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Lukyanchuk A, Muraki N, Kawai T, Sato T, Hata K, Ito T, Tajima A. Long-term exposure to diesel exhaust particles induces concordant changes in DNA methylation and transcriptome in human adenocarcinoma alveolar basal epithelial cells. Epigenetics Chromatin 2024; 17:24. [PMID: 39103936 DOI: 10.1186/s13072-024-00549-3] [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: 03/08/2024] [Accepted: 07/19/2024] [Indexed: 08/07/2024] Open
Abstract
BACKGROUND Diesel exhaust particles (DEP), which contain hazardous compounds, are emitted during the combustion of diesel. As approximately one-third of the vehicles worldwide use diesel, there are growing concerns about the risks posed by DEP to human health. Long-term exposure to DEP is associated with airway hyperresponsiveness, pulmonary fibrosis, and inflammation; however, the molecular mechanisms behind the effects of DEP on the respiratory tract are poorly understood. Such mechanisms can be addressed by examining transcriptional and DNA methylation changes. Although several studies have focused on the effects of short-term DEP exposure on gene expression, research on the transcriptional effects and genome-wide DNA methylation changes caused by long-term DEP exposure is lacking. Hence, in this study, we investigated transcriptional and DNA methylation changes in human adenocarcinoma alveolar basal epithelial A549 cells caused by prolonged exposure to DEP and determined whether these changes are concordant. RESULTS DNA methylation analysis using the Illumina Infinium MethylationEPIC BeadChips showed that the methylation levels of DEP-affected CpG sites in A549 cells changed in a dose-dependent manner; the extent of change increased with increasing dose reaching the statistical significance only in samples exposed to 30 µg/ml DEP. Four-week exposure to 30 µg/ml of DEP significantly induced DNA hypomethylation at 24,464 CpG sites, which were significantly enriched for DNase hypersensitive sites, genomic regions marked by H3K4me1 and H3K27ac, and several transcription factor binding sites. In contrast, 9,436 CpG sites with increased DNA methylation levels were significantly overrepresented in genomic regions marked by H3K27me3 as well as H3K4me1 and H3K27ac. In parallel, gene expression profiling by RNA sequencing demonstrated that long-term exposure to DEP altered the expression levels of 2,410 genes, enriching 16 gene sets including Xenobiotic metabolism, Inflammatory response, and Senescence. In silico analysis revealed that the expression levels of 854 genes correlated with the methylation levels of the DEP-affected cis-CpG sites. CONCLUSIONS To our knowledge, this is the first report of genome-wide transcriptional and DNA methylation changes and their associations in A549 cells following long-term exposure to DEP.
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Affiliation(s)
- Alexandra Lukyanchuk
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-8640, Japan
- Krasnoyarsk State Medical University Named After Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
| | - Naomi Muraki
- Health Effects Research Group, Environment Research Division, Japan Automobile Research Institute, Tsukuba, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-8640, Japan
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Human Molecular Genetics, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Tsuyoshi Ito
- Health Effects Research Group, Environment Research Division, Japan Automobile Research Institute, Tsukuba, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-8640, Japan.
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Xu F, Tong Y, Yang W, Cai Y, Yu M, Liu L, Meng Q. Identifying a survival-associated cell type based on multi-level transcriptome analysis in idiopathic pulmonary fibrosis. Respir Res 2024; 25:126. [PMID: 38491375 PMCID: PMC10941445 DOI: 10.1186/s12931-024-02738-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/19/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a progressive disease with a five-year survival rate of less than 40%. There is significant variability in survival time among IPF patients, but the underlying mechanisms for this are not clear yet. METHODS AND RESULTS We collected single-cell RNA sequence data of 13,223 epithelial cells taken from 32 IPF patients and bulk RNA sequence data from 456 IPF patients in GEO. Based on unsupervised clustering analysis at the single-cell level and deconvolution algorithm at bulk RNA sequence data, we discovered a special alveolar type 2 cell subtype characterized by high expression of CCL20 (referred to as ATII-CCL20), and found that IPF patients with a higher proportion of ATII-CCL20 had worse prognoses. Furthermore, we uncovered the upregulation of immune cell infiltration and metabolic functions in IPF patients with a higher proportion of ATII-CCL20. Finally, the comprehensive decision tree and nomogram were constructed to optimize the risk stratification of IPF patients and provide a reference for accurate prognosis evaluation. CONCLUSIONS Our study by integrating single-cell and bulk RNA sequence data from IPF patients identified a special subtype of ATII cells, ATII-CCL20, which was found to be a risk cell subtype associated with poor prognosis in IPF patients. More importantly, the ATII-CCL20 cell subtype was linked with metabolic functions and immune infiltration.
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Affiliation(s)
- Fei Xu
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yun Tong
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Wenjun Yang
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yiyang Cai
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Meini Yu
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Lei Liu
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Qingkang Meng
- Department of Pharmacogenomics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
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3
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Feng X, Pan C, Liu S, Hu H, Ma Y. Identification of core genes affecting IMF deposition in bovine. Anim Biotechnol 2023; 34:2887-2899. [PMID: 36137229 DOI: 10.1080/10495398.2022.2124167] [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] [Indexed: 11/01/2022]
Abstract
Intramuscular fat (IMF) content is an important economic factor in beef production. However, knowledge on the key factors controlling bovine IMF is limited. In this study, using weighted gene co-expression network analysis (WGCNA), nine modules were identified and the number of transcripts in these modules ranged from 36 to 3191. Two modules were found to be significantly associated with fat deposition and three genes (TCAP, MYH7, and TNNC1) were further identified by Protein-protein interaction (PPI), which may be the hub genes regulating bovine IMF deposition. In addition, considering the genetic variation, the PCK1 gene was found by functional enrichment analysis of overlapping genes, which was previously reported to be involved in IMF deposition. We noted that the core promoter region of buffalo PCK1 binds to transcription factors involved in lipid metabolism while cattle PCK1 binds transcription factors involved in muscle development. The results suggest that PCK1 participated in IMF deposition of buffalo and cattle in different ways. In summary, gene expression networks and new candidate genes associated with IMF deposition identified in this study. This would lay the foundation for further research into the molecular regulatory mechanisms underlying bovine IMF deposition.
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Affiliation(s)
- Xue Feng
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Cuili Pan
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Shuang Liu
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Honghong Hu
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, China
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4
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Maus M, López-Polo V, Mateo L, Lafarga M, Aguilera M, De Lama E, Meyer K, Sola A, Lopez-Martinez C, López-Alonso I, Guasch-Piqueras M, Hernandez-Gonzalez F, Chaib S, Rovira M, Sanchez M, Faner R, Agusti A, Diéguez-Hurtado R, Ortega S, Manonelles A, Engelhardt S, Monteiro F, Stephan-Otto Attolini C, Prats N, Albaiceta G, Cruzado JM, Serrano M. Iron accumulation drives fibrosis, senescence and the senescence-associated secretory phenotype. Nat Metab 2023; 5:2111-2130. [PMID: 38097808 PMCID: PMC10730403 DOI: 10.1038/s42255-023-00928-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/11/2023] [Indexed: 12/21/2023]
Abstract
Fibrogenesis is part of a normal protective response to tissue injury that can become irreversible and progressive, leading to fatal diseases. Senescent cells are a main driver of fibrotic diseases through their secretome, known as senescence-associated secretory phenotype (SASP). Here, we report that cellular senescence, and multiple types of fibrotic diseases in mice and humans are characterized by the accumulation of iron. We show that vascular and hemolytic injuries are efficient in triggering iron accumulation, which in turn can cause senescence and promote fibrosis. Notably, we find that senescent cells persistently accumulate iron, even when the surge of extracellular iron has subdued. Indeed, under normal conditions of extracellular iron, cells exposed to different types of senescence-inducing insults accumulate abundant ferritin-bound iron, mostly within lysosomes, and present high levels of labile iron, which fuels the generation of reactive oxygen species and the SASP. Finally, we demonstrate that detection of iron by magnetic resonance imaging might allow non-invasive assessment of fibrotic burden in the kidneys of mice and in patients with renal fibrosis. Our findings suggest that iron accumulation plays a central role in senescence and fibrosis, even when the initiating events may be independent of iron, and identify iron metabolism as a potential therapeutic target for senescence-associated diseases.
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Grants
- SAF2017-82613-R "la Caixa" Foundation (Caixa Foundation)
- of M. Serrano was funded by the IRB and “laCaixa” Foundation, and by grants from the Spanish Ministry of Science co-funded by the European Regional Development Fund (ERDF) (SAF2017-82613-R), European Research Council (ERC-2014-AdG/669622), and grant RETOS COLABORACION RTC2019-007125-1 from MCIN/AEI, and Secretaria d'Universitats i Recerca del Departament d'Empresa i Coneixement of Catalonia (Grup de Recerca consolidat 2017 SGR 282)
- M.M. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement (No 794744) and from the Spanish Ministry of Science and Innovation (MCIN) (RYC2020-030652-I /AEI /10.13039/501100011033)
- V.L.P. was recipient of a predoctoral contract from Spanish Ministry of Education (FPU-18/05917).
- K.M. was recipient of fellowships from the German Cardiac, the German Research Foundation, and a postdoctoral contract Juan de la Cierva from the MCIN.
- F.H.G. was supported by the PhD4MD Collaborative Research Training Programme for Medical Doctors (IRB Barcelona/Hospital Clinic/IDIBAPS).
- M. Sanchez was funded by grants PID2021-122436OB-I00 from MCIN/ AEI /10.13039/501100011033 / FEDER, UE, and RETOS COLABORACION RTC2019-007074-1 from MCIN/AEI /10.13039/501100011033.
- G.A. was funded by Instituto de Salud Carlos III through project PI 20/01360, FEDER funds.
- J.M.C was funded by Instituto de Salud Carlos III through projects PI18/00910 and PI21/00931 (Co-funded by European Regional Development Fund. ERDF, a way to build Europe), and thanks CERCA Programme / Generalitat de Catalunya for institutional support.
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Affiliation(s)
- Mate Maus
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Vall d'Hebron Institute of Oncology, Barcelona, Spain.
| | - Vanessa López-Polo
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Lidia Mateo
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Miguel Lafarga
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria-IDIVAL, Santander, Spain
| | - Mònica Aguilera
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Eugenia De Lama
- Radiology Department, Hospital Universitari de Bellvitge, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Kathleen Meyer
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - Anna Sola
- Nephrology and Renal Transplantation Research Group. Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Cecilia Lopez-Martinez
- Departamento de Biología Funcional, Instituto Universitario de Oncología del principado de Asturias, Universidad de Oviedo, Oviedo, Spain
- Unidad de Cuidados Intensivos Cardiológicos. Hospital Universitario Central de Asturias, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Ines López-Alonso
- Departamento de Morfología y Biología Celular, Universidad de Oviedo, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | | | - Fernanda Hernandez-Gonzalez
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Department of Pulmonary Medicine, Respiratory Institute, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Selim Chaib
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Miguel Rovira
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Mayka Sanchez
- Iron Metabolism: Regulation and Diseases Group, Department of Basic Sciences, Universitat Internacional de Catalunya (UIC), Sant Cugat del Vallès, Spain
| | - Rosa Faner
- Biomedicine Department, University of Barcelona, IDIBAPS, CIBERES, Barcelona, Spain
| | - Alvar Agusti
- Universitat de Barcelona, Institut Respiratori, Hospital Clinic, IDIBAPS, CIBERES, Barcelona, Spain
| | - Rodrigo Diéguez-Hurtado
- Deparment of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Sagrario Ortega
- Transgenics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Anna Manonelles
- Nephrology and Renal Transplantation Research Group. Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Nephrology Department, Bellvitge University Hospital, Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, University of Barcelona, Hospitalet de Llobregat, Barcelona, Spain
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology, Technical University of Munich (TUM), Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Freddy Monteiro
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Neus Prats
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Guillermo Albaiceta
- Departamento de Biología Funcional, Instituto Universitario de Oncología del principado de Asturias, Universidad de Oviedo, Oviedo, Spain
- Unidad de Cuidados Intensivos Cardiológicos. Hospital Universitario Central de Asturias, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
- CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Josep M Cruzado
- Nephrology and Renal Transplantation Research Group. Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Nephrology Department, Bellvitge University Hospital, Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, University of Barcelona, Hospitalet de Llobregat, Barcelona, Spain
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Altos Labs, Cambridge Institute of Science, Cambridge, UK.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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5
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Al-Mutairy EA, Al Qattan S, Khalid M, Al-Enazi AA, Al-Saif MM, Imtiaz F, Ramzan K, Raveendran V, Alaiya A, Meyer BF, Atamas SP, Collison KS, Khabar KS, Hasday JD, Al-Mohanna F. Wild-type S100A3 and S100A13 restore calcium homeostasis and mitigate mitochondrial dysregulation in pulmonary fibrosis patient-derived cells. Front Cell Dev Biol 2023; 11:1282868. [PMID: 38099297 PMCID: PMC10720433 DOI: 10.3389/fcell.2023.1282868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
Patients with digenic S100A3 and S100A13 mutations exhibited an atypical and progressive interstitial pulmonary fibrosis, with impaired intracellular calcium homeostasis and mitochondrial dysfunction. Here we provide direct evidence of a causative effect of the mutation on receptor mediated calcium signaling and calcium store responses in control cells transfected with mutant S100A3 and mutant S100A13. We demonstrate that the mutations lead to increased mitochondrial mass and hyperpolarization, both of which were reversed by transfecting patient-derived cells with the wild type S100A3 and S100A13, or extracellular treatment with the recombinant proteins. In addition, we demonstrate increased secretion of inflammatory mediators in patient-derived cells and in control cells transfected with the mutant-encoding constructs. These findings indicate that treatment of patients' cells with recombinant S100A3 and S100A13 proteins is sufficient to normalize most of cellular responses, and may therefore suggest the use of these recombinant proteins in the treatment of this devastating disease.
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Affiliation(s)
- Eid A. Al-Mutairy
- Department of Cell Biology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Somaya Al Qattan
- Department of Cell Biology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Mohammed Khalid
- Department of Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Azizah A. Al-Enazi
- Department of Cell Biology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Maher M. Al-Saif
- BioMolecular Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Faiqa Imtiaz
- Clinical Genomics, Center of Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Khushnooda Ramzan
- Clinical Genomics, Center of Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Vineesh Raveendran
- Department of Cell Biology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Ayodele Alaiya
- Stem Cell Therapy Program, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Brian F. Meyer
- Clinical Genomics, Center of Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sergei P. Atamas
- University of Maryland School of Medicine, Baltimore, MD, United States
- Baltimore VA Medical Center, Baltimore, MD, United States
| | - Kate S. Collison
- Department of Cell Biology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Khalid S. Khabar
- BioMolecular Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Jeffrey D. Hasday
- University of Maryland School of Medicine, Baltimore, MD, United States
- Baltimore VA Medical Center, Baltimore, MD, United States
| | - Futwan Al-Mohanna
- Department of Cell Biology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
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6
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Zhou Y, Lin Z, Xie S, Gao Y, Zhou H, Chen F, Fu Y, Yang C, Ke C. Interplay of chronic obstructive pulmonary disease and colorectal cancer development: unravelling the mediating role of fatty acids through a comprehensive multi-omics analysis. J Transl Med 2023; 21:587. [PMID: 37658368 PMCID: PMC10474711 DOI: 10.1186/s12967-023-04278-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/14/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) patients often exhibit gastrointestinal symptoms, A potential association between COPD and Colorectal Cancer (CRC) has been indicated, warranting further examination. METHODS In this study, we collected COPD and CRC data from the National Health and Nutrition Examination Survey, genome-wide association studies, and RNA sequence for a comprehensive analysis. We used weighted logistic regression to explore the association between COPD and CRC incidence risk. Mendelian randomization analysis was performed to assess the causal relationship between COPD and CRC, and cross-phenotype meta-analysis was conducted to pinpoint crucial loci. Multivariable mendelian randomization was used to uncover mediating factors connecting the two diseases. Our results were validated using both NHANES and GEO databases. RESULTS In our analysis of the NHANES dataset, we identified COPD as a significant contributing factor to CRC development. MR analysis revealed that COPD increased the risk of CRC onset and progression (OR: 1.16, 95% CI 1.01-1.36). Cross-phenotype meta-analysis identified four critical genes associated with both CRC and COPD. Multivariable Mendelian randomization suggested body fat percentage, omega-3, omega-6, and the omega-3 to omega-6 ratio as potential mediating factors for both diseases, a finding consistent with the NHANES dataset. Further, the interrelation between fatty acid-related modules in COPD and CRC was demonstrated via weighted gene co-expression network analysis and Kyoto Encyclopedia of Genes and Genomes enrichment results using RNA expression data. CONCLUSIONS This study provides novel insights into the interplay between COPD and CRC, highlighting the potential impact of COPD on the development of CRC. The identification of shared genes and mediating factors related to fatty acid metabolism deepens our understanding of the underlying mechanisms connecting these two diseases.
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Affiliation(s)
- Youtao Zhou
- The First Clinical Medical School, Guangzhou Medical University, Guangzhou, China
| | - Zikai Lin
- Nanshan School, Guangzhou Medical University, Guangzhou, China
| | - Shuojia Xie
- Nanshan School, Guangzhou Medical University, Guangzhou, China
| | - Yuan Gao
- The First Clinical Medical School, Guangzhou Medical University, Guangzhou, China
| | - Haobin Zhou
- The First Clinical Medical School, Guangzhou Medical University, Guangzhou, China
| | - Fengzhen Chen
- The First Clinical Medical School, Guangzhou Medical University, Guangzhou, China
| | - Yuewu Fu
- Department of General Surgery, School of Medicine, The First Affiliated Hospital, Ji'nan University, Guangzhou, China
| | - Cuiyan Yang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Chuanfeng Ke
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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7
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Su M, Liu J, Wu X, Chen X, Xiao Q, Jiang N. Construction of a TFs-miRNA-mRNA network related to idiopathic pulmonary fibrosis. ANNALS OF TRANSLATIONAL MEDICINE 2023; 11:78. [PMID: 36819574 PMCID: PMC9929790 DOI: 10.21037/atm-22-6161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/07/2023] [Indexed: 01/18/2023]
Abstract
Background The transcription factors (TFs)-microRNA (miRNA)-messenger RNA (mRNA) network plays an important role in a variety of diseases. However, the relationship between the TFs-miRNA-mRNA network and idiopathic pulmonary fibrosis (IPF) remains unclear. Methods The GSE110147 and GSE53845 datasets from the Gene Expression Omnibus (GEO) database were used to process differentially expressed genes (DEGs) analysis, gene set enrichment analysis (GSEA), weighted gene co-expression network analysis (WGCNA), as well as Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The GSE13316 dataset was used to perform differentially expressed miRNAs (DEMs) analysis and TFs prediction. Finally, a TFs-miRNA-mRNA network related to IPF was constructed, and its function was evaluated by Gene Ontology (GO) and KEGG analyses. Also, 19 TFs in the network were verified by quantitative real time polymerase chain reaction (qRT-PCR). Results Through our analysis, 53 DEMs and 2,630 DEGs were screened. The GSEA results suggested these genes were mainly related to protein digestion and absorption. The WGCNA results showed that these DEGs were divided into eight modules, and the GO and KEGG analyses results of blue module genes showed that these 86 blue module genes were mainly enriched in cilium assembly and cilium organization. Moreover, a TFs-miRNA-mRNA network comprising 25 TFs, 11 miRNAs, and 60 mRNAs was constructed. Ultimately, the functional enrichment analysis showed that the TFs-miRNA-mRNA network was mainly related to the cell cycle and the phosphatidylinositol 3 kinase-protein kinase B (PI3K-Akt) signaling pathway. Furthermore, experimental verification of the TFs showed that ARNTL, TRIM28, EZH2, BCOR, and ASXL1 were sufficiently up-regulated in the transforming growth factor (TGF)-β1 treatment groups, while BCL6, BHLHE40, FOXA1, and EGR1 were significantly down-regulated. Conclusions The novel TFs-miRNA-mRNA network that we constructed could provide new insights into the underlying molecular mechanisms of IPF. ARNTL, TRIM28, EZH2, BCOR, ASXL1, BCL6, BHLHE40, FOXA1, and EGR1 may play important roles in IPF and become effective biomarkers for diagnosis and treatment.
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Affiliation(s)
- Minhong Su
- Department of Respiratory and Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Junfang Liu
- Department of Respiratory and Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiping Wu
- Department of Respiratory and Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xin Chen
- Department of Respiratory and Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Qiang Xiao
- Department of Pulmonary and Critical Care Medicine, Shunde Hospital, Southern Medical University, Foshan, China
| | - Ning Jiang
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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8
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Cellular and Molecular Mechanisms in Idiopathic Pulmonary Fibrosis. Adv Respir Med 2023; 91:26-48. [PMID: 36825939 PMCID: PMC9952569 DOI: 10.3390/arm91010005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/06/2023] [Accepted: 01/12/2023] [Indexed: 02/04/2023]
Abstract
The respiratory system is a well-organized multicellular organ, and disruption of cellular homeostasis or abnormal tissue repair caused by genetic deficiency and exposure to risk factors lead to life-threatening pulmonary disease including idiopathic pulmonary fibrosis (IPF). Although there is no clear etiology as the name reflected, its pathological progress is closely related to uncoordinated cellular and molecular signals. Here, we review the advances in our understanding of the role of lung tissue cells in IPF pathology including epithelial cells, mesenchymal stem cells, fibroblasts, immune cells, and endothelial cells. These advances summarize the role of various cell components and signaling pathways in the pathogenesis of idiopathic pulmonary fibrosis, which is helpful to further study the pathological mechanism of the disease, provide new opportunities for disease prevention and treatment, and is expected to improve the survival rate and quality of life of patients.
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Lv J, Xiao J, Jia Q, Meng X, Yang Z, Pu S, Li M, Yu T, Zhang Y, Wang H, Liu L, Li Z, Chen X, Yang H, Li Y, Qiao M, Duan A, Shao H, Li B. Identification of key pathways and genes in the progression of silicosis based on WGCNA. Inhal Toxicol 2022; 34:304-318. [PMID: 35913820 DOI: 10.1080/08958378.2022.2102700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Silicosis, induced by inhaling silica particles in workplaces, is one of the most common occupational diseases. The prognosis of silicosis and its consequent fibrosis is extremely poor due to limited treatment modalities and lack of understanding of the disease mechanisms. In this study, a Wistar rat model for silicosis fibrosis was established by intratracheal instillation of silica (0, 50, 100 and 200 mg/mL, 1 mL) with the evidence of Hematoxylin and Eosin (HE) and Masson staining and the expressions of inflammatory and fibrotic proteins of rats' lung tissues. RNA of lung tissues of rats exposed to 200 mg/mL silica particles and normal saline for 14 d and 28 d was extracted and sequenced to detect differentially expressed genes (DEGs) and to identify silicosis fibrosis-associated modules and hub genes by Weighted gene co-expression network analysis (WGCNA). Predictions of gene functions and signaling pathways were conducted using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. In this study, it has been demonstrated the promising role of the Hippo signaling pathway in silicosis fibrosis, which will be conducive to elucidating the specific mechanism of pulmonary fibrosis induced by silica and to determining molecular initiating event (MIE) and adverse outcome pathway (AOP) of silicosis fibrosis.
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Affiliation(s)
- Jiaqi Lv
- Department of Toxicology, Key Lab of Chemical Safety and health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jingwei Xiao
- Department of Toxicology, Key Lab of Chemical Safety and health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qiang Jia
- Department of Toxicology, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong Academy of Occupational Health and Occupational Medicine, Jinan, China
| | - Xiangjing Meng
- Department of Toxicology, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong Academy of Occupational Health and Occupational Medicine, Jinan, China
| | - Zhifeng Yang
- Department of Toxicology, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong Academy of Occupational Health and Occupational Medicine, Jinan, China
| | - Shuangshuang Pu
- Department of Toxicology, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong Academy of Occupational Health and Occupational Medicine, Jinan, China
| | - Ming Li
- Department of Toxicology, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong Academy of Occupational Health and Occupational Medicine, Jinan, China
| | - Tao Yu
- Department of Toxicology, Key Lab of Chemical Safety and health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi Zhang
- Department of Toxicology, Key Lab of Chemical Safety and health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Haihua Wang
- Department of Toxicology, Key Lab of Chemical Safety and health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Li Liu
- Department of Toxicology, Key Lab of Chemical Safety and health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhongsheng Li
- Department of Toxicology, Key Lab of Chemical Safety and health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiao Chen
- Department of Toxicology, Key Lab of Chemical Safety and health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Haitao Yang
- Department of Toxicology, Key Lab of Chemical Safety and health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yulu Li
- Department of Toxicology, Key Lab of Chemical Safety and health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mengyun Qiao
- Department of Toxicology, Key Lab of Chemical Safety and health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Airu Duan
- Department of Toxicology, Key Lab of Chemical Safety and health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hua Shao
- Department of Toxicology, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong Academy of Occupational Health and Occupational Medicine, Jinan, China
| | - Bin Li
- Department of Toxicology, Key Lab of Chemical Safety and health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
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Consensus Gene Co-Expression Network Analysis Identifies Novel Genes Associated with Severity of Fibrotic Lung Disease. Int J Mol Sci 2022; 23:ijms23105447. [PMID: 35628257 PMCID: PMC9141193 DOI: 10.3390/ijms23105447] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/07/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a severe fibrotic lung disease characterized by irreversible scarring of the lung parenchyma leading to dyspnea, progressive decline in lung function, and respiratory failure. We analyzed lung transcriptomic data from independent IPF cohorts using weighted gene co-expression network analysis (WGCNA) to identify gene modules based on their preservation status in these cohorts. The consensus gene modules were characterized by leveraging existing clinical and molecular data such as lung function, biological processes, pathways, and lung cell types. From a total of 32 consensus gene modules identified, two modules were found to be significantly correlated with the disease, lung function, and preserved in other IPF datasets. The upregulated gene module was enriched for extracellular matrix, collagen metabolic process, and BMP signaling while the downregulated module consisted of genes associated with tube morphogenesis, blood vessel development, and cell migration. Using a combination of connectivity-based and trait-based significance measures, we identified and prioritized 103 "hub" genes (including 25 secretory candidate biomarkers) by their similarity to known IPF genetic markers. Our validation studies demonstrate the dysregulated expression of CRABP2, a retinol-binding protein, in multiple lung cells of IPF, and its correlation with the decline in lung function.
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Garcia AN, Casanova NG, Kempf CL, Bermudez T, Valera DG, Song JH, Sun X, Cai H, Moreno-Vinasco L, Gregory T, Oita RC, Hernon VR, Camp SM, Rogers C, Kyubwa EM, Menon N, Axtelle J, Rappaport J, Bime C, Sammani S, Cress AE, Garcia JGN. eNAMPT Is a Novel Damage-associated Molecular Pattern Protein That Contributes to the Severity of Radiation-induced Lung Fibrosis. Am J Respir Cell Mol Biol 2022; 66:497-509. [PMID: 35167418 PMCID: PMC9116358 DOI: 10.1165/rcmb.2021-0357oc] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/17/2021] [Indexed: 11/24/2022] Open
Abstract
The paucity of therapeutic strategies to reduce the severity of radiation-induced lung fibrosis (RILF), a life-threatening complication of intended or accidental ionizing radiation exposure, is a serious unmet need. We evaluated the contribution of eNAMPT (extracellular nicotinamide phosphoribosyltransferase), a damage-associated molecular pattern (DAMP) protein and TLR4 (Toll-like receptor 4) ligand, to the severity of whole-thorax lung irradiation (WTLI)-induced RILF. Wild-type (WT) and Nampt+/- heterozygous C57BL6 mice and nonhuman primates (NHPs, Macaca mulatta) were exposed to a single WTLI dose (9.8 or 10.7 Gy for NHPs, 20 Gy for mice). WT mice received IgG1 (control) or an eNAMPT-neutralizing polyclonal or monoclonal antibody (mAb) intraperitoneally 4 hours after WTLI and weekly thereafter. At 8-12 weeks after WTLI, NAMPT expression was assessed by immunohistochemistry, biochemistry, and plasma biomarker studies. RILF severity was determined by BAL protein/cells, hematoxylin and eosin, and trichrome blue staining and soluble collagen assays. RNA sequencing and bioinformatic analyses identified differentially expressed lung tissue genes/pathways. NAMPT lung tissue expression was increased in both WTLI-exposed WT mice and NHPs. Nampt+/- mice and eNAMPT polyclonal antibody/mAb-treated mice exhibited significantly attenuated WTLI-mediated lung fibrosis with reduced: 1) NAMPT and trichrome blue staining; 2) dysregulated lung tissue expression of smooth muscle actin, p-SMAD2/p-SMAD1/5/9, TGF-β, TSP1 (thrombospondin-1), NOX4, IL-1β, and NRF2; 3) plasma eNAMPT and IL-1β concentrations; and 4) soluble collagen. Multiple WTLI-induced dysregulated differentially expressed lung tissue genes/pathways with known tissue fibrosis involvement were each rectified in mice receiving eNAMPT mAbs.The eNAMPT/TLR4 inflammatory network is essentially involved in radiation pathobiology, with eNAMPT neutralization an effective therapeutic strategy to reduce RILF severity.
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Affiliation(s)
| | | | | | | | | | | | | | - Hua Cai
- Department of Anesthesiology, University of California Los Angeles, Los Angeles, California
| | | | | | | | | | | | | | | | | | | | - Jay Rappaport
- Tulane National Primate Research Center, New Orleans, Louisiana
| | | | | | - Anne E. Cress
- Department of Cell and Molecular Medicine, University of Arizona Health Sciences, Tucson, Arizona
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12
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Gu HY, Qu WQ, Peng HH, Yu YF, Jiang ZZ, Qi BW, Yu AX. Stemness Subtypes and Scoring System Predict Prognosis and Efficacy of Immunotherapy in Soft Tissue Sarcoma. Front Immunol 2022; 13:796606. [PMID: 35464409 PMCID: PMC9022121 DOI: 10.3389/fimmu.2022.796606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 03/07/2022] [Indexed: 11/29/2022] Open
Abstract
Tumor stemness has been reported to play important roles in cancers. However, a comprehensive analysis of tumor stemness remains to be performed to investigate the specific mechanisms and practical values of stemness in soft tissue sarcomas (STS). Here, we applied machine learning to muti-omic data of patients from TCGA-SARC and GSE21050 cohorts to reveal important roles of stemness in STS. We demonstrated limited roles of existing mRNAsi in clinical application. Therefore, based on stemness-related signatures (SRSs), we identified three stemness subtypes with distinct stemness, immune, and metabolic characteristics using consensus clustering. The low-stemness subtype had better prognosis, activated innate and adaptive immunity (e.g., infiltrating B, DC, Th1, CD8+ T, activated NK, gamma delta T cells, and M1 macrophages), more enrichment of metabolic pathways, more sites with higher methylation level, higher gene mutations, CNA burdens, and immunogenicity indicators. Furthermore, the 16 SRS-based stemness prognostic index (SPi) was developed, and we found that low-SPi patients with low stemness had better prognosis and other characteristics similar to those in the low-stemness subtype. Besides, low-stemness subtype and low-SPi patients could benefit from immunotherapy. The predictive value of SPi in immunotherapy was more accurate after the addition of MSI into SPi. MSIlowSPilow patients might be more sensitive to immunotherapy. In conclusion, we highlighted mechanisms and practical values of the stemness in STS. We also recommended the combination of MSI and SPi which is a promising tool to predict prognosis and achieve precise treatments of immunotherapy in STS.
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Affiliation(s)
- Hui-Yun Gu
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wen-Qiang Qu
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hai-Heng Peng
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yi-Feng Yu
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhe-Zhen Jiang
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Bai-Wen Qi
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ai-Xi Yu
- Department of Orthopedics Trauma and Microsurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
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13
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Liu J, Gu L, Li W. The Prognostic Value of Integrated Analysis of Inflammation and Hypoxia-Related Genes in Idiopathic Pulmonary Fibrosis. Front Immunol 2022; 13:730186. [PMID: 35309336 PMCID: PMC8929415 DOI: 10.3389/fimmu.2022.730186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/14/2022] [Indexed: 02/05/2023] Open
Abstract
Currently, the aetiology and pathogenesis of idiopathic pulmonary fibrosis (IPF) are still largely unclear. Moreover, patients with IPF exhibit a considerable difference in clinical presentation, treatment, and prognosis. Optimal biomarkers or models for IPF prognosis are lacking. Therefore, this study quantified the levels of various hallmarks using a single-sample gene set enrichment analysis algorithm. The hazard ration was calculated using Univariate Cox regression analysis based on the transcriptomic profile of bronchoalveolar lavage cells and clinical survival information. Afterwards, weighted Gene Co-expression Network Analysis was performed to construct a network between gene expression, inflammation response, and hypoxia. Subsequently, univariate Cox, random forest, and multivariate Cox regressions were applied to develop a robust inflammation and hypoxia-related gene signature for predicting clinical outcomes in patients with IPF. Furthermore, a nomogram was constructed to calculate risk assessment. The inflammation response and hypoxia were identified as latent risk factors for patients with IPF. Five genes, including HS3ST1, WFDC2, SPP1, TFPI, and CDC42EP2, were identified that formed the inflammation-hypoxia-related gene signature. Kaplan-Meier plotter showed that the patients with high-risk scores had a worse prognosis than those with low-risk scores in training and validation cohorts. The time-dependent concordance index and the receiver operating characteristic analysis revealed that the risk model could accurately predict the clinical outcome of patients with IPF. Therefore, this study contributes to elucidating the role of inflammation and hypoxia in IPF, which can aid in assessing individual prognosis and personalised treatment decisions.
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Affiliation(s)
- Jun Liu
- Reproductive Medicine Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
- Medical Research Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Liming Gu
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Wenli Li
- Reproductive Medicine Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
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Peng Y, Wang ZN, Xu AR, Fang ZF, Chen SY, Hou XT, Zhou ZQ, Lin HM, Xie JX, Tang XX, Wang DY, Zhong NS. Mucus Hypersecretion and Ciliary Impairment in Conducting Airway Contribute to Alveolar Mucus Plugging in Idiopathic Pulmonary Fibrosis. Front Cell Dev Biol 2022; 9:810842. [PMID: 35174169 PMCID: PMC8842394 DOI: 10.3389/fcell.2021.810842] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/14/2021] [Indexed: 12/20/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease attributed to the complex interplay of genetic and environmental risks. The muco-ciliary clearance (MCC) system plays a critical role in maintaining the conduit for air to and from the alveoli, but it remains poorly understood whether the MCC abnormalities in conducting airway are involved in IPF pathogenesis. In this study, we obtained the surgically resected bronchi and peripheral lung tissues from 31 IPF patients and 39 control subjects, and we sought to explore the morphologic characteristics of MCC in conducting airway by using immunostaining and scanning and transmission electron microscopy. In the submucosal regions of the bronchi, we found that the areas of mucus glands (MUC5B+) were significantly larger in IPF patients as compared with control subjects (p < 0.05). In the surface epithelium of three airway regions (bronchi, proximal bronchioles, and distal bronchioles), increased MUC5B and MUC5AC expression of secretory cells, decreased number of ciliated cells, and increased ciliary length were observed in IPF patients than control subjects (all p < 0.05). In addition, the mRNA expression levels of MUC5B were up-regulated in both the bronchi and peripheral lung of IPF patients than those of control subjects (p < 0.05), accompanied with 93.55% IPF subjects who had obvious MUC5B+ mucus plugs in alveolar regions. No MUC5B rs35705950 single-nucleotide polymorphism allele was detected in both IPF patients and control subjects. Our study shows that mucus hypersecretion and ciliary impairment in conducting airway are major causes of mucus plugs in alveolar regions and may be closely related to the alveolar injuries in IPF patients.
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Affiliation(s)
- Yang Peng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China.,Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Zhao-Ni Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Ai-Ru Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Zhang-Fu Fang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Shi-Ying Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Xiao-Tao Hou
- Guangzhou KingMed Center for Clinical Laboratory Co., Ltd., Guangzhou, China
| | - Zi-Qing Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Hui-Min Lin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Jia-Xing Xie
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Xiao Xiao Tang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - De-Yun Wang
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nan-Shan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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Matrix Metalloproteinase 7 Expression and Apical Epithelial Defects in Atp8b1 Mutant Mouse Model of Pulmonary Fibrosis. Biomolecules 2022; 12:biom12020283. [PMID: 35204783 PMCID: PMC8961514 DOI: 10.3390/biom12020283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 02/04/2023] Open
Abstract
Abnormalities in airway epithelia and lung parenchyma are found in Atp8b1 mutant mice, which develop pulmonary fibrosis after hyperoxic insult. Microarray and ingenuity pathway analysis (IPA) show numerous transcripts involved in ciliogenesis are downregulated in 14-month (14 M) -old Atp8b1 mouse lung compared with wild-type C57BL/6. Lung epithelium of Atp8b1 mice demonstrate apical abnormalities of ciliated and club cells in the bronchial epithelium on transmission electron microscopy (TEM). Matrix metalloproteinase 7 (MMP7) regulates of ciliogenesis and is a biomarker for idiopathic pulmonary fibrosis (IPF) in humans. Mmp7 transcript and protein expression are significantly upregulated in 14 M Atp8b1 mutant mouse lung. MMP7 expression is also increased in bronchoalveolar lavage fluid (BAL). Immunohistochemistry is localized MMP7 to bronchial epithelial cells in the Atp8b1 mutant. In conclusion, MMP7 is upregulated in the aged Atp8b1 mouse model, which displays abnormal ciliated cell and club cell morphology. This mouse model can facilitate the exploration of the role of MMP7 in epithelial integrity and ciliogenesis in IPF. The Atp8b1 mutant mouse is proposed as a model for IPF.
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Elliot S, Catanuto P, Pereira-simon S, Xia X, Shahzeidi S, Roberts E, Ludlow J, Hamdan S, Daunert S, Parra J, Stone R, Pastar I, Tomic-Canic M, Glassberg MK. Urine-derived exosomes from individuals with IPF carry pro-fibrotic cargo. eLife 2022; 11:79543. [PMID: 36454035 PMCID: PMC9714968 DOI: 10.7554/elife.79543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNA) and other components contained in extracellular vesicles may reflect the presence of a disease. Lung tissue, sputum, and sera of individuals with idiopathic pulmonary fibrosis (IPF) show alterations in miRNA expression. We designed this study to test whether urine and/or tissue derived exosomal miRNAs from individuals with IPF carry cargo that can promote fibrosis. METHODS Exosomes were isolated from urine (U-IPFexo), lung tissue myofibroblasts (MF-IPFexo), serum from individuals with IPF (n=16) and age/sex-matched controls without lung disease (n=10). We analyzed microRNA expression of isolated exosomes and their in vivo bio-distribution. We investigated the effect on ex vivo skin wound healing and in in vivo mouse lung models. RESULTS U-IPFexo or MF-IPFexo expressed miR-let-7d, miR-29a-5p, miR-181b-3p and miR-199a-3p consistent with previous reports of miRNA expression obtained from lung tissue/sera from patients with IPF. In vivo bio-distribution experiments detected bioluminescent exosomes in the lung of normal C57Bl6 mice within 5 min after intravenous infusion, followed by distribution to other organs irrespective of exosome source. Exosomes labeled with gold nanoparticles and imaged by transmission electron microscopy were visualized in alveolar epithelial type I and type II cells. Treatment of human and mouse lung punches obtained from control, non-fibrotic lungs with either U-IPFexo or MF-IPFexo produced a fibrotic phenotype. A fibrotic phenotype was also induced in a human ex vivo skin model and in in vivo lung models. CONCLUSIONS Our results provide evidence of a systemic feature of IPF whereby exosomes contain pro-fibrotic miRNAs when obtained from a fibrotic source and interfere with response to tissue injury as measured in skin and lung models. FUNDING This work was supported in part by Lester and Sue Smith Foundation and The Samrick Family Foundation and NIH grants R21 AG060338 (SE and MKG), U01 DK119085 (IP, RS, MTC).
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Affiliation(s)
- Sharon Elliot
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of MedicineMiamiUnited States
| | - Paola Catanuto
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of MedicineMiamiUnited States
| | - Simone Pereira-simon
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of MedicineMiamiUnited States
| | - Xiaomei Xia
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep, University of MiamiMiamiUnited States
| | | | - Evan Roberts
- Cancer Modeling Shared Resource Sylvester Comprehensive Cancer Center, University of MiamiMiamiUnited States
| | | | - Suzana Hamdan
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of MedicineMiamiUnited States,Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami Miller School of MedicineMiamiUnited States
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of MedicineMiamiUnited States,Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami Miller School of MedicineMiamiUnited States,Miami Clinical and Translational Science Institute, University of Miami Miller School of MedicineMiamiUnited States
| | - Jennifer Parra
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep, University of MiamiMiamiUnited States
| | - Rivka Stone
- Wound Healing and Regenerative Medicine Research Program, Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of MiamiMiamiUnited States
| | - Irena Pastar
- Wound Healing and Regenerative Medicine Research Program, Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of MiamiMiamiUnited States
| | - Marjana Tomic-Canic
- Wound Healing and Regenerative Medicine Research Program, Dr Phillip Frost Department of Dermatology and Cutaneous Surgery, University of MiamiMiamiUnited States
| | - Marilyn K Glassberg
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of MedicineMiamiUnited States,Department of Medicine, Division of Pulmonary, Critical Care and Sleep, University of MiamiMiamiUnited States,Department of Medicine, Stritch School of Medicine, Loyola University ChicagoChicagoUnited States
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17
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De Sadeleer LJ, McDonough JE, Schupp JC, Yan X, Vanstapel A, Van Herck A, Everaerts S, Geudens V, Sacreas A, Goos T, Aelbrecht C, Nawrot TS, Martens DS, Schols D, Claes S, Verschakelen JA, Verbeken EK, Ackermann M, Decottignies A, Mahieu M, Hackett TL, Hogg JC, Vanaudenaerde BM, Verleden SE, Kaminski N, Wuyts WA. Lung Microenvironments and Disease Progression in Fibrotic Hypersensitivity Pneumonitis. Am J Respir Crit Care Med 2022; 205:60-74. [PMID: 34724391 PMCID: PMC8865586 DOI: 10.1164/rccm.202103-0569oc] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Rationale: Fibrotic hypersensitivity pneumonitis (fHP) is an interstitial lung disease caused by sensitization to an inhaled allergen. Objectives: To identify the molecular determinants associated with progression of fibrosis. Methods: Nine fHP explant lungs and six unused donor lungs (as controls) were systematically sampled (4 samples/lung). According to microcomputed tomography measures, fHP cores were clustered into mild, moderate, and severe fibrosis groups. Gene expression profiles were assessed using weighted gene co-expression network analysis, xCell, gene ontology, and structure enrichment analysis. Gene expression of the prevailing molecular traits was also compared with idiopathic pulmonary fibrosis (IPF). The explant lung findings were evaluated in separate clinical fHP cohorts using tissue, BAL samples, and computed tomography scans. Measurements and Main Results: We found six molecular traits that associated with differential lung involvement. In fHP, extracellular matrix and antigen presentation/sensitization transcriptomic signatures characterized lung zones with only mild structural and histological changes, whereas signatures involved in honeycombing and B cells dominated the transcriptome in the most severely affected lung zones. With increasing disease severity, endothelial function was progressively lost, and progressive disruption in normal cellular homeostatic processes emerged. All six were also found in IPF, with largely similar associations with disease microenvironments. The molecular traits correlated with in vivo disease behavior in a separate clinical fHP cohort. Conclusions: We identified six molecular traits that characterize the morphological progression of fHP and associate with in vivo clinical behavior. Comparing IPF with fHP, the transcriptome landscape was determined considerably by local disease extent rather than by diagnosis alone.
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Affiliation(s)
- Laurens J. De Sadeleer
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA),,Unit for Interstitial Lung Diseases, Department of Respiratory Diseases
| | - John E. McDonough
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA),,Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Jonas C. Schupp
- Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut;,Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
| | - Xiting Yan
- Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Arno Vanstapel
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA),,Department of Histopathology, and
| | - Anke Van Herck
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA)
| | - Stephanie Everaerts
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA),,Unit for Interstitial Lung Diseases, Department of Respiratory Diseases
| | - Vincent Geudens
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA)
| | - Annelore Sacreas
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA)
| | - Tinne Goos
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA),,Unit for Interstitial Lung Diseases, Department of Respiratory Diseases
| | - Celine Aelbrecht
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA)
| | - Tim S. Nawrot
- Department of Public Health and Primary Care, and,Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Dries S. Martens
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Dominique Schols
- Department of Microbiology, Immunology, and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Sandra Claes
- Department of Microbiology, Immunology, and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | | | | | - Maximilian Ackermann
- Institute of Functional and Clinical Anatomy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany;,Institute of Pathology and Molecular Pathology, Helios University Clinic Wuppertal, University of Witten/Herdecke, Wuppertal, Germany
| | - Anabelle Decottignies
- Telomeres Research Group, Genetic and Epigenetic Alterations of Genomes, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Manon Mahieu
- Telomeres Research Group, Genetic and Epigenetic Alterations of Genomes, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Tillie-Louise Hackett
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada; and
| | - James C. Hogg
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada; and
| | - Bart M. Vanaudenaerde
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA)
| | - Stijn E. Verleden
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA),,Antwerp Surgical Training, Anatomy and Research Centre, Antwerp University, Antwerp, Belgium
| | - Naftali Kaminski
- Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Wim A. Wuyts
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA),,Unit for Interstitial Lung Diseases, Department of Respiratory Diseases
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Qiu L, Gong G, Wu W, Li N, Li Z, Chen S, Li P, Chen T, Zhao H, Hu C, Fang Z, Wang Y, Liu H, Cui P, Zhang G. A novel prognostic signature for idiopathic pulmonary fibrosis based on five-immune-related genes. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1570. [PMID: 34790776 PMCID: PMC8576669 DOI: 10.21037/atm-21-4545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/02/2021] [Indexed: 01/04/2023]
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is a highly fatal lung disease of unknown etiology with a median survival after diagnosis of only 2–3 years. Its poor prognosis is due to the limited therapy options available as well as the lack of effective prognostic indicators. This study aimed to construct a novel prognostic signature for IPF to assist in the personalized management of IPF patients during treatment. Methods Differentially-expressed genes (DEGs) in IPF patients versus healthy individuals were analyzed using the “limma” package of R software. Immune-related genes (IRGs) were obtained from the ImmPort database. Univariate Cox regression analysis was adopted to screen significantly prognostic IRGs for IPF patients. Multiple Cox regression analysis was used to identify optimal prognostic IRGs and construct a prognostic signature. Results Compared with healthy individuals, there were a total of 52 prognosis-related DEGs in the bronchoalveolar lavage (BAL) samples of IPF patients, of which 37 genes were identified as IRGs. Of these, five genes (CXCL14, SLC40A1, RNASE3, CCR3, and RORA) were significantly associated with overall survival (OS) in IPF patients, and were utilized for establishment of the prognostic signature. IPF patients were divided into high- and low-risk groups based on the prognostic signature. Marked differences in the OS probability were observed between high- and low-risk IPF patients. The area under curves (AUCs) of the receiver operating characteristic (ROC) curve for the prognostic signature in the training and validation cohorts were 0.858 and 0.837, respectively. The expression levels between RNASE3 and SLC40A1 (P<0.01, r=0.394), between RORA and CXCL14 (P<0.01, r=−0.355), between CCR3 and CXCL14 (P<0.01, r=0.258), as well as between RNASE3 and CCR3 (P<0.01, r=0.293) were significantly correlated. Conclusions We developed a validated and reproducible IRG-based prognostic signature that should be helpful in the personalized management of patients with IPF, providing new insights into the relationship between the immune system and IPF.
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Affiliation(s)
- Lingxiao Qiu
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China.,Henan Provincial Medical Key Laboratory for Interstitial Lung Disease and Lung Transplantation, Zhengzhou, China
| | - Gencheng Gong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenjuan Wu
- Department of Geriatric Medicine, Henan Provincial People's Hospital, Zhengzhou, China
| | - Nana Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhaonan Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shanshan Chen
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Medical Key Laboratory for Interstitial Lung Disease and Lung Transplantation, Zhengzhou, China
| | - Ping Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Medical Key Laboratory for Interstitial Lung Disease and Lung Transplantation, Zhengzhou, China.,Zhengzhou Key Laboratory for Chronic Respiratory Disease, Zhengzhou, China
| | - Tengfei Chen
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huasi Zhao
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chunling Hu
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zeming Fang
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yan Wang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongping Liu
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Panpan Cui
- School of Nursing and Heath, Zhengzhou University, Zhengzhou, China
| | - Guojun Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Medical Key Laboratory for Interstitial Lung Disease and Lung Transplantation, Zhengzhou, China.,Zhengzhou Key Laboratory for Chronic Respiratory Disease, Zhengzhou, China
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Li Y, Dong W, Zhang P, Zhang T, Ma L, Qu M, Ma X, Zhou X, He Q. Comprehensive Analysis of Regulatory Factors and Immune-Associated Patterns to Decipher Common and BRCA1/2 Mutation-Type-Specific Critical Regulation in Breast Cancer. Front Cell Dev Biol 2021; 9:750897. [PMID: 34733851 PMCID: PMC8558486 DOI: 10.3389/fcell.2021.750897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/22/2021] [Indexed: 11/13/2022] Open
Abstract
Background: BRCA1/2 mutations are closely related to high lifetime risk of breast cancer (BC). The objective of this study was to identify the genes, regulators, and immune-associated patterns underlying disease pathology in BC with BRCA1/2 somatic mutations and their associations with clinical traits. Methods: RNA sequencing data and clinical information from The Cancer Genome Atlas (TCGA; N = 36 BRCA1-mutant BC; N = 49 BRCA2-mutant BC; and N = 117 BRCA1/2-wild-type BC samples) were used for discovery, which included consensus network analysis, function enrichment, and analysis of hub genes; other TCGA data (N = 117 triple-negative BC) and two Gene Expression Omnibus database expression profiles were used as validation cohorts. Results: Consensus network analysis helped to identify specific co-expressed modules that showed positive correlations with tumor stage, number of positive lymph nodes, and margin status in BRCA1/2-mutant BC but lacking correlations in BRCA1/2-wild-type BC. Functional enrichment suggested potential mechanisms in BRCA1/2 carriers that could regulate the cell cycle, immune response, cellular metabolic processes, and cell migration, via enriched pathways including p53 and JAK-STAT signaling. Consensus network analysis identified the specific and common carcinogenic mechanisms involving BRCA mutations. Regulators cross-linking these modules include E2F or IRF transcription factor family, associated with cell cycle or immune response regulation module, respectively. Eight hub genes, including ISG15, BUB1, and TTK, were upregulated in several BRCA1/2-mutant BC datasets and showed prognostic value in BC. Furthermore, their genetic expression was related to higher levels of immune infiltration in BRCA1/2-mutant BC, which manifested as recruitment of T helper cells (Th1 cells), follicular helper T cells, and regulatory T cells, and T cell exhaustion. Moreover, important indicators for evaluation of BC immunotherapy, tumor mutational burden and neoantigen load also positively correlated with expression of some hub genes. Conclusion: We constructed a BRCA1/2 mutation-type-specific co-expressed gene network with related transcription factors and immune-associated patterns that could regulate and influence tumor metastasis and immune microenvironment, providing novel insights into the pathological process of this disease and the corresponding BRCA mutations.
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Affiliation(s)
- Yue Li
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Wei Dong
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Pengqian Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ting Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ling Ma
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Meng Qu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xingcong Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiaoyan Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qian He
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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20
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Fanidis D, Moulos P, Aidinis V. Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis. Sci Rep 2021; 11:21712. [PMID: 34741074 PMCID: PMC8571330 DOI: 10.1038/s41598-021-01069-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/21/2021] [Indexed: 11/22/2022] Open
Abstract
Idiopathic pulmonary fibrosis is a lethal lung fibroproliferative disease with limited therapeutic options. Differential expression profiling of affected sites has been instrumental for involved pathogenetic mechanisms dissection and therapeutic targets discovery. However, there have been limited efforts to comparatively analyse/mine the numerous related publicly available datasets, to fully exploit their potential on the validation/creation of novel research hypotheses. In this context and towards that goal, we present Fibromine, an integrated database and exploration environment comprising of consistently re-analysed, manually curated transcriptomic and proteomic pulmonary fibrosis datasets covering a wide range of experimental designs in both patients and animal models. Fibromine can be accessed via an R Shiny application (http://www.fibromine.com/Fibromine) which offers dynamic data exploration and real-time integration functionalities. Moreover, we introduce a novel benchmarking system based on transcriptomic datasets underlying characteristics, resulting to dataset accreditation aiming to aid the user on dataset selection. Cell specificity of gene expression can be visualised and/or explored in several scRNA-seq datasets, in an effort to link legacy data with this cutting-edge methodology and paving the way to their integration. Several use case examples are presented, that, importantly, can be reproduced on-the-fly by a non-specialist user, the primary target and potential user of this endeavour.
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Affiliation(s)
- Dionysios Fanidis
- Institute for Bioinnovation, Biomedical Sciences Research Center ″Alexander Fleming″, 16672, Athens, Greece
| | - Panagiotis Moulos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center ″Alexander Fleming″, 16672, Athens, Greece.
| | - Vassilis Aidinis
- Institute for Bioinnovation, Biomedical Sciences Research Center ″Alexander Fleming″, 16672, Athens, Greece.
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21
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Identification of the Molecular Subgroups in Idiopathic Pulmonary Fibrosis by Gene Expression Profiles. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:7922594. [PMID: 34646338 PMCID: PMC8505108 DOI: 10.1155/2021/7922594] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 08/27/2021] [Indexed: 12/30/2022]
Abstract
Background Idiopathic Pulmonary Fibrosis (IPF) is one of the most common idiopathic interstitial pneumonia, which can occur all over the world. The median survival time of patients is about 3-5 years, and the mortality is relatively high. Objective To reveal the potential molecular characteristics of IPF and deepen the understanding of the molecular mechanism of IPF. In order to provide some guidance for the clinical treatment, new drug development, and prognosis judgment of IPF. Although the preliminary conclusion of this study has certain guiding significance for the treatment of IPF and so on, it needs more accurate analytical approaches and large sample clinical trials to verify. Methods 220 patients with IPF were divided into different subgroups according to the gene expression profiles, which were obtained from the Gene Expression Omnibus (GEO) database. In addition, these subgroups present different expression forms and clinical features. Therefore, weighted gene coexpression analysis (WGCNA) was used to seek the differences between subtypes. And six subgroup-specific WGCNA modules were identified. Results Combined with the characteristics of WGCNA and KEGG enrichment modules, the autophagic pathway was only upregulated in subgroup I and enriched significantly. The differentiation pathways of Th1 and Th2 cells were only upregulated and enriched in subgroup II. At the same time, combined with clinical information, IPF patients in subgroup II were older and more serious, which may be closely related to the differentiation of Th1 and Th2 cells. In contrast, the neuroactive ligand-receptor interaction pathway and Ca+ signaling pathway were significantly upregulated and enriched in subgroup III. Although there was no significant difference in prognosis between subgroup I and subgroup III, their intrinsic biological characteristics were very different. These results suggest that the subtypes may represent risk factors of age and intrinsic biological characteristics and may also partly reflect the severity of the disease. Conclusion In conclusion, current studies have improved our understanding of IPF-related molecular mechanisms. At the same time, because the results show that patients from different subgroups may have their own unique gene expression patterns, it reminds us that patients in each subgroup should receive more personalized treatment.
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22
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Irini F, Kia AN, Shannon D, Jannusch T, Murphy F, Sheehan B. Associations between mobility patterns and COVID-19 deaths during the pandemic: A network structure and rank propagation modelling approach. ARRAY 2021; 11:100075. [PMID: 35083428 PMCID: PMC8419690 DOI: 10.1016/j.array.2021.100075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/28/2021] [Accepted: 06/27/2021] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND From February 2020, both urban and rural Ireland witnessed the rapid proliferation of the COVID-19 disease throughout its counties. During this period, the national COVID-19 responses included stay-at-home directives issued by the state, subject to varying levels of enforcement. METHODS In this paper, we present a new method to assess and rank the causes of Ireland COVID-19 deaths as it relates to mobility activities within each county provided by Google while taking into consideration the epidemiological confirmed positive cases reported per county. We used a network structure and rank propagation modelling approach using Personalised PageRank to reveal the importance of each mobility category linked to cases and deaths. Then a novel feature-selection method using relative prominent factors finds important features related to each county's death. Finally, we clustered the counties based on features selected with the network results using a customised network clustering algorithm for the research problem. FINDINGS Our analysis reveals that the most important mobility trend categories that exhibit the strongest association to COVID-19 cases and deaths include retail and recreation and workplaces. This is the first time a network structure and rank propagation modelling approach has been used to link COVID-19 data to mobility patterns. The infection determinants landscape illustrated by the network results aligns soundly with county socio-economic and demographic features. The novel feature selection and clustering method presented clusters useful to policymakers, managers of the health sector, politicians and even sociologists. Finally, each county has a different impact on the national total.
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Affiliation(s)
- Furxhi Irini
- Transgero Limited, Newcastle West, Limerick, Ireland,Kemmy Business School, University of Limerick, Ireland
| | - Arash Negahdari Kia
- Kemmy Business School, University of Limerick, Ireland,Corresponding author
| | | | - Tim Jannusch
- Kemmy Business School, University of Limerick, Ireland,Institut for Insurance Studies, TH, Köln, Germany
| | - Finbarr Murphy
- Transgero Limited, Newcastle West, Limerick, Ireland,Kemmy Business School, University of Limerick, Ireland
| | - Barry Sheehan
- Kemmy Business School, University of Limerick, Ireland
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23
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Xu L, Liu F, Li H, Li M, Xie Y, Li Z, Guo Y. Comprehensive characterization of pathological stage-related genes of papillary thyroid cancer along with survival prediction. J Cell Mol Med 2021; 25:8390-8404. [PMID: 34342109 PMCID: PMC8419169 DOI: 10.1111/jcmm.16799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 06/08/2021] [Accepted: 07/09/2021] [Indexed: 02/05/2023] Open
Abstract
It is crucial to understand the differences across papillary thyroid cancer (PTC) stages, so as to provide a basis for individualized treatments. Here, comprehensive function characterization of PTC stage‐related genes was performed and a new prognostic signature was developed for advanced patients. Two gene modules were confirmed to be closely associated with PTC stages and further six hub genes were identified that yield excellent diagnostic efficiency between tumour and normal tissues. Genetic alteration analysis indicates that they are much conservative since mutations in the DNA of them rarely occur, but changes of DNA methylation on these six genes show that 12 DNA methylation sites are significantly associated with their corresponding genes' expression. Validation data set testing also suggests that these six stage‐related hub genes would be probably potential biomarkers for marking four stages. Subsequently, a 21‐mRNA‐based prognostic risk model was constructed for PTC stage III/IV patients and it could effectively predict the survival of patients with strong prognostic ability. Functional analysis shows that differential expression genes between high‐ and low‐risk patients would promote the progress of PTC to some extent. Moreover, tumour microenvironment (TME) of high‐risk patients may be more conducive to tumour growth by ESTIMATE analysis.
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Affiliation(s)
- Lei Xu
- College of Chemistry, Sichuan University, Chengdu, China
| | - Feng Liu
- Department of Thyroid Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Haiyan Li
- College of Chemistry, Sichuan University, Chengdu, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, China
| | - Yongmei Xie
- Department of Thyroid Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Zhihui Li
- Department of Thyroid Surgery, West China Hospital of Sichuan University, Chengdu, China.,Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital of Sichuan University, Chengdu, China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu, China
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Abstract
PURPOSE OF REVIEW Pulmonary fibrosis is a chronic and progressive lung disease involving unclear pathological mechanisms. The present review presents and discusses the major and recent advances in our knowledge of the pathogenesis of lung fibrosis. RECENT FINDINGS The past months have deepened our understanding on the cellular actors of fibrosis with a better characterization of the abnormal lung epithelial cells observed during lung fibrosis. Better insight has been gained into fibroblast biology and the role of immune cells during fibrosis. Mechanistically, senescence appears as a key driver of the fibrotic process. Extracellular vesicles have been discovered as participating in the impaired cellular cross-talk during fibrosis and deeper understanding has been made on developmental signaling in lung fibrosis. SUMMARY This review emphasizes the contribution of different cell types and mechanisms during pulmonary fibrosis, highlights new insights for identification of potential therapeutic strategies, and underlines where future research is needed to answer remaining open questions.
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25
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Zhang H, Song M, Guo J, Ma J, Qiu M, Yang Z. The function of non-coding RNAs in idiopathic pulmonary fibrosis. Open Med (Wars) 2021; 16:481-490. [PMID: 33817326 PMCID: PMC8005778 DOI: 10.1515/med-2021-0231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 01/20/2021] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
Non-coding ribonucleic acids (ncRNAs) are a diverse group of RNA molecules that are mostly not translated into proteins after transcription, including long non-coding RNAs (lncRNAs) with longer than 200 nucleotides non-coding transcripts and microRNAs (miRNAs) which are only 18–22 nucleotides. As families of evolutionarily conserved ncRNAs, lncRNAs activate and repress genes via a variety of mechanisms at both transcriptional and translational levels, whereas miRNAs regulate protein-coding gene expression mainly through mRNA silencing. ncRNAs are widely involved in biological functions, such as proliferation, differentiation, migration, angiogenesis, and apoptosis. Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with a poor prognosis. The etiology of IPF is still unclear. Increasing evidence shows the close correlations between the development of IPF and aberrant expressions of ncRNAs than thought previously. In this study, we provide an overview of ncRNAs participated in pathobiology of IPF, seeking the early diagnosis biomarker and aiming for potential therapeutic applications for IPF.
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Affiliation(s)
- Hui Zhang
- Department of Cardiovascular Diseases, First Affiliated Hospital of Baotou Medical College, Baotou, Inner Mongolia, China
| | - Miao Song
- Department of Cardiovascular Diseases, First Affiliated Hospital of Baotou Medical College, Baotou, Inner Mongolia, China.,Department of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia, China
| | - Jianing Guo
- Comfort Medical Center, Central hospital of Ulanqab, Ulanqab, Inner Mongolia, China
| | - Junbing Ma
- Department of Cardiovascular Diseases, First Affiliated Hospital of Baotou Medical College, Baotou, Inner Mongolia, China
| | - Min Qiu
- Department of Cardiovascular Diseases, First Affiliated Hospital of Baotou Medical College, Baotou, Inner Mongolia, China.,Department of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia, China
| | - Zheng Yang
- Department of Cardiovascular Diseases, First Affiliated Hospital of Baotou Medical College, Baotou, Inner Mongolia, China
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26
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Xia Y, Lei C, Yang D, Luo H. Construction and validation of a bronchoalveolar lavage cell-associated gene signature for prognosis prediction in idiopathic pulmonary fibrosis. Int Immunopharmacol 2021; 92:107369. [PMID: 33493738 DOI: 10.1016/j.intimp.2021.107369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/14/2020] [Accepted: 01/03/2021] [Indexed: 01/22/2023]
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive interstitial lung disease. It is urgent to identify biomarkers to precisely predict mortality. METHODS Gene expression data of bronchoalveolar lavage (BAL) cells and clinical information were downloaded from the Gene Expression Omnibus database. We identified key modules associated with prognosis using weighted gene co-expression network analysis (WGCNA). Then we screened genes with the least absolute shrinkage and selection operator Cox regression. Finally, we constructed a prognostic gene signature using multivariate Cox regression. The risk model was evaluated using the time-dependent receiver operating characteristic (ROC) curve and the concordance index. Additionally, the risk model was validated using an external independent dataset. RESULTS Two key modules, strongly associated with inflammation and immune response, were identified by WGCNA. Four genes, including TLR2, CCR2, HTRA1, and SFN, were screened to construct the prognostic model. The patients with a high-risk score had a significantly worse prognosis than patients with a low-risk score. Time-dependent ROC analysis showed that the risk model had a moderate predictive performance for overall survival in the training and external validation datasets. CONCLUSIONS Our study provides new insights into the prognostic value of BAL cells in IPF and it may be helpful to assist clinicians in making treatment decisions for the personalized management of IPF.
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Affiliation(s)
- Yuechong Xia
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Research Unit of Respiratory Disease, Central South University, Changsha, Hunan, China; Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, Hunan, China
| | - Cheng Lei
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Research Unit of Respiratory Disease, Central South University, Changsha, Hunan, China; Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, Hunan, China
| | - Danhui Yang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Research Unit of Respiratory Disease, Central South University, Changsha, Hunan, China; Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, Hunan, China
| | - Hong Luo
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Research Unit of Respiratory Disease, Central South University, Changsha, Hunan, China; Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, Hunan, China.
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Periera-Simon S, Xia X, Catanuto P, Coronado R, Kurtzberg J, Bellio M, Lee YS, Khan A, Smith R, Elliot SJ, Glassberg MK. Anti-fibrotic effects of different sources of MSC in bleomycin-induced lung fibrosis in C57BL6 male mice. Respirology 2021; 26:161-170. [PMID: 32851725 DOI: 10.1111/resp.13928] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 07/14/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND OBJECTIVE IPF is a fatal and debilitating lung disorder increasing in incidence worldwide. To date, two approved treatments only slow disease progression, have multiple side effects and do not provide a cure. MSC have promising therapeutic potential as a cell-based therapy for many lung disorders based on the anti-fibrotic properties of the MSC. METHODS Critical questions remain surrounding the optimal source, timing and efficacy of cell-based therapies. The present study examines the most effective sources of MSC. Human MSC were derived from adipose, WJ, chorionic membrane (CSC) and chorionic villi (CVC). MSC were injected into the ageing mouse model of BLM-induced lung fibrosis. RESULTS All sources decreased Aschroft and hydroxyproline levels when injected into BLM-treated mice at day 10 with the exception of CSC cells that did not change hydroxyproline levels. There were also decreases in mRNA expression of αv -integrin and TNFα in all sources except CSC. Only ASC- and WJ-derived cells reduced AKT and MMP-2 activation, while Cav-1 was increased by ASC treatment as previously reported. BLM-induced miR dysregulation of miR-29 and miR-199 was restored only by ASC treatment. CONCLUSION Our data suggest that sources of MSC may differ in the pathway(s) involved in repair.
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Affiliation(s)
- Simone Periera-Simon
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Xiaomei Xia
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Paola Catanuto
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Joanne Kurtzberg
- Marcus Center for Cellular Cures at Duke, Duke University School of Medicine, Durham, NC, USA
| | - Michael Bellio
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Yee-Shuan Lee
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Aisha Khan
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Robin Smith
- Department of Medicine, Rutgers University, New Brunswick, NJ, USA
| | - Sharon J Elliot
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Marilyn K Glassberg
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, The University of Arizona School of Medicine, Phoenix, AZ, USA
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28
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Zhu K, Xu A, Xia W, Li P, Han R, Wang E, Zhou S, Wang R. Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis. Int J Med Sci 2021; 18:3412-3424. [PMID: 34522168 PMCID: PMC8436110 DOI: 10.7150/ijms.61309] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/30/2021] [Indexed: 12/29/2022] Open
Abstract
Rationale: Idiopathic pulmonary fibrosis (IPF) is one of the most aggressive forms of idiopathic interstitial pneumonia. Some miRNAs may be associated with IPF and may affect the occurrence and development of IPF in various pathways. Many miRNAs and genes that may be involved in the development of IPF have been discovered using chip and high throughput technologies. Methods: We analyzed one miRNA and four mRNA databases. We identified hub genes and pathways related to IPF using GO, KEGG enrichment analysis, gene set variation analysis (GSVA), PPI network construction, and hub gene analysis. A comprehensive analysis of differentially expressed miRNAs (DEMs), predicted miRNA target genes, and differentially expressed genes (DEGs) led to the creation of a miRNA-mRNA regulatory network in IPF. Results: We found 203 DEGs and 165 DEMs that were associated with IPF. The findings of enrichment analyses showed that these DEGs were mainly involved in antimicrobial humoral response, antimicrobial humoral immune response mediated by antimicrobial peptide, extracellular matrix organization, cell killing, and organ or tissue specific immune response. The VEGFA, CDH5, and WNT3A genes overlapped between hub genes and the miRNA-mRNA regulatory network. The miRNAs including miR-199b-5p, miR-140-5p, miR-199a-5p, miR-125A-5p, and miR-107 that we predicted would regulate the VEGFA, CDH5, and WNT3A genes, which were also associated with IPF or other fibrosis-related diseases. GSVA indicated that metabolic processes of UTP and IMP, immune response, regulation of Th2 cell cytokine production, and positive regulation of NK cell-mediated immunity are associated with the pathogenesis and treatment of IPF. These pathways also interact with VEGFA, CDH5, and WNT3A. Conclusion: These findings provide a new research direction for the diagnosis and treatment of IPF.
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Affiliation(s)
- Ke Zhu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Aiqun Xu
- Department of General Medicine, Hefei Second People's Hospital, Hefei 230001, China
| | - Wanli Xia
- Department of Thoracic Surgery, the first affiliated hospital of Anhui medical university, Hefei 230022, China
| | - Pulin Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Rui Han
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Enze Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Sijing Zhou
- Hefei Third Clinical College of Anhui Medical University, Hefei 230022, China.,Hefei Prevention and Treatment Center for Occupational Diseases, Hefei 230022, China
| | - Ran Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
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29
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Veith C, Hristova M, Danyal K, Habibovic A, Dustin CM, McDonough JE, Vanaudenaerde BM, Kreuter M, Schneider MA, Kahn N, van Schooten FJ, Boots AW, van der Vliet A. Profibrotic epithelial TGF-β1 signaling involves NOX4-mitochondria cross talk and redox-mediated activation of the tyrosine kinase FYN. Am J Physiol Lung Cell Mol Physiol 2020; 320:L356-L367. [PMID: 33325804 DOI: 10.1152/ajplung.00444.2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is characterized by a disturbed redox balance and increased production of reactive oxygen species (ROS), which is believed to contribute to epithelial injury and fibrotic lung scarring. The main pulmonary sources of ROS include mitochondria and NADPH oxidases (NOXs), of which the NOX4 isoform has been implicated in IPF. Non-receptor SRC tyrosine kinases (SFK) are important for cellular homeostasis and are often dysregulated in lung diseases. SFK activation by the profibrotic transforming growth factor-β (TGF-β) is thought to contribute to pulmonary fibrosis, but the relevant SFK isoform and its relationship to NOX4 and/or mitochondrial ROS in the context of profibrotic TGF-β signaling is not known. Here, we demonstrate that TGF-β1 can rapidly activate the SRC kinase FYN in human bronchial epithelial cells, which subsequently induces mitochondrial ROS (mtROS) production, genetic damage shown by the DNA damage marker γH2AX, and increased expression of profibrotic genes. Moreover, TGF-β1-induced activation of FYN involves initial activation of NOX4 and direct cysteine oxidation of FYN, and both FYN and mtROS contribute to TGF-β-induced induction of NOX4. NOX4 expression in lung tissues of IPF patients is positively correlated with disease severity, although FYN expression is down-regulated in IPF and does not correlate with disease severity. Collectively, our findings highlight a critical role for FYN in TGF-β1-induced mtROS production, DNA damage response, and induction of profibrotic genes in bronchial epithelial cells, and suggest that altered expression and activation of NOX4 and FYN may contribute to the pathogenesis of pulmonary fibrosis.
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Affiliation(s)
- Carmen Veith
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont.,Department of Pharmacology and Toxicology, NUTRIM School of Nutrition, Translational Research and Metabolism, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Milena Hristova
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Karamatullah Danyal
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Aida Habibovic
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Christopher M Dustin
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - John E McDonough
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven, Belgium
| | - Bart M Vanaudenaerde
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven, Belgium
| | - Michael Kreuter
- Center for Interstitial and Rare Lung Diseases, Pneumology, Thoraxklinik, Heidelberg University Hospital, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Marc A Schneider
- Translational Research Unit, Thoraxklinik, Heidelberg University Hospital, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Nicolas Kahn
- Center for Interstitial and Rare Lung Diseases, Pneumology, Thoraxklinik, Heidelberg University Hospital, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Frederik J van Schooten
- Department of Pharmacology and Toxicology, NUTRIM School of Nutrition, Translational Research and Metabolism, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Agnes W Boots
- Department of Pharmacology and Toxicology, NUTRIM School of Nutrition, Translational Research and Metabolism, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Albert van der Vliet
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
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30
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Jolliffe DA, Stefanidis C, Wang Z, Kermani NZ, Dimitrov V, White JH, McDonough JE, Janssens W, Pfeffer P, Griffiths CJ, Bush A, Guo Y, Christenson S, Adcock IM, Chung KF, Thummel KE, Martineau AR. Vitamin D Metabolism Is Dysregulated in Asthma and Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2020; 202:371-382. [PMID: 32186892 DOI: 10.1164/rccm.201909-1867oc] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Rationale: Vitamin D deficiency is common in patients with asthma and chronic obstructive pulmonary disease (COPD). Low 25-hydroxyvitamin D (25[OH]D) levels may represent a cause or a consequence of these conditions.Objectives: To determine whether vitamin D metabolism is altered in asthma or COPD.Methods: We conducted a longitudinal study in 186 adults to determine whether the 25(OH)D response to six oral doses of 3 mg vitamin D3, administered over 1 year, differed between those with asthma or COPD versus control subjects. Serum concentrations of vitamin D3, 25(OH)D3, and 1α,25-dihydroxyvitamin D3 (1α,25[OH]2D3) were determined presupplementation and postsupplementation in 93 adults with asthma, COPD, or neither condition, and metabolite-to-parent compound molar ratios were compared between groups to estimate hydroxylase activity. Additionally, we analyzed 14 datasets to compare expression of 1α,25(OH)2D3-inducible gene expression signatures in clinical samples taken from adults with asthma or COPD versus control subjects.Measurements and Main Results: The mean postsupplementation 25(OH)D increase in participants with asthma (20.9 nmol/L) and COPD (21.5 nmol/L) was lower than in control subjects (39.8 nmol/L; P = 0.001). Compared with control subjects, patients with asthma and COPD had lower molar ratios of 25(OH)D3-to-vitamin D3 and higher molar ratios of 1α,25(OH)2D3-to-25(OH)D3 both presupplementation and postsupplementation (P ≤ 0.005). Intergroup differences in 1α,25(OH)2D3-inducible gene expression signatures were modest and variable if statistically significant.Conclusions: Attenuation of the 25(OH)D response to vitamin D supplementation in asthma and COPD associated with reduced molar ratios of 25(OH)D3-to-vitamin D3 and increased molar ratios of 1α,25(OH)2D3-to-25(OH)D3 in serum, suggesting that vitamin D metabolism is dysregulated in these conditions.
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Affiliation(s)
- David A Jolliffe
- Asthma UK Centre for Applied Research, Institute of Population Health Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Christos Stefanidis
- Asthma UK Centre for Applied Research, Institute of Population Health Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Zhican Wang
- Department of Pharmaceutics, University of Washington, Seattle, Washington
| | | | - Vassil Dimitrov
- Department of Physiology, McGill University, Montreal, Quebec, Canada
| | - John H White
- Department of Physiology, McGill University, Montreal, Quebec, Canada
| | | | - Wim Janssens
- Laboratory of Respiratory Diseases and Thoracic Surgery, Department of Chronic Diseases, Metabolism and Ageing, Katholieke Universiteit Leuven, Leuven, Belgium; and
| | - Paul Pfeffer
- Asthma UK Centre for Applied Research, Institute of Population Health Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Christopher J Griffiths
- Asthma UK Centre for Applied Research, Institute of Population Health Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Andrew Bush
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Yike Guo
- Data Science Institute, William Penney Laboratory and
| | - Stephanie Christenson
- Division of Pulmonary, Critical Care, Allergy, & Sleep Medicine, Department of Medicine, University of California, San Francisco, California
| | - Ian M Adcock
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Kian Fan Chung
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Kenneth E Thummel
- Department of Pharmaceutics, University of Washington, Seattle, Washington
| | - Adrian R Martineau
- Asthma UK Centre for Applied Research, Institute of Population Health Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
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Pathology of Idiopathic Pulmonary Fibrosis Assessed by a Combination of Microcomputed Tomography, Histology, and Immunohistochemistry. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:2427-2435. [PMID: 32919981 DOI: 10.1016/j.ajpath.2020.09.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/16/2020] [Accepted: 09/01/2020] [Indexed: 01/08/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fibrotic disease with the histology of usual interstitial pneumonia (UIP). Although the pathologist's visual inspection is central in histologic assessments, three-dimensional microcomputed tomography (microCT) assessment may complement the pathologist's scoring. We examined associations between the histopathologic features of UIP and IPF in explanted lungs and quantitative microCT measurements, including alveolar surface density, total lung volume taken up by tissue (%), and terminal bronchiolar number. Sixty frozen samples from 10 air-inflated explanted lungs with severe IPF and 36 samples from 6 donor control lungs were scanned with microCT and processed for histologic analysis. An experienced pathologist scored three major UIP criteria (patchy fibrosis, honeycomb, and fibroblastic foci), five additional pathologic changes, and immunohistochemical staining for CD68-, CD4-, CD8-, and CD79a-positive cells, graded on a 0 to 3+ scale. The alveolar surface density and terminal bronchiolar number decreased and the tissue percentage increased in lungs with IPF compared with controls. In lungs with IPF, lower alveolar surface density and higher tissue percentage were correlated with greater scores of patchy fibrosis, fibroblastic foci, honeycomb, CD79a-positive cells, and lymphoid follicles. A decreased number of terminal bronchioles was correlated with honeycomb score but not with the other scores. The three-dimensional microCT measurements reflect the pathological UIP and IPF criteria and suggest that the reduction in the terminal bronchioles may be associated with honeycomb cyst formation.
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Xia Y, Lei C, Yang D, Luo H. Identification of key modules and hub genes associated with lung function in idiopathic pulmonary fibrosis. PeerJ 2020; 8:e9848. [PMID: 33194355 PMCID: PMC7485506 DOI: 10.7717/peerj.9848] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive interstitial lung disease, characterized by a decline in lung function. To date, the pathophysiologic mechanisms associated with lung dysfunction remain unclear, and no effective therapy has been identified to improve lung function. Methods In the present study, we used weighted gene co-expression network analysis (WGCNA) to identify key modules and hub genes associated with lung function in IPF. Three datasets, containing clinical information, were downloaded from Gene Expression Omnibus. WGCNA was performed on the GSE32537 dataset. Differentially expressed gene s (DEGs) between IPF patients and healthy controls were also identified to filter hub genes. The relationship between hub genes and lung function was then validated using the GSE47460 and GSE24206 datasets. Results The red module, containing 267 genes, was positively correlated with the St. George’s Respiratory Questionnaire score (r = 0.37, p < 0.001) and negatively correlated with the percent predicted forced vital capacity (FVC% predicted) (r = − 0.46, p < 0.001) and the percent predicted diffusion capacity of the lung for carbon monoxide (Dlco% predicted) (r = − 0.42, p < 0.001). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis suggested that the genes in the red module were primarily involved in inflammation and immune pathways. Based on Module Membership and Gene Significance, 32 candidate hub genes were selected in the red module to construct a protein-protein interaction network . Based on the identified DEGs and the degree of connectivity in the network, we identified three hub genes, including interleukin 6 (IL6), suppressor of cytokine signaling-3 (SOCS3), and serpin family E member 1 (SERPINE1). In the GSE47460 dataset, Spearman correlation coefficients between Dlco% predicted and expression levels of IL6, SERPINE1, SOCS3 were –0.32, –0.41, and –0.46, respectively. Spearman correlation coefficients between FVC% predicted and expression levels of IL6, SERPINE1, SOCS3 were –0.29, –0.33, and –0.27, respectively. In the GSE24206 dataset, all three hub genes were upregulated in patients with advanced IPF. Conclusion We identified three hub genes that negatively correlated with the lung function of IPF patients. Our results provide insights into the pathogenesis underlying the progressive disruption of lung function, and the identified hub genes may serve as biomarkers and potential therapeutictargets for the treatment of IPF patients.
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Affiliation(s)
- Yuechong Xia
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Research Unit of Respiratory Disease, Central South University, Changsha, Hunan, China.,Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, Hunan, China
| | - Cheng Lei
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Research Unit of Respiratory Disease, Central South University, Changsha, Hunan, China.,Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, Hunan, China
| | - Danhui Yang
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Research Unit of Respiratory Disease, Central South University, Changsha, Hunan, China.,Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, Hunan, China
| | - Hong Luo
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Research Unit of Respiratory Disease, Central South University, Changsha, Hunan, China.,Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, Hunan, China
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Longitudinal blood transcriptomic analysis to identify molecular regulatory patterns of bovine respiratory disease in beef cattle. Genomics 2020; 112:3968-3977. [PMID: 32650099 DOI: 10.1016/j.ygeno.2020.07.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/19/2020] [Accepted: 07/04/2020] [Indexed: 12/16/2022]
Abstract
Bovine respiratory disease (BRD) is the most common disease in beef cattle and leads to considerable economic losses in both beef and dairy cattle. It is important to uncover the molecular mechanisms underlying BRD and to identify biomarkers for early identification of BRD cattle in order to address its impact on production and welfare. In this study, a longitudinal transcriptomic analysis was conducted using blood samples collected from 24 beef cattle at three production stages in the feedlot: 1) arrival (Entry group); 2) when identified as sick (diagnosed as BRD) and separated for treatment (Pulled); 3) prior to marketing (Close-out, representing healthy animals). Expressed genes were significantly different in the same animal among Entry, Pulled and Close-out stages (false discovery rate (FDR) < 0.01 & |Fold Change| > 2). Beef steers at both Entry and Pulled stages presented obvious difference in GO terms (FDR < 0.05) and affected biological functions (FDR < 0.05 & |Z-score| > 2) when compared with animals at Close-out. However, no significant functional difference was observed between Entry and Pulled animals. The interferon signaling pathway showed the most significant difference between animals at Entry/Pulled and Close-out stages (P < .001 & |Z-score| > 2), suggesting the animals initiated antiviral responses at an early stage of infection. Six key genes including IFI6, IFIT3, ISG15, MX1, and OAS2 were identified as biomarkers to predict and recognize sick cattle at Entry. A gene module with 169 co-expressed genes obtained from WGCNA analysis was most positively correlated (R = 0.59, P = 6E-08) with sickness, which was regulated by 11 transcription factors. Our findings provide an initial understanding of the BRD infection process in the field and suggests a subset of novel marker genes for identifying BRD in cattle at an early stage of infection.
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Li X, Kim SE, Chen TY, Wang J, Yang X, Tabib T, Tan J, Guo B, Fung S, Zhao J, Sembrat J, Rojas M, Shiva S, Lafyatis R, St Croix C, Alder JK, Di YP, Kass DJ, Zhang Y. Toll interacting protein protects bronchial epithelial cells from bleomycin-induced apoptosis. FASEB J 2020; 34:9884-9898. [PMID: 32596871 DOI: 10.1096/fj.201902636rr] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 04/10/2020] [Accepted: 04/20/2020] [Indexed: 12/16/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is characterized by altered epithelial cell phenotypes, which are associated with myofibroblast accumulation in the lung. Atypical alveolar epithelial cells in IPF express molecular markers of airway epithelium. Polymorphisms within and around Toll interacting protein (TOLLIP) are associated with the susceptibility to IPF and mortality. However, the functional role of TOLLIP in IPF is unknown. Using lung tissues from IPF and control subjects, we showed that expression of TOLLIP gene in the lung parenchyma is globally lower in IPF compared to controls. Lung cells expressing significant levels of TOLLIP include macrophages, alveolar type II, and basal cells. TOLLIP protein expression is lower in the parenchyma of IPF lungs but is expressed in the atypical epithelial cells of the distal fibrotic regions. Using overexpression and silencing approaches, we demonstrate that TOLLIP protects cells from bleomycin-induced apoptosis using primary bronchial epithelial cells and BEAS-2B cells. The protective effects are mediated by reducing mitochondrial reactive oxygen species (ROS) levels and upregulating autophagy. Therefore, global downregulation of the TOLLIP gene in IPF lungs may predispose injured lung epithelial cells to apoptosis and to the development of IPF.
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Affiliation(s)
- Xiaoyun Li
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sharon E Kim
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ting-Yun Chen
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA.,Institute of Allied Health Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Juan Wang
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pulmonary Medicine, Tianjin Medical University, Tianjin, China
| | - Xia Yang
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pulmonary Medicine, Tianjin Medical University, Tianjin, China
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jiangning Tan
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brandon Guo
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sonia Fung
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jing Zhao
- Department of Physiology and Cell Biology, Ohio State University, Columbus, OH, USA
| | - John Sembrat
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mauricio Rojas
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sruti Shiva
- Vascular Medicine Institute and Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Claudette St Croix
- Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jonathan K Alder
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
| | - Y Peter Di
- Department of Environmental and Occupational Health, University of Pittsburgh, PA, USA
| | - Daniel J Kass
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine and the Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
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Chen Y, Jiang B, Wang W, Su D, Xia F, Li X. Identifying the Transcriptional Regulatory Network Associated With Extrathyroidal Extension in Papillary Thyroid Carcinoma by Comprehensive Bioinformatics Analysis. Front Genet 2020; 11:453. [PMID: 32477405 PMCID: PMC7232969 DOI: 10.3389/fgene.2020.00453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 04/14/2020] [Indexed: 12/31/2022] Open
Abstract
Extrathyroidal extension (ETE) affects papillary thyroid cancer (PTC) prognosis. The objective of this study was to identify biomarkers for ETE and explore the mechanisms controlling its development in PTC. We performed a comprehensive bioinformatics analysis using several datasets. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) on 58 paired PTC samples from The Cancer Genome Atlas (TCGA) were used to detect ETE-related mRNA and long noncoding (lnc) RNA modules and construct an lncRNA/mRNA network. An independent TCGA dataset containing 438 samples was utilized to validate and characterize the WGCNA results. Functional annotation was used to identify the biological functions and related pathways of ETE modules. Two independent RNA sequencing datasets were combined to crossvalidate relationships between lncRNAs and mRNAs by Pearson correlation analysis. Transcription factors (TFs) for affected genes were predicted using the binding motif data from Ensembl Biomart to construct a TF/lncRNA/mRNA network. Other two independent datasets were used to crossvalidate TF-mRNA associations. Finally, receiver operating characteristic, survival analyses, and Cox proportional hazard regression model were performed to explore the significance of hub genes in ETE diagnosis and PTC prognosis. Three mRNA modules and two lncRNA modules were significantly associated with ETE. Enrichment analysis showed extracellular matrix changes was closely related to the development of ETE. A TF/lncRNA/mRNA regulatory network was constructed containing 33 validated hub genes, 64 lncRNAs, and 64 TFs, all differentially expressed between ETE and non-ETE samples. Unc-5 family C-terminal like [area under the curve (AUC): 0.711], sushi repeat containing protein X-linked 2 (AUC: 0.706), lysyl oxidase (AUC: 0.704), collagen type I alpha 1 chain (AUC: 0.704), and collagen type X alpha 1 chain (AUC: 0.704) were the most highly significant hub genes for ETE diagnosis. The Cox proportional hazard regression model constructed with hub genes showed significant survival differences between low- and high-risk groups (p = 0.00025) and performed good prediction for PTC prognosis(AUC = 0.794; C-index = 0.895). The identification of 33 biomarkers and TF/lncRNA/mRNA regulatory network would provide new insights into the molecular mechanisms of ETE besides the prognosis model may have important clinical implications in the improvement of PTC risk stratification, therapeutic decision-making, and prognosis prediction.
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Affiliation(s)
- Yong Chen
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Bo Jiang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Wenlong Wang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Duntao Su
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Fada Xia
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Xinying Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
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Schruf E, Schroeder V, Le HQ, Schönberger T, Raedel D, Stewart EL, Fundel-Clemens K, Bluhmki T, Weigle S, Schuler M, Thomas MJ, Heilker R, Webster MJ, Dass M, Frick M, Stierstorfer B, Quast K, Garnett JP. Recapitulating idiopathic pulmonary fibrosis related alveolar epithelial dysfunction in a human iPSC-derived air-liquid interface model. FASEB J 2020; 34:7825-7846. [PMID: 32297676 DOI: 10.1096/fj.201902926r] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/29/2020] [Accepted: 03/26/2020] [Indexed: 02/06/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal disease of unknown cause that is characterized by progressive fibrotic lung remodeling. An abnormal emergence of airway epithelial-like cells within the alveolar compartments of the lung, herein termed bronchiolization, is often observed in IPF. However, the origin of this dysfunctional distal lung epithelium remains unknown due to a lack of suitable human model systems. In this study, we established a human induced pluripotent stem cell (iPSC)-derived air-liquid interface (ALI) model of alveolar epithelial type II (ATII)-like cell differentiation that allows us to investigate alveolar epithelial progenitor cell differentiation in vitro. We treated this system with an IPF-relevant cocktail (IPF-RC) to mimic the pro-fibrotic cytokine milieu present in IPF lungs. Stimulation with IPF-RC during differentiation increases secretion of IPF biomarkers and RNA sequencing (RNA-seq) of these cultures reveals significant overlap with human IPF patient data. IPF-RC treatment further impairs ATII differentiation by driving a shift toward an airway epithelial-like expression signature, providing evidence that a pro-fibrotic cytokine environment can influence the proximo-distal differentiation pattern of human lung epithelial cells. In conclusion, we show for the first time, the establishment of a human model system that recapitulates aspects of IPF-associated bronchiolization of the lung epithelium in vitro.
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Affiliation(s)
- Eva Schruf
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Victoria Schroeder
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Huy Q Le
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Tanja Schönberger
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Dagmar Raedel
- Nonclinical Drug Safety, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Emily L Stewart
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Katrin Fundel-Clemens
- Global Computational Biology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Teresa Bluhmki
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Sabine Weigle
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Michael Schuler
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Matthew J Thomas
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Ralf Heilker
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Megan J Webster
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Martin Dass
- Nonclinical Drug Safety, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Manfred Frick
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Birgit Stierstorfer
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Karsten Quast
- Global Computational Biology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - James P Garnett
- Immunology & Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany.,Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
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37
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Regulation of the Extracellular Matrix by Ciliary Machinery. Cells 2020; 9:cells9020278. [PMID: 31979260 PMCID: PMC7072529 DOI: 10.3390/cells9020278] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/13/2020] [Accepted: 01/19/2020] [Indexed: 12/14/2022] Open
Abstract
The primary cilium is an organelle involved in cellular signalling. Mutations affecting proteins involved in cilia assembly or function result in diseases known as ciliopathies, which cause a wide variety of phenotypes across multiple tissues. These mutations disrupt various cellular processes, including regulation of the extracellular matrix. The matrix is important for maintaining tissue homeostasis through influencing cell behaviour and providing structural support; therefore, the matrix changes observed in ciliopathies have been implicated in the pathogenesis of these diseases. Whilst many studies have associated the cilium with processes that regulate the matrix, exactly how these matrix changes arise is not well characterised. This review aims to bring together the direct and indirect evidence for ciliary regulation of matrix, in order to summarise the possible mechanisms by which the ciliary machinery could regulate the composition, secretion, remodelling and organisation of the matrix.
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Laporte M, Stevaert A, Raeymaekers V, Boogaerts T, Nehlmeier I, Chiu W, Benkheil M, Vanaudenaerde B, Pöhlmann S, Naesens L. Hemagglutinin Cleavability, Acid Stability, and Temperature Dependence Optimize Influenza B Virus for Replication in Human Airways. J Virol 2019; 94:e01430-19. [PMID: 31597759 PMCID: PMC6912116 DOI: 10.1128/jvi.01430-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 09/28/2019] [Indexed: 12/15/2022] Open
Abstract
Influenza A virus (IAV) and influenza B virus (IBV) cause yearly epidemics with significant morbidity and mortality. When zoonotic IAVs enter the human population, the viral hemagglutinin (HA) requires adaptation to achieve sustained virus transmission. In contrast, IBV has been circulating in humans, its only host, for a long period of time. Whether this entailed adaptation of IBV HA to the human airways is unknown. To address this question, we compared two seasonal IAVs (A/H1N1 and A/H3N2) and two IBVs (B/Victoria and B/Yamagata lineages) with regard to host-dependent activity of HA as the mediator of membrane fusion during viral entry. We first investigated proteolytic activation of HA by covering all type II transmembrane serine protease (TTSP) and kallikrein enzymes, many of which proved to be present in human respiratory epithelium. The IBV HA0 precursor is cleaved by a broader panel of TTSPs and activated with much higher efficiency than IAV HA0. Accordingly, knockdown of a single protease, TMPRSS2, abrogated spread of IAV but not IBV in human respiratory epithelial cells. Second, the HA fusion pH values proved similar for IBV and human-adapted IAVs (with one exception being the HA of 1918 IAV). Third, IBV HA exhibited higher expression at 33°C, a temperature required for membrane fusion by B/Victoria HA. This indicates pronounced adaptation of IBV HA to the mildly acidic pH and cooler temperature of human upper airways. These distinct and intrinsic features of IBV HA are compatible with extensive host adaptation during prolonged circulation of this respiratory virus in the human population.IMPORTANCE Influenza epidemics are caused by influenza A and influenza B viruses (IAV and IBV, respectively). IBV causes substantial disease; however, it is far less studied than IAV. While IAV originates from animal reservoirs, IBV circulates in humans only. Virus spread requires that the viral hemagglutinin (HA) is active and sufficiently stable in human airways. We resolve here how these mechanisms differ between IBV and IAV. Whereas human IAVs rely on one particular protease for HA activation, this is not the case for IBV. Superior activation of IBV by several proteases should enhance shedding of infectious particles. IBV HA exhibits acid stability and a preference for 33°C, indicating pronounced adaptation to the human upper airways, where the pH is mildly acidic and a cooler temperature exists. These adaptive features are rationalized by the long existence of IBV in humans and may have broader relevance for understanding the biology and evolution of respiratory viruses.
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MESH Headings
- Cell Line
- Epithelial Cells/pathology
- Epithelial Cells/virology
- Gene Expression Regulation
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/metabolism
- Host-Pathogen Interactions/genetics
- Humans
- Hydrogen-Ion Concentration
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/metabolism
- Influenza A Virus, H1N1 Subtype/pathogenicity
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/metabolism
- Influenza A Virus, H3N2 Subtype/pathogenicity
- Influenza B virus/genetics
- Influenza B virus/metabolism
- Influenza B virus/pathogenicity
- Influenza, Human/pathology
- Influenza, Human/virology
- Kallikreins/classification
- Kallikreins/genetics
- Kallikreins/metabolism
- Lung/pathology
- Lung/virology
- Membrane Fusion
- Membrane Proteins/classification
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Proteolysis
- Respiratory Mucosa/pathology
- Respiratory Mucosa/virology
- Serine Endopeptidases/deficiency
- Serine Endopeptidases/genetics
- Serine Proteases/classification
- Serine Proteases/genetics
- Serine Proteases/metabolism
- Species Specificity
- Temperature
- Virus Internalization
- Virus Replication/genetics
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Affiliation(s)
- Manon Laporte
- Katholieke Universiteit Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Annelies Stevaert
- Katholieke Universiteit Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Valerie Raeymaekers
- Katholieke Universiteit Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Talitha Boogaerts
- Katholieke Universiteit Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, Göttingen, Germany
| | - Winston Chiu
- Katholieke Universiteit Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Mohammed Benkheil
- Katholieke Universiteit Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Bart Vanaudenaerde
- Katholieke Universiteit Leuven, Department of Chronic Diseases, Metabolism and Ageing, Laboratory of Pneumology, University Hospital Leuven, Leuven, Belgium
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, University Göttingen, Göttingen, Germany
| | - Lieve Naesens
- Katholieke Universiteit Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
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McDonough JE, Ahangari F, Li Q, Jain S, Verleden SE, Herazo-Maya J, Vukmirovic M, DeIuliis G, Tzouvelekis A, Tanabe N, Chu F, Yan X, Verschakelen J, Homer RJ, Manatakis DV, Zhang J, Ding J, Maes K, De Sadeleer L, Vos R, Neyrinck A, Benos PV, Bar-Joseph Z, Tantin D, Hogg JC, Vanaudenaerde BM, Wuyts WA, Kaminski N. Transcriptional regulatory model of fibrosis progression in the human lung. JCI Insight 2019; 4:131597. [PMID: 31600171 PMCID: PMC6948862 DOI: 10.1172/jci.insight.131597] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/04/2019] [Indexed: 11/17/2022] Open
Abstract
To develop a systems biology model of fibrosis progression within the human lung we performed RNA sequencing and microRNA analysis on 95 samples obtained from 10 idiopathic pulmonary fibrosis (IPF) and 6 control lungs. Extent of fibrosis in each sample was assessed by microCT-measured alveolar surface density (ASD) and confirmed by histology. Regulatory gene expression networks were identified using linear mixed-effect models and dynamic regulatory events miner (DREM). Differential gene expression analysis identified a core set of genes increased or decreased before fibrosis was histologically evident that continued to change with advanced fibrosis. DREM generated a systems biology model (www.sb.cs.cmu.edu/IPFReg) that identified progressively divergent gene expression tracks with microRNAs and transcription factors that specifically regulate mild or advanced fibrosis. We confirmed model predictions by demonstrating that expression of POU2AF1, previously unassociated with lung fibrosis but proposed by the model as regulator, is increased in B lymphocytes in IPF lungs and that POU2AF1-knockout mice were protected from bleomycin-induced lung fibrosis. Our results reveal distinct regulation of gene expression changes in IPF tissue that remained structurally normal compared with moderate or advanced fibrosis and suggest distinct regulatory mechanisms for each stage.
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Affiliation(s)
- John E. McDonough
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Farida Ahangari
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Qin Li
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Siddhartha Jain
- Carnegie Mellon University of Computer Science, Pittsburgh, Pennsylvania, USA
| | - Stijn E. Verleden
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Jose Herazo-Maya
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Milica Vukmirovic
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Giuseppe DeIuliis
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Argyrios Tzouvelekis
- Division of Immunology, Biomedical Sciences Research Center “Alexander Fleming”, Athens, Greece
| | - Naoya Tanabe
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
| | - Fanny Chu
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
| | - Xiting Yan
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Johny Verschakelen
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Robert J. Homer
- Department of Pathology, Yale University School of Medicine, New Haven,Connecticut, USA
- Pathology and Laboratory Medicine Service, VA CT HealthCare System, West Haven, Connecticut, USA
| | - Dimitris V. Manatakis
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Junke Zhang
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jun Ding
- Carnegie Mellon University of Computer Science, Pittsburgh, Pennsylvania, USA
| | - Karen Maes
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Laurens De Sadeleer
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Robin Vos
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Arne Neyrinck
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ziv Bar-Joseph
- Carnegie Mellon University of Computer Science, Pittsburgh, Pennsylvania, USA
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - James C. Hogg
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
| | | | - Wim A. Wuyts
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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40
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Sellarés J, Molina-Molina M. Serum Biomarkers in Diffuse Interstitial Lung Diseases. Arch Bronconeumol 2019; 56:349-350. [PMID: 31699442 DOI: 10.1016/j.arbres.2019.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 08/04/2019] [Indexed: 10/25/2022]
Affiliation(s)
- Jacobo Sellarés
- Servicio de Neumología, Instituto del Tórax, Hospital Clínico, IDIBAPS, Universidad de Barcelona, Barcelona, España; Centro de Investigación Biomédica en Red-Enfermedades Respiratorias (CIBERES); Barcelona Respiratory Network
| | - María Molina-Molina
- Centro de Investigación Biomédica en Red-Enfermedades Respiratorias (CIBERES); Barcelona Respiratory Network; Unidad Funcional de Intersticio Pulmonar (UFIP), Servicio de Neumología, Hospital Universitario de Bellvitge, IDIBELL, L'Hospitalet de Llobregat, Barcelona, España.
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41
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Song SY, Meng XW, Xia Z, Liu H, Zhang J, Chen QC, Liu HY, Ji FH, Peng K. Cognitive impairment and transcriptomic profile in hippocampus of young mice after multiple neonatal exposures to sevoflurane. Aging (Albany NY) 2019; 11:8386-8417. [PMID: 31582589 PMCID: PMC6814607 DOI: 10.18632/aging.102326] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 09/22/2019] [Indexed: 02/06/2023]
Abstract
Children with repeated inhalational anesthesia may develop cognitive disorders. This study aimed to investigate the transcriptome-wide response of hippocampus in young mice that had been exposed to multiple sevoflurane in the neonatal period. Mice received 3% sevoflurane for 2 h on postnatal day (PND) 6, 8, and 10, followed by arterial blood gas test on PND 10, behavioral experiments on PND 31–36, and RNA sequencing (RNA-seq) of hippocampus on PND 37. Functional annotation and protein-protein interaction analyses of differentially expressed genes (DEGs) and quantitative reverse transcription polymerase chain reaction (qPCR) were performed. Neonatal sevoflurane exposures induced cognitive and social behavior disorders in young mice. RNA-seq identified a total of 314 DEGs. Several enriched biological processes (ion channels, brain development, learning, and memory) and signaling pathways (oxytocin signaling pathway and glutamatergic, cholinergic, and GABAergic synapses) were highlighted. As hub-proteins, Pten was involved in nervous system development, synapse assembly, learning, memory, and behaviors, Nos3 and Pik3cd in oxytocin signaling pathway, and Cdk16 in exocytosis and phosphorylation. Some top DEGs were validated by qPCR. This study revealed a transcriptome-wide profile in mice hippocampus after multiple neonatal exposures to sevoflurane, promoting better understanding of underlying mechanisms and investigation of preventive strategies.
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Affiliation(s)
- Shao-Yong Song
- Department of Anesthesiology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xiao-Wen Meng
- Department of Anesthesiology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - ZhengYuan Xia
- Department of Anesthesiology, University of Hong Kong, Hong Kong, China.,Department of Anesthesiology and Pain Medicine, University of California Davis Health System, Sacramento, CA 95817, USA
| | - Hong Liu
- Department of Anesthesiology and Pain Medicine, University of California Davis Health System, Sacramento, CA 95817, USA
| | - Juan Zhang
- Department of Anesthesiology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Qing-Cai Chen
- Department of Anesthesiology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Hua-Yue Liu
- Department of Anesthesiology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Fu-Hai Ji
- Department of Anesthesiology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Ke Peng
- Department of Anesthesiology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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