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He J, Hu J, Liu H. A three-gene random forest model for diagnosing idiopathic pulmonary fibrosis based on circadian rhythm-related genes in lung tissue. Expert Rev Respir Med 2023; 17:1307-1320. [PMID: 38285622 DOI: 10.1080/17476348.2024.2311262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/24/2024] [Indexed: 01/31/2024]
Abstract
BACKGROUND The disorder of circadian rhythm could be a key factor mediating fibrotic lung disease Therefore, our study aims to determine the diagnostic value of circadian rhythm-related genes (CRRGs) in IPF. METHODS We retrieved the data on CRRGs from previous studies and the GSE150910 dataset. The participants from the GSE150910 dataset were divided into training and internal validation sets. Next, we used several various bioinformatics methods and machine learning algorithms to screen genes. Next, we identified SEMA5A, COL7A1, and TUBB3, which were included in the random forest (RF) diagnostic model. Finally, external validation was conducted on data retrieved from the GSE184316 datasets. RESULTS The results revealed that the RF diagnostic model could diagnose patients with IPF in the internal validation set with the area under the ROC curve (AUC) value of 0.905 and in the external validation with the AUC value of 0.767. Furthermore, real-time quantitative PCR and western blotting results revealed a significant decrease in SEMA5A (p < 0.05) expression level and an increase in COL7A1 and TUBB3 expression levels in TGF-β1-treated normal human lung fibroblasts. CONCLUSION We constructed an RF diagnostic model based on SEMA5A, COL7A1, and TUBB3 expression in lung tissue for diagnosing patients with IPF.
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Affiliation(s)
- Jie He
- Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, China
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Jun Hu
- Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, China
- Department of Otolaryngology - Head and Neck Surgery, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Hairong Liu
- Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, China
- Department of Geriatric Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
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Wang X, Wang M, Chen S, Wei B, Gao Y, Huang L, Liu C, Huang T, Yu M, Zhao SH, Li X. Ammonia exposure causes lung injuries and disturbs pulmonary circadian clock gene network in a pig study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 205:111050. [PMID: 32827960 DOI: 10.1016/j.ecoenv.2020.111050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 07/13/2020] [Accepted: 07/17/2020] [Indexed: 06/11/2023]
Abstract
Ammonia toxicity to respiratory system in pig faming is of particular concern, but the molecular mechanism remains still unclear. The present study was devoted to assess the impacts of the ammonia exposure on the lung tissues based on a pig study using 80 ppm ammonia exposing to piglets for different days. The histology analysis revealed ammonia exposure induced lung injury and inflammatory response, as indicated by epithelial-mesenchymal transition (EMT), significant thickening of alveolar septa, infiltration of inflammatory cells and excessive mucus production. The transcriptome analysis revealed many more up-regulated genes in exposure groups when compared with the control group, and these genes were significantly enriched in the GO term of extracellular exosome, proteolysis, and regulation of circadian rhythm. The study discovered the induction of seven genes (CRY2, CIART, CREM, NR1D1, NR1D2, PER1 and PER3) that encode repressors of circadian clock. One gene (ARNTL) that encodes activator of circadian clock was down-regulated after ammonia exposure. The results of this study suggest that ammonia exposure disturbed the pulmonary circadian clock gene expression, which may establish new evidence for further understanding the toxicity of ammonia to lungs.
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Affiliation(s)
- Xiaotong Wang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengyao Wang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangzhao Chen
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China
| | - Baoxin Wei
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yun Gao
- College of Engineering, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China
| | - Longhui Huang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chun Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tao Huang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mei Yu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shu-Hong Zhao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoping Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China.
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microRNA-25 as a novel modulator of circadian Period2 gene oscillation. Exp Mol Med 2020; 52:1614-1626. [PMID: 32968200 PMCID: PMC8080691 DOI: 10.1038/s12276-020-00496-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 06/22/2020] [Accepted: 07/06/2020] [Indexed: 01/02/2023] Open
Abstract
Circadian clock controls an organism’s biological rhythm and regulates its physiological processes in response to external time cues. Most living organisms have their own time-keeping mechanism that is maintained by transcriptional–translational autoregulatory feedback loops involving several core clock genes, such as Period. Recent studies have found the relevance between the modulation of circadian oscillation and posttranscriptional modifications by microRNAs (miRNAs). However, there are limited studies on candidate miRNAs that regulate circadian oscillation. Here, we characterize the functions of novel miRNA-25 regulating circadian Period2 (Per2) expression. Using several in silico algorithms, we identified novel miR-25-3p that, together with miR-24-3p, targets the Per2 gene. Luciferase reporter assays validated that miR-25-3p and miR-24-3p repressed Per2 expression and confirmed their predicted binding sites in the 3′-untranslated region (UTR) of Per2 mRNA. Real-time bioluminescence analyses using Per2::Luc mouse embryonic fibroblasts confirmed that PER2 protein oscillation patterns were responsive to miR-25-3p and miR-24-3. The overexpression of miR-25-3p or miR-24-3p resulted in the dampening and period shortening of the PER2::LUC oscillation, while inhibition of either miRNA increased the relative amplitude of the PER2::LUC oscillation. Notably, endogenous miR-25-3p expression in the suprachiasmatic nucleus (SCN) showed no circadian rhythmicity, but the expression levels differed in various brain regions and peripheral tissues. These results suggest that the posttranscriptional regulation of miR-25-3p and miR-24-3p may differ according to Per2 gene expression in different tissue regions. In summary, we found that novel miR-25-3p was involved in fine-tuning circadian rhythmicity by regulating Per2 oscillation at the posttranscriptional level and that it functioned synergistically with miR-24-3p to affect Per2 oscillation. A newly identified microRNA plays a key role in fine-tuning the genetic interactions governing the circadian rhythms in mammals, according to researchers in South Korea. Numerous studies have suggested that the Period genes, which negatively regulate the CLOCK and BMAL1 genes to produce a 24-hour feedback loop, may be further modified by microRNAs after they are transcribed. Kyungjin Kim at Daegu Gyeongbuk Institute of Science and Technology, South Korea, and co-workers confirmed that a novel microRNA, miR-25-3p, reduces the expression of a Period gene, Per2, in mice. When miR-25-3p is over-expressed, it dampens and shortens the oscillations of Per2 levels. Interestingly, the researchers showed that natural miR-25-3p expression levels varied across different parts of the brain, supporting the theory that different tissues of the body maintain their own unique circadian cycles.
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Tamimi F, Abusamak M, Akkanti B, Chen Z, Yoo SH, Karmouty-Quintana H. The case for chronotherapy in Covid-19-induced acute respiratory distress syndrome. Br J Pharmacol 2020; 177:4845-4850. [PMID: 32442317 PMCID: PMC7280566 DOI: 10.1111/bph.15140] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/07/2020] [Accepted: 05/09/2020] [Indexed: 12/27/2022] Open
Abstract
Coronavirus disease 2019 (COVID‐19), the disease resulting from infection by a novel coronavirus, SARS‐Cov2, has rapidly spread since November 2019 leading to a global pandemic. SARS‐Cov2 has infected over four million people and caused over 290,000 deaths worldwide. Although most cases are mild, a subset of patients develop a severe and atypical presentation of acute respiratory distress syndrome (ARDS) that is characterised by a cytokine release storm (CRS). Paradoxically, treatment with anti‐inflammatory agents and immune regulators has been associated with worsening of ARDS. We hypothesize that the intrinsic circadian clock of the lung and the immune system may regulate individual components of CRS, and thus, chronotherapy may be used to effectively manage ARDS in COVID‐19 patients. LINKED ARTICLES This article is part of a themed issue on The Pharmacology of COVID‐19. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v177.21/issuetoc
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Affiliation(s)
- Faleh Tamimi
- Faculty of Dentistry, McGill University, Montreal, Quebec, Canada.,College of Dental Medicine, Qatar University, Doha, Qatar
| | | | - Bindu Akkanti
- Divisions of Critical Care, Pulmonary and Sleep Medicine, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Harry Karmouty-Quintana
- Divisions of Critical Care, Pulmonary and Sleep Medicine, Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA.,Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
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Fan BS, Zhang EH, Cheng MH, Wu ZT, Han B, Yu JG. Diurnal Variation of the Peripheral Cholinergic Antiinflammatory Function in Mice. CNS Neurosci Ther 2016; 22:764-70. [PMID: 27306582 DOI: 10.1111/cns.12578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 05/03/2016] [Accepted: 05/13/2016] [Indexed: 11/28/2022] Open
Abstract
AIMS Cholinergic antiinflammatory (CAI) pathway functions importantly in inflammation via α7 nicotinic acetylcholine receptors (α7nAChR). The present work tested circadian rhythm in peripheral CAI activity and validities of CAI activity and glucocorticoids in chronotherapy for lipopolysaccharide (LPS)-induced shock. METHODS Vesicular acetylcholine transporter (VAChT) expressed in liver and kidney was examined every 3 h in C57BL/6 mice. Proinflammatory cytokines in serum and survival time in shock were monitored after LPS injection every 3 h. Mifepristone, antagonist of glucocorticoid receptors, and methyllycaconitine (MLA), antagonist of α7nAChR, were administrated before LPS to block antiinflammatory function of endogenous glucocorticoids and acetylcholine. RESULTS Both levels of tumor necrosis factor α, interleukin 1β, and interleukin 6 and mortality exhibited diurnal variations with prominent peaks when LPS was given at 15:00, and the minimum mortality occurred at 00:00. Expression of VAChT increased during resting period. MLA increased serum proinflammatory cytokines slightly, but not affected survival rate. Both differences in cytokines and in survival times between LPS injection at 15:00 and 00:00 were eliminated by mifepristone, but not by MLA. CONCLUSION Peripheral CAI pathway exerts more powerful antiinflammatory effect during resting period. Glucocorticoids appear to be efficient in chronotherapy for septic shock.
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Affiliation(s)
- Bo-Shi Fan
- Department of Pharmacology, Second Military Medical University, Shanghai, China
| | | | - Ming-He Cheng
- Department of Pharmacology, Second Military Medical University, Shanghai, China
| | - Zhao-Tang Wu
- Department of Physiology, Second Military Medical University, Shanghai, China
| | - Bing Han
- Department of Pharmacy, Minhang Hospital, Fudan University, Shanghai, China
| | - Jian-Guang Yu
- Department of Pharmacology, Second Military Medical University, Shanghai, China
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Sundar IK, Ahmad T, Yao H, Hwang JW, Gerloff J, Lawrence BP, Sellix MT, Rahman I. Influenza A virus-dependent remodeling of pulmonary clock function in a mouse model of COPD. Sci Rep 2015; 4:9927. [PMID: 25923474 PMCID: PMC4413879 DOI: 10.1038/srep09927] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 03/23/2015] [Indexed: 12/18/2022] Open
Abstract
Daily oscillations of pulmonary function depend on the rhythmic activity of the circadian timing system. Environmental tobacco/cigarette smoke (CS) disrupts circadian clock leading to enhanced inflammatory responses. Infection with influenza A virus (IAV) increases hospitalization rates and death in susceptible individuals, including patients with Chronic Obstructive Pulmonary Disease (COPD). We hypothesized that molecular clock disruption is enhanced by IAV infection, altering cellular and lung function, leading to severity in airway disease phenotypes. C57BL/6J mice exposed to chronic CS, BMAL1 knockout (KO) mice and wild-type littermates were infected with IAV. Following infection, we measured diurnal rhythms of clock gene expression in the lung, locomotor activity, pulmonary function, inflammatory, pro-fibrotic and emphysematous responses. Chronic CS exposure combined with IAV infection altered the timing of clock gene expression and reduced locomotor activity in parallel with increased lung inflammation, disrupted rhythms of pulmonary function, and emphysema. BMAL1 KO mice infected with IAV showed pronounced detriments in behavior and survival, and increased lung inflammatory and pro-fibrotic responses. This suggests that remodeling of lung clock function following IAV infection alters clock-dependent gene expression and normal rhythms of lung function, enhanced emphysematous and injurious responses. This may have implications for the pathobiology of respiratory virus-induced airway disease severity and exacerbations.
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Affiliation(s)
- Isaac K. Sundar
- Department of Environmental Medicine Lung Biology and Disease
Program, University of Rochester Medical Center, Rochester, NY,
USA
| | - Tanveer Ahmad
- Department of Environmental Medicine Lung Biology and Disease
Program, University of Rochester Medical Center, Rochester, NY,
USA
| | - Hongwei Yao
- Department of Environmental Medicine Lung Biology and Disease
Program, University of Rochester Medical Center, Rochester, NY,
USA
| | - Jae-woong Hwang
- Department of Environmental Medicine Lung Biology and Disease
Program, University of Rochester Medical Center, Rochester, NY,
USA
| | - Janice Gerloff
- Department of Environmental Medicine Lung Biology and Disease
Program, University of Rochester Medical Center, Rochester, NY,
USA
| | - B. Paige Lawrence
- Department of Environmental Medicine Lung Biology and Disease
Program, University of Rochester Medical Center, Rochester, NY,
USA
| | - Michael T. Sellix
- Department of Medicine, Division of Endocrinology, Diabetes and
Metabolism, University of Rochester Medical Center, Rochester,
NY, USA
| | - Irfan Rahman
- Department of Environmental Medicine Lung Biology and Disease
Program, University of Rochester Medical Center, Rochester, NY,
USA
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