] [Accepted: 08/25/2021] [Indexed: 12/14/2022] Open
Abstract
Approximately 7% of pregnant women in the United States use electronic-cigarette (e-cig) devices during pregnancy. There is, however, no scientific evidence to support e-cig use as being 'safe' during pregnancy. Little is known about the effects of fetal exposures to e-cig aerosols on lung alveologenesis. In the present study, we tested the hypothesis that in utero exposure to e-cig aerosol impairs lung alveologenesis and pulmonary function in neonates. Pregnant BALB/c mice were exposed 2 h a day for 20 consecutive days during gestation to either filtered air or cinnamon-flavored e-cig aerosol (36 mg/mL of nicotine). Lung tissue was collected in offspring during lung alveologenesis on postnatal day (PND) 5 and PND11. Lung function was measured at PND11. Exposure to e-cig aerosol in utero led to a significant decrease in body weights at birth which was sustained through PND5. At PND5, in utero e-cig exposures dysregulated genes related to Wnt signaling and epigenetic modifications in both females (~ 120 genes) and males (40 genes). These alterations were accompanied by reduced lung fibrillar collagen content at PND5-a time point when collagen content is close to its peak to support alveoli formation. In utero exposure to e-cig aerosol also increased the Newtonian resistance of offspring at PND11, suggesting a narrowing of the conducting airways. At PND11, in females, transcriptomic dysregulation associated with epigenetic alterations was sustained (17 genes), while WNT signaling dysregulation was largely resolved (10 genes). In males, at PND11, the expression of only 4 genes associated with epigenetics was dysregulated, while 16 Wnt related-genes were altered. These data demonstrate that in utero exposures to cinnamon-flavored e-cig aerosols alter lung structure and function and induce sex-specific molecular signatures during lung alveologenesis in neonatal mice. This may reflect epigenetic programming affecting lung disease development later in life.
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Affiliation(s)
- Kerin M. Cahill
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Skip Bertman Dr., Baton Rouge, LA 70803 USA
| | - Manas R. Gartia
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Sushant Sahu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA 70504 USA
| | - Sarah R. Bergeron
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Skip Bertman Dr., Baton Rouge, LA 70803 USA
| | - Linda M. Heffernan
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Skip Bertman Dr., Baton Rouge, LA 70803 USA
| | - Daniel B. Paulsen
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Arthur L. Penn
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Skip Bertman Dr., Baton Rouge, LA 70803 USA
| | - Alexandra Noël
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Skip Bertman Dr., Baton Rouge, LA 70803 USA
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Jeong J, Oh C, Kim J, Yoo CG, Kim KI. LSD1-S112A exacerbates the pathogenesis of CSE/LPS-induced chronic obstructive pulmonary disease in mice. BMB Rep 2021. [PMID: 34078525 PMCID: PMC8560461 DOI: 10.5483/bmbrep.2021.54.10.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lysine-specific demethylase 1 (LSD1) is an epigenetic regulator that modulates the chromatin status, contributing to gene activation or repression. The post-translational modification of LSD1 is critical for the regulation of many of its biological processes. Phosphorylation of serine 112 of LSD1 by protein kinase C alpha (PKCα) is crucial for regulating inflammation, but its physiological significance is not fully understood. This study aimed to investigate the role of Lsd1-S112A, a phosphorylation defective mutant, in the cigarette smoke extract/LPS-induced chronic obstructive pulmonary disease (COPD) model using Lsd1SA/SA mice and to explore the potential mechanism underpinning the development of COPD. We found that Lsd1SA/SA mice exhibited increased susceptibility to CSE/LPS-induced COPD, including high inflammatory cell influx into the bronchoalveolar lavage fluid and airspace enlargement. Additionally, the high gene expression associated with the inflammatory response and oxidative stress was observed in cells and mice containing Lsd1-S112A. Similar results were obtained from the mouse embryonic fibroblasts exposed to a PKCα inhibitor, Go6976. Thus, the lack of LSD1 phosphorylation exacerbates CSE/LPS-induced COPD by elevating inflammation and oxidative stress.
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Affiliation(s)
- Jiyeong Jeong
- Research Institute of Women's Health, Sookmyung Women's University, Seoul 04310, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Chaeyoon Oh
- Department of Biological Sciences, Cellular Heterogeneity Research Center, Sookmyung Women's University, Seoul 04310, Korea
| | - Jiwon Kim
- Department of Biological Sciences, Cellular Heterogeneity Research Center, Sookmyung Women's University, Seoul 04310, Korea
| | - Chul-Gyu Yoo
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Keun Il Kim
- Research Institute of Women's Health, Sookmyung Women's University, Seoul 04310, Korea
- Department of Biological Sciences, Cellular Heterogeneity Research Center, Sookmyung Women's University, Seoul 04310, Korea
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Gene commander in the trash heap: Transcriptional regulation and ubiquitination modification mediated by RNF6 in carcinogenesis. Exp Cell Res 2021; 401:112396. [PMID: 33485842 DOI: 10.1016/j.yexcr.2020.112396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/13/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023]
Abstract
RING finger protein 6 (RNF6), a RING finger protein, has been identified as a potential tumor promoter in several cancers. However, the exact mechanism of RNF6 in cancer remains elusive. As in various diseases, RNF6 may be involved in regulating cell growth, cell proliferation, invasion, cell cycle progression, apoptosis and cell adhesion through E3 ligase-mediated ubiquitination. Thus, the research on RNF6 is mainly focused on the ubiquitination of RNF6 in recent years. This article summarizes the role of RNF6 ubiquitination in various physiological and pathological mechanisms, such as Akt/mTOR signaling pathway, Wnt/β-catenin pathway, RNF6/ERα/Bcl-xL axis, and provides knowledge and understanding for the treatment of diseases.
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Two-hybrid screening of FAM13A protein partners in lung epithelial cells. BMC Res Notes 2020; 12:804. [PMID: 31900205 PMCID: PMC6942259 DOI: 10.1186/s13104-019-4840-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/02/2019] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES Family with sequence similarity 13 member A (FAM13A) genetic variants have been associated with several chronic respiratory diseases including chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF), idiopathic pulmonary fibrosis (IPF) and lung cancer. The FAM13A protein includes a RhoGTPase activating protein (RhoGAP) domain known to participate in various cellular mechanisms including cell proliferation. While intensive genomic studies have been performed to reveal its involvement in lung diseases, the biological role of FAM13A protein is still not completely elucidated. RESULTS We therefore performed a two-hybrid screening to identify protein partners of FAM13A using a human lung cancer cDNA library. We identified several protein partners with a high confidence score. Researchers in the field of chronic lung diseases may benefit from this two-hybrid screening data which may reveal new research pathways to decipher.
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Schmidt H, Braubach P, Schilpp C, Lochbaum R, Neuland K, Thompson K, Jonigk D, Frick M, Dietl P, Wittekindt OH. IL-13 Impairs Tight Junctions in Airway Epithelia. Int J Mol Sci 2019; 20:ijms20133222. [PMID: 31262043 PMCID: PMC6651493 DOI: 10.3390/ijms20133222] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 06/27/2019] [Indexed: 12/12/2022] Open
Abstract
Interleukin-13 (IL-13) drives symptoms in asthma with high levels of T-helper type 2 cells (Th2-cells). Since tight junctions (TJ) constitute the epithelial diffusion barrier, we investigated the effect of IL-13 on TJ in human tracheal epithelial cells. We observed that IL-13 increases paracellular permeability, changes claudin expression pattern and induces intracellular aggregation of the TJ proteins zonlua occludens protein 1, as well as claudins. Furthermore, IL-13 treatment increases expression of ubiquitin conjugating E2 enzyme UBE2Z. Co-localization and proximity ligation assays further showed that ubiquitin and the proteasomal marker PSMA5 co-localize with TJ proteins in IL-13 treated cells, showing that TJ proteins are ubiquitinated following IL-13 exposure. UBE2Z upregulation occurs within the first day after IL-13 exposure. Proteasomal aggregation of ubiquitinated TJ proteins starts three days after IL-13 exposure and transepithelial electrical resistance (TEER) decrease follows the time course of TJ-protein aggregation. Inhibition of JAK/STAT signaling abolishes IL-13 induced effects. Our data suggest that that IL-13 induces ubiquitination and proteasomal aggregation of TJ proteins via JAK/STAT dependent expression of UBE2Z, resulting in opening of TJs. This may contribute to barrier disturbances in pulmonary epithelia and lung damage of patients with inflammatory lung diseases.
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Affiliation(s)
- Hanna Schmidt
- Institute of General Physiology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Peter Braubach
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 130625 Hannover, Germany
- German Center of Lung Research (DZL), Partnersite BREATH, 306245 Hannover, Germany
| | - Carolin Schilpp
- Institute of General Physiology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Robin Lochbaum
- Institute of General Physiology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Kathrin Neuland
- Institute of General Physiology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Kristin Thompson
- Institute of General Physiology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Danny Jonigk
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 130625 Hannover, Germany
- German Center of Lung Research (DZL), Partnersite BREATH, 306245 Hannover, Germany
| | - Manfred Frick
- Institute of General Physiology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Paul Dietl
- Institute of General Physiology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Oliver H Wittekindt
- Institute of General Physiology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
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Liu W, Zhang Q, Fang Y, Wang Y. The deubiquitinase USP38 affects cellular functions through interacting with LSD1. Biol Res 2018; 51:53. [PMID: 30497519 PMCID: PMC6263071 DOI: 10.1186/s40659-018-0201-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/18/2018] [Indexed: 02/08/2023] Open
Abstract
Background Deubiquitination is a posttranslational protein modification prevalent in mammalian cells. Deubiquitinases regulate the functions of the target protein by removing its ubiquitin chain. In this study, the effects of the deubiquitinase USP38’s functions on the LSD1 protein and on cell physiology were investigated. Materials and methods Western blotting, real-time quantitative PCR, immunoprecipitation, denaturing immunoprecipitation and luciferase reporter assays were used to analyze the protein stability, protein interactions and changes in the ubiquitin chain. Cell proliferation assays, colony formation assays, drug treatments and western blotting were used to explore the functions of USP38 in cells. Results The deubiquitinase USP38 stabilizes protein LSD1 in cells by binding LSD1 and cleaving its ubiquitin chain to prevent the degradation of LSD1 by the intracellular proteasome. USP38 enhances the ability of LSD1 to activate signaling pathways and hence promotes cellular abilities of proliferation and colony formation through interacting with LSD1. Furthermore, USP38 enhances the drug tolerance of human colon cancer cells. Conclusions USP38 is an LSD1-specific deubiquitinase that affects cellular physiology through interacting with LSD1.
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Affiliation(s)
- Wenbin Liu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, Hubei, China. .,College of Health Sciences and Nursing, Wuhan Polytechnic University, No. 68 Southern Xuefu Road, Wuhan, 430023, Hubei, China.
| | - Qi Zhang
- College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yuanyuan Fang
- College of Health Sciences and Nursing, Wuhan Polytechnic University, No. 68 Southern Xuefu Road, Wuhan, 430023, Hubei, China
| | - Yanan Wang
- College of Health Sciences and Nursing, Wuhan Polytechnic University, No. 68 Southern Xuefu Road, Wuhan, 430023, Hubei, China
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The Overlap of Lung Tissue Transcriptome of Smoke Exposed Mice with Human Smoking and COPD. Sci Rep 2018; 8:11881. [PMID: 30089872 PMCID: PMC6082828 DOI: 10.1038/s41598-018-30313-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/23/2018] [Indexed: 01/09/2023] Open
Abstract
Genome-wide mRNA profiling in lung tissue from human and animal models can provide novel insights into the pathogenesis of chronic obstructive pulmonary disease (COPD). While 6 months of smoke exposure are widely used, shorter durations were also reported. The overlap of short term and long-term smoke exposure in mice is currently not well understood, and their representation of the human condition is uncertain. Lung tissue gene expression profiles of six murine smoking experiments (n = 48) were obtained from the Gene Expression Omnibus (GEO) and analyzed to identify the murine smoking signature. The "human smoking" gene signature containing 386 genes was previously published in the lung eQTL study (n = 1,111). A signature of mild COPD containing 7 genes was also identified in the same study. The lung tissue gene signature of "severe COPD" (n = 70) contained 4,071 genes and was previously published. We detected 3,723 differentially expressed genes in the 6 month-exposure mice datasets (FDR <0.1). Of those, 184 genes (representing 48% of human smoking) and 1,003 (representing 27% of human COPD) were shared with the human smoking-related genes and the COPD severity-related genes, respectively. There was 4-fold over-representation of human and murine smoking-related genes (P = 6.7 × 10-26) and a 1.4 fold in the severe COPD -related genes (P = 2.3 × 10-12). There was no significant enrichment of the mice and human smoking-related genes in mild COPD signature. These data suggest that murine smoke models are strongly representative of molecular processes of human smoking but less of COPD.
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Zhang Y, Li W, Feng Y, Guo S, Zhao X, Wang Y, He Y, He W, Chen L. Prioritizing chronic obstructive pulmonary disease (COPD) candidate genes in COPD-related networks. Oncotarget 2017; 8:103375-103384. [PMID: 29262568 PMCID: PMC5732734 DOI: 10.18632/oncotarget.21874] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/04/2017] [Indexed: 12/16/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a multi-factor disease, which could be caused by many factors, including disturbances of metabolism and protein-protein interactions (PPIs). In this paper, a weighted COPD-related metabolic network and a weighted COPD-related PPI network were constructed base on COPD disease genes and functional information. Candidate genes in these weighted COPD-related networks were prioritized by making use of a gene prioritization method, respectively. Literature review and functional enrichment analysis of the top 100 genes in these two networks suggested the correlation of COPD and these genes. The performance of our gene prioritization method was superior to that of ToppGene and ToppNet for genes from the COPD-related metabolic network or the COPD-related PPI network after assessing using leave-one-out cross-validation, literature validation and functional enrichment analysis. The top-ranked genes prioritized from COPD-related metabolic and PPI networks could promote the better understanding about the molecular mechanism of this disease from different perspectives. The top 100 genes in COPD-related metabolic network or COPD-related PPI network might be potential markers for the diagnosis and treatment of COPD.
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Affiliation(s)
- Yihua Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Wan Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yuyan Feng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Shanshan Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Xilei Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yahui Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yuehan He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Weiming He
- Institute of Opto-Electronics, Harbin Institute of Technology, Harbin, Heilongjiang Province, China
| | - Lina Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
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Obeidat M, Nie Y, Fishbane N, Li X, Bossé Y, Joubert P, Nickle DC, Hao K, Postma DS, Timens W, Sze MA, Shannon CP, Hollander Z, Ng RT, McManus B, Miller BE, Rennard S, Spira A, Hackett TL, Lam W, Lam S, Faner R, Agusti A, Hogg JC, Sin DD, Paré PD. Integrative Genomics of Emphysema-Associated Genes Reveals Potential Disease Biomarkers. Am J Respir Cell Mol Biol 2017; 57:411-418. [PMID: 28459279 DOI: 10.1165/rcmb.2016-0284oc] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Chronic obstructive pulmonary disease is the third leading cause of death worldwide. Gene expression profiling across multiple regions of the same lung identified genes significantly related to emphysema. We sought to determine whether the lung and epithelial expression of 127 emphysema-related genes was also related to lung function in independent cohorts, and whether any of these genes could be used as biomarkers in the peripheral blood of patients with chronic obstructive pulmonary disease. To that end, we examined whether the expression levels of these genes were under genetic control in lung tissue (n = 1,111). We then determined whether the mRNA levels of these genes in lung tissue (n = 727), small airway epithelial cells (n = 238), and peripheral blood (n = 620) were significantly related to lung function measurements. The expression of 63 of the 127 genes (50%) was under genetic control in lung tissue. The lung and epithelial mRNA expression of a subset of the emphysema-associated genes, including ASRGL1, LPHN2, and EDNRB, was strongly associated with lung function. In peripheral blood, the expression of 40 genes was significantly associated with lung function. Twenty-nine of these genes (73%) were also associated with lung function in lung tissue, but with the opposite direction of effect for 24 of the 29 genes, including those involved in hypoxia and B cell-related responses. The integrative genomics approach uncovered a significant overlap of emphysema genes associations with lung function between lung and blood with opposite directions between the two. These results support the use of peripheral blood to detect disease biomarkers.
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Affiliation(s)
- Ma'en Obeidat
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Yunlong Nie
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Nick Fishbane
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Xuan Li
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Yohan Bossé
- 2 Department of Molecular Medicine.,3 Institut Universitaire de Cardiologie et de Pneumologie de Québec, and
| | - Philippe Joubert
- 3 Institut Universitaire de Cardiologie et de Pneumologie de Québec, and.,4 Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University, Québec, Quebec, Canada
| | - David C Nickle
- 5 Merck Research Laboratories, Genetics and Pharmacogenomics, Boston, Massachusetts
| | - Ke Hao
- 6 Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Wim Timens
- 8 Department of Pathology and Medical Biology, GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Marc A Sze
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Casey P Shannon
- 9 Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - Zsuzsanna Hollander
- 9 Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - Raymond T Ng
- 9 Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - Bruce McManus
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada.,9 Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | | | - Stephen Rennard
- 11 Division of Pulmonary and Critical Care Medicine, University of Nebraska Medical Center, Omaha, Nebraska.,12 Clinical Discovery Unit, Early Clinical Development, AstraZeneca, Cambridge, United Kingdom
| | - Avrum Spira
- 13 Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Tillie-Louise Hackett
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada.,14 Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wan Lam
- 15 Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Stephen Lam
- 15 Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Rosa Faner
- 16 Fundacio Clinic per a la Recerca Biomedica, Barcelona, Spain
| | - Alvar Agusti
- 16 Fundacio Clinic per a la Recerca Biomedica, Barcelona, Spain
| | - James C Hogg
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada.,17 Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; and
| | - Don D Sin
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada.,18 Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter D Paré
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada.,18 Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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12
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Brazee P, Dada LA, Sznajder JI. Role of Linear Ubiquitination in Health and Disease. Am J Respir Cell Mol Biol 2017; 54:761-8. [PMID: 26848516 DOI: 10.1165/rcmb.2016-0014tr] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The covalent attachment of ubiquitin to target proteins is one of the most prevalent post-translational modifications, regulating a myriad of cellular processes including cell growth, survival, and metabolism. Recently, a novel RING E3 ligase complex was described, called linear ubiquitin assembly complex (LUBAC), which is capable of connecting ubiquitin molecules in a novel head-to-tail fashion via the N-terminal methionine residue. LUBAC is a heteromeric complex composed of heme-oxidized iron-responsive element-binding protein 2 ubiquitin ligase-1L (HOIL-1L), HOIL-1L-interacting protein, and shank-associated RH domain-interacting protein (SHARPIN). The essential role of LUBAC-generated linear chains for activation of nuclear factor-κB (NF-κB) signaling was first described in the activation of tumor necrosis factor-α receptor signaling complex. A decade of research has identified additional pathways that use LUBAC for downstream signaling, including CD40 ligand and the IL-1β receptor, as well as cytosolic pattern recognition receptors including nucleotide-binding oligomerization domain containing 2 (NOD2), retinoic acid-inducible gene 1 (RIG-1), and the NOD-like receptor family, pyrin domain containing 3 inflammasome (NLRP3). Even though the three components of the complex are required for full activation of NF-κB, the individual components of LUBAC regulate specific cell type- and stimuli-dependent effects. In humans, autosomal defects in LUBAC are associated with both autoinflammation and immunodeficiency, with additional disorders described in mice. Moreover, in the lung epithelium, HOIL-1L ubiquitinates target proteins independently of the other LUBAC components, adding another layer of complexity to the function and regulation of LUBAC. Although many advances have been made, the diverse functions of linear ubiquitin chains and the regulation of LUBAC are not yet completely understood. In this review, we discuss the various roles of linear ubiquitin chains and point to areas of study that would benefit from further investigation into LUBAC-mediated signaling pathways in lung pathophysiology.
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Affiliation(s)
- Patricia Brazee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University, Chicago, Illinois
| | - Laura A Dada
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University, Chicago, Illinois
| | - Jacob I Sznajder
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University, Chicago, Illinois
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13
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Sheridan JA, Zago M, Nair P, Li PZ, Bourbeau J, Tan WC, Hamid Q, Eidelman DH, Benedetti AL, Baglole CJ. Decreased expression of the NF-κB family member RelB in lung fibroblasts from Smokers with and without COPD potentiates cigarette smoke-induced COX-2 expression. Respir Res 2015; 16:54. [PMID: 25943190 PMCID: PMC4427974 DOI: 10.1186/s12931-015-0214-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/21/2015] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Heightened inflammation, including expression of COX-2, is associated with COPD pathogenesis. RelB is an NF-κB family member that attenuates COX-2 in response to cigarette smoke by a mechanism that may involve the miRNA miR-146a. There is no information on the expression of RelB in COPD or if RelB prevents COX-2 expression through miR-146a. METHODS RelB, Cox-2 and miR-146a levels were evaluated in lung fibroblasts and blood samples derived from non-smokers (Normal) and smokers (At Risk) with and without COPD by qRT-PCR. RelB and COX-2 protein levels were evaluated by western blot. Human lung fibroblasts from Normal subjects and smokers with and without COPD, along with RelB knock-down (siRNA) in Normal cells, were exposed to cigarette smoke extract (CSE) in vitro and COX-2 mRNA/protein and miR-146a levels assessed. RESULTS Basal expression of RelB mRNA and protein were significantly lower in lung cells derived from smokers with and without COPD, the latter of which expressed more Cox-2 mRNA and protein in response to CSE. Knock-down of RelB in Normal fibroblasts increased Cox-2 mRNA and protein induction by CSE. Basal miR-146a levels were not different between the three groups, and only Normal fibroblasts increased miR-146a expression in response to smoke. There was a positive correlation between systemic RelB and Cox-2 mRNA levels and circulating miR-146a levels were higher only in GOLD stage I subjects. CONCLUSIONS Our data indicate that RelB attenuates COX-2 expression in lung structural cells, such that loss of pulmonary RelB may be an important determinant in the aberrant, heightened inflammation associated with COPD pathogenesis.
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Affiliation(s)
- Jared A Sheridan
- Department of Medicine, 1001 Decarie Blvd, Montreal, QC, H4A 3J1, Canada.
| | - Michela Zago
- Department of Medicine, 1001 Decarie Blvd, Montreal, QC, H4A 3J1, Canada.
| | | | - Pei Z Li
- Respiratory Epidemiology and Clinical Research Unit, Montreal Chest Institute, McGill University, Montreal, QC, Canada.
| | - Jean Bourbeau
- Respiratory Epidemiology and Clinical Research Unit, Montreal Chest Institute, McGill University, Montreal, QC, Canada.
| | - Wan C Tan
- The UBC James Hogg Research Centre, University of British Columbia, Vancouver, BC, Canada.
| | - Qutayba Hamid
- Department of Medicine, 1001 Decarie Blvd, Montreal, QC, H4A 3J1, Canada.
- Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC, H4A 3J1, Canada.
| | - David H Eidelman
- Department of Medicine, 1001 Decarie Blvd, Montreal, QC, H4A 3J1, Canada.
- Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC, H4A 3J1, Canada.
| | - Andrea L Benedetti
- Department of Epidemiology and Biostatistics, 1001 Decarie Blvd, Montreal, QC, H4A 3J1, Canada.
| | - Carolyn J Baglole
- Department of Medicine, 1001 Decarie Blvd, Montreal, QC, H4A 3J1, Canada.
- Research Institute of the McGill University Health Centre, 1001 Decarie Blvd, Montreal, QC, H4A 3J1, Canada.
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