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Bandyopadhyay G, Jehrio MG, Baker C, Bhattacharya S, Misra RS, Huyck HL, Chu C, Myers JR, Ashton J, Polter S, Cochran M, Bushnell T, Dutra J, Katzman PJ, Deutsch GH, Mariani TJ, Pryhuber GS. Bulk RNA sequencing of human pediatric lung cell populations reveals unique transcriptomic signature associated with postnatal pulmonary development. Am J Physiol Lung Cell Mol Physiol 2024; 326:L604-L617. [PMID: 38442187 DOI: 10.1152/ajplung.00385.2023] [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: 12/07/2023] [Revised: 02/19/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024] Open
Abstract
Postnatal lung development results in an increasingly functional organ prepared for gas exchange and pathogenic challenges. It is achieved through cellular differentiation and migration. Changes in the tissue architecture during this development process are well-documented and increasing cellular diversity associated with it are reported in recent years. Despite recent progress, transcriptomic and molecular pathways associated with human postnatal lung development are yet to be fully understood. In this study, we investigated gene expression patterns associated with healthy pediatric lung development in four major enriched cell populations (epithelial, endothelial, and nonendothelial mesenchymal cells, along with lung leukocytes) from 1-day-old to 8-yr-old organ donors with no known lung disease. For analysis, we considered the donors in four age groups [less than 30 days old neonates, 30 days to < 1 yr old infants, toddlers (1 to < 2 yr), and children 2 yr and older] and assessed differentially expressed genes (DEG). We found increasing age-associated transcriptional changes in all four major cell types in pediatric lung. Transition from neonate to infant stage showed highest number of DEG compared with the number of DEG found during infant to toddler- or toddler to older children-transitions. Profiles of differential gene expression and further pathway enrichment analyses indicate functional epithelial cell maturation and increased capability of antigen presentation and chemokine-mediated communication. Our study provides a comprehensive reference of gene expression patterns during healthy pediatric lung development that will be useful in identifying and understanding aberrant gene expression patterns associated with early life respiratory diseases.NEW & NOTEWORTHY This study presents postnatal transcriptomic changes in major cell populations in human lung, namely endothelial, epithelial, mesenchymal cells, and leukocytes. Although human postnatal lung development continues through early adulthood, our results demonstrate that greatest transcriptional changes occur in first few months of life during neonate to infant transition. These early transcriptional changes in lung parenchyma are particularly notable for functional maturation and activation of alveolar type II cell genes.
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Affiliation(s)
- Gautam Bandyopadhyay
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Matthew G Jehrio
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Cameron Baker
- UR Genomics Research Center, University of Rochester Medical Center, Rochester, New York, United States
| | - Soumyaroop Bhattacharya
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
- Program in Pediatric Molecular and Personalized Medicine, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Ravi S Misra
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Heidie L Huyck
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - ChinYi Chu
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
- Program in Pediatric Molecular and Personalized Medicine, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Jason R Myers
- UR Genomics Research Center, University of Rochester Medical Center, Rochester, New York, United States
| | - John Ashton
- UR Genomics Research Center, University of Rochester Medical Center, Rochester, New York, United States
| | - Steven Polter
- UR Flow Cytometry Core Facility, University of Rochester Medical Center, Rochester, New York, United States
| | - Matthew Cochran
- UR Flow Cytometry Core Facility, University of Rochester Medical Center, Rochester, New York, United States
| | - Timothy Bushnell
- UR Flow Cytometry Core Facility, University of Rochester Medical Center, Rochester, New York, United States
| | - Jennifer Dutra
- UR Clinical & Translational Science Institute Informatics, University of Rochester Medical Center, Rochester, New York, United States
| | - Philip J Katzman
- Department of Pathology, University of Rochester Medical Center, Rochester, New York, United States
| | - Gail H Deutsch
- Department of Pathology, Seattle Children's Hospital, Seattle, Washington, United States
| | - Thomas J Mariani
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
- Program in Pediatric Molecular and Personalized Medicine, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
| | - Gloria S Pryhuber
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, United States
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Koo HK, Morrow J, Kachroo P, Tantisira K, Weiss ST, Hersh CP, Silverman EK, DeMeo DL. Sex-specific associations with DNA methylation in lung tissue demonstrate smoking interactions. Epigenetics 2021; 16:692-703. [PMID: 32962511 PMCID: PMC8143227 DOI: 10.1080/15592294.2020.1819662] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/08/2020] [Accepted: 08/18/2020] [Indexed: 01/01/2023] Open
Abstract
Cigarette smoking impacts DNA methylation, but the investigation of sex-specific features of lung tissue DNA methylation in smokers has been limited. Women appear more susceptible to cigarette smoke, and often develop more severe lung disease at an earlier age with less smoke exposure. We aimed to analyse whether there are sex differences in DNA methylation in lung tissue and whether these DNA methylation marks interact with smoking. We collected lung tissue samples from former smokers who underwent lung tissue resection. One hundred thirty samples from white subjects were included for this analysis. Regression models for sex as a predictor of methylation were adjusted for age, presence of COPD, smoking variables and technical batch variables revealed 710 associated sites. 294 sites demonstrated robust sex-specific methylation associations in foetal lung tissue. Pathway analysis identified 6 nominally significant pathways including the mitophagy pathway. Three CpG sites demonstrated a suggested interaction between sex and pack-years of smoking: GPR132, ANKRD44 and C19orf60. All of them were nominally significant in both male- and female-specific models, and the effect estimates were in opposite directions for male and female; GPR132 demonstrated significant association between DNA methylation and gene expression in lung tissue (P < 0.05). Sex-specific associations with DNA methylation in lung tissue are wide-spread and may reveal genes and pathways relevant to sex differences for lung damaging effects of cigarette smoking.
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Affiliation(s)
- Hyeon-Kyoung Koo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Ilsan Paik Hospital, Inje University College of Medicine, Ilsan, Republic of Korea
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Kelan Tantisira
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
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3
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Bhattacharyya U, Thelma BK. Age-related gene expression alterations by SARS-CoV-2 infection contribute to poor prognosis in elderly. J Genet 2020. [PMID: 33168795 PMCID: PMC7584866 DOI: 10.1007/s12041-020-01233-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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4
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Transcriptome Profiling across Five Tissues of Giant Panda. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3852586. [PMID: 32851066 PMCID: PMC7436357 DOI: 10.1155/2020/3852586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/03/2020] [Accepted: 06/01/2020] [Indexed: 11/18/2022]
Abstract
Gene differential expression studies can serve to explore and understand the laws and characteristics of animal life activities, and the difference in gene expression between different animal tissues has been well demonstrated and studied. However, for the world-famous rare and protected species giant panda (Ailuropoda melanoleuca), only the transcriptome of the blood and spleen has been reported separately. Here, in order to explore the transcriptome differences between the different tissues of the giant panda, transcriptome profiles of the heart, liver, spleen, lung, and kidney from five captive giant pandas were constructed with Illumina HiSeq 2500 platform. The comparative analysis of the intertissue gene expression patterns was carried out based on the generated RNA sequencing datasets. Analyses of Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network were performed according to the identified differentially expressed genes (DEGs). We generated 194.52 GB clean base data from twenty-five sequencing libraries and identified 18,701 genes, including 3492 novel genes. With corrected p value <0.05 and |log2FoldChange| >2, we finally obtained 921, 553, 574, 457, and 638 tissue-specific DEGs in the heart, liver, spleen, lung, and kidney, respectively. In addition, we identified TTN, CAV3, LDB3, TRDN, and ACTN2 in the heart; FGA, AHSG, and SERPINC1 in the liver; CD19, CD79B, and IL21R in the spleen; NKX2-4 and SFTPB in the lung; GC and HRG in the kidney as hub genes in the PPI network. The results of the analyses showed a similar gene expression pattern between the spleen and lung. This study provided for the first time the heart, liver, lung, and kidney's transcriptome resources of the giant panda, and it provided a valuable resource for further genetic research or other potential research.
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The Effects of Age, Cigarette Smoking, Sex, and Race on the Qualitative Characteristics of Lung Transcriptome. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6418460. [PMID: 32802863 PMCID: PMC7424369 DOI: 10.1155/2020/6418460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/29/2020] [Indexed: 11/18/2022]
Abstract
The within-sample relative expression orderings (REOs) of genes, which are stable qualitative transcriptional characteristics, can provide abundant information for a disease. Methods based on REO comparisons have been proposed for identifying differentially expressed genes (DEGs) at the individual level and for detecting disease-associated genes based on one-phenotype disease data by reusing data of normal samples from other sources. Here, we evaluated the effects of common potential confounding factors, including age, cigarette smoking, sex, and race, on the REOs of gene pairs within normal lung tissues transcriptome. Our results showed that age has little effect on REOs within lung tissues. We found that about 0.23% of the significantly stable REOs of gene pairs in nonsmokers' lung tissues are reversed in smokers' lung tissues, introduced by 344 DEGs between the two groups of samples (RankCompV2, FDR <0.05), which are enriched in metabolism of xenobiotics by cytochrome P450, glutathione metabolism, and other pathways (hypergeometric test, FDR <0.05). Comparison between the normal lung tissue samples of males and females revealed fewer reversal REOs introduced by 24 DEGs between the sex groups, among which 19 DEGs are located on sex chromosomes and 5 DEGs involving in spermatogenesis and regulation of oocyte are located on autosomes. Between the normal lung tissue samples of white and black people, we identified 22 DEGs (RankCompV2, FDR <0.05) which introduced a few reversal REOs between the two races. In summary, the REO-based study should take into account the confounding factors of cigarette smoking, sex, and race.
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6
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Small-world networks of prognostic genes associated with lung adenocarcinoma development. Genomics 2020; 112:4078-4088. [PMID: 32659327 DOI: 10.1016/j.ygeno.2020.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/26/2020] [Accepted: 07/07/2020] [Indexed: 11/23/2022]
Abstract
The present study investigates the role of network topology in lung adenocarcinoma (LUAD) development. Analysis of sex- and stage-specific whole-genome expression data revealed that co-expressed and highly connected prognostic genes common to all cancer stages form a small-world network in each stage of LUAD. These small-world networks are present within stage-specific scale-free networks, conserved across the cancer stages, and linked to cancer-specific events. The presence of small-world networks across the cancer stages presents a synchronized system in the disordered environment of cancer, resulting in the evolution of malignancy. Our study reported that these small-world networks are resilient to random and systematic attacks, indicating the least opportunity to introduce perturbations by drugs as a therapeutic intervention. We concluded that highly clustered small-world networks could be controlled through transcriptional modulation for the improved treatment of LUAD.
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7
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Stearman RS, Bui QM, Speyer G, Handen A, Cornelius AR, Graham BB, Kim S, Mickler EA, Tuder RM, Chan SY, Geraci MW. Systems Analysis of the Human Pulmonary Arterial Hypertension Lung Transcriptome. Am J Respir Cell Mol Biol 2020; 60:637-649. [PMID: 30562042 DOI: 10.1165/rcmb.2018-0368oc] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is characterized by increased pulmonary artery pressure and vascular resistance, typically leading to right heart failure and death. Current therapies improve quality of life of the patients but have a modest effect on long-term survival. A detailed transcriptomics and systems biology view of the PAH lung is expected to provide new testable hypotheses for exploring novel treatments. We completed transcriptomics analysis of PAH and control lung tissue to develop disease-specific and clinical data/tissue pathology gene expression classifiers from expression datasets. Gene expression data were integrated into pathway analyses. Gene expression microarray data were collected from 58 PAH and 25 control lung tissues. The strength of the dataset and its derived disease classifier was validated using multiple approaches. Pathways and upstream regulators analyses was completed with standard and novel graphical approaches. The PAH lung dataset identified expression patterns specific to PAH subtypes, clinical parameters, and lung pathology variables. Pathway analyses indicate the important global role of TNF and transforming growth factor signaling pathways. In addition, novel upstream regulators and insight into the cellular and innate immune responses driving PAH were identified. Finally, WNT-signaling pathways may be a major determinant underlying the observed sex differences in PAH. This study provides a transcriptional framework for the PAH-diseased lung, supported by previously reported findings, and will be a valuable resource to the PAH research community. Our investigation revealed novel potential targets and pathways amenable to further study in a variety of experimental systems.
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Affiliation(s)
- Robert S Stearman
- 1 Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Quan M Bui
- 1 Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Gil Speyer
- 2 Quantitative Medicine and Systems Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona.,3 Research Computing, Arizona State University, Tempe, Arizona
| | - Adam Handen
- 4 Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Amber R Cornelius
- 1 Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Brian B Graham
- 5 Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado, Aurora, Colorado; and
| | - Seungchan Kim
- 6 Department of Electrical and Computer Engineering, Center for Computational Systems Biology, Roy G. Perry College of Engineering, Prairie View A&M University, Prairie View, Texas
| | - Elizabeth A Mickler
- 1 Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Rubin M Tuder
- 5 Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado, Aurora, Colorado; and
| | - Stephen Y Chan
- 4 Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Mark W Geraci
- 1 Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
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8
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van den Berge M, Brandsma CA, Faiz A, de Vries M, Rathnayake SNH, Paré PD, Sin DD, Bossé Y, Laviolette M, Nickle DC, Hao K, Obeidat M, Dragani TA, Colombo F, Timens W, Postma DS. Differential lung tissue gene expression in males and females: implications for the susceptibility to develop COPD. Eur Respir J 2019; 54:13993003.02567-2017. [PMID: 31164434 DOI: 10.1183/13993003.02567-2017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 04/04/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Dept of Pulmonary Diseases, Groningen, The Netherlands .,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Shared first authorship; both authors contributed equally
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Dept of Pathology and Medical Biology, Groningen, The Netherlands.,Shared first authorship; both authors contributed equally
| | - Alen Faiz
- University of Groningen, University Medical Center Groningen, Dept of Pulmonary Diseases, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life Sciences, Sydney, Australia
| | - Maaike de Vries
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Dept of Pathology and Medical Biology, Groningen, The Netherlands
| | - Senani N H Rathnayake
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life Sciences, Sydney, Australia
| | - Peter D Paré
- The University of British Columbia, Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada.,Respiratory Division, University of British Columbia, Vancouver, BC, Canada
| | - Don D Sin
- The University of British Columbia, Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada.,Respiratory Division, University of British Columbia, Vancouver, BC, Canada
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada.,Dept of Molecular Medicine, Laval University, Québec, QC, Canada
| | - Michel Laviolette
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
| | | | - Ke Hao
- Merck Research Laboratories, Boston, MA, USA
| | - Ma'en Obeidat
- The University of British Columbia, Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Tommaso A Dragani
- Research Unit "Genetic Epidemiology and Pharmacogenomics", Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Francesca Colombo
- Dept of Predictive and Preventive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Dept of Pathology and Medical Biology, Groningen, The Netherlands.,Shared last authorship; both authors contributed equally
| | - Dirkje S Postma
- University of Groningen, University Medical Center Groningen, Dept of Pulmonary Diseases, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Shared last authorship; both authors contributed equally
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9
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Age-related gene and miRNA expression changes in airways of healthy individuals. Sci Rep 2019; 9:3765. [PMID: 30842487 PMCID: PMC6403379 DOI: 10.1038/s41598-019-39873-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 02/01/2019] [Indexed: 12/15/2022] Open
Abstract
Knowledge on age-related miRNA changes in healthy individuals and their interaction with mRNAs is lacking. We studied age-related mRNA and miRNA expression changes and their interactions in normal airways. RNA and small RNA sequencing was performed on bronchial biopsies of 86 healthy individuals (age: 18–73) to determine age-related expression changes. Per age-related miRNA we determined the enrichment of age-related predicted targets and their correlation. We identified 285 age-related genes and 27 age-related miRNAs. Pathway enrichment showed that genes higher expressed with age were involved in synapse-related processes. Genes lower expressed with age were involved in cell cycle regulation, the immune system and DNA damage/repair. MiR-146a-5p, miR-146b-5p and miR-142-5p were lower expressed with increasing age and we found a significant enrichment for predicted targets of these miRNAs among genes that were higher expressed with age. The expression levels of the enriched predicted targets RIMS2 and IGSF1 were negatively correlated with both miR-146a-5p and miR-146b-5p. RIMS2 was present in the enriched process, i.e. positive regulation of synaptic transmission. In conclusion, genes decreased with ageing are involved in several of the ageing hallmarks. Genes higher expressed with ageing were involved in synapse-related processes, of which RIMS2 is potentially regulated by two age-related miRNAs.
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10
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Gomez-Verjan JC, Vazquez-Martinez ER, Rivero-Segura NA, Medina-Campos RH. The RNA world of human ageing. Hum Genet 2018; 137:865-879. [DOI: 10.1007/s00439-018-1955-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/29/2018] [Indexed: 12/15/2022]
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11
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Nino CL, Perez GF, Isaza N, Gutierrez MJ, Gomez JL, Nino G. Characterization of Sex-Based Dna Methylation Signatures in the Airways During Early Life. Sci Rep 2018; 8:5526. [PMID: 29615635 PMCID: PMC5882800 DOI: 10.1038/s41598-018-23063-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 03/06/2018] [Indexed: 12/17/2022] Open
Abstract
Human respiratory conditions are largely influenced by the individual’s sex resulting in overall higher risk for males. Sex-based respiratory differences are present at birth suggesting a strong genetic component. Our objective was to characterize early life sex-based genomic signatures determined by variable X-chromosome methylation in the airways. We compared male versus female genome-wide DNA methylation in nasal airway samples from newborns and infants aged 1–6 months (N = 12). We analyzed methylation signals across CpG sites mapped to each X-linked gene using an unsupervised classifier (principal components) followed by an internal evaluation and an exhaustive cross-validation. Results were validated in an independent population of children (N = 72) following the same algorithm. X-linked genes with significant sex-based differential methylation in the nasal airway of infants represented only about 50% of the unique protein coding transcripts. X-linked genes without significant sex-based differential methylation included genes with evidence of escaping X-inactivation and female-biased airway expression. These genes showed similar methylation patterns in males and females suggesting unbalanced X-chromosome dosage. In conclusion, we identified that the human airways have already sex-based DNA methylation signatures at birth. These early airway epigenomic marks may determine sex-based respiratory phenotypes and overall predisposition to develop respiratory disorders later in life.
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Affiliation(s)
- Cesar L Nino
- Department of Electronics Engineering, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Geovanny F Perez
- Division of Pulmonary and Sleep Medicine, Children's National Medical Center, Washington, DC, USA.,Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Center for Genetic Medicine, Children's National Medical Center, Washington, DC, USA
| | - Natalia Isaza
- Division of Neonatology, Children's National Medical Center, Washington, DC, USA
| | - Maria J Gutierrez
- Division of Pediatric Allergy Immunology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jose L Gomez
- Division of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New-Haven, CT, USA
| | - Gustavo Nino
- Division of Pulmonary and Sleep Medicine, Children's National Medical Center, Washington, DC, USA. .,Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA. .,Center for Genetic Medicine, Children's National Medical Center, Washington, DC, USA.
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