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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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Bhattacharya S, Myers JA, Baker C, Guo M, Danopoulos S, Myers JR, Bandyopadhyay G, Romas ST, Huyck HL, Misra RS, Dutra J, Holden-Wiltse J, McDavid AN, Ashton JM, Al Alam D, Potter SS, Whitsett JA, Xu Y, Pryhuber GS, Mariani TJ. Single-Cell Transcriptomic Profiling Identifies Molecular Phenotypes of Newborn Human Lung Cells. Genes (Basel) 2024; 15:298. [PMID: 38540357 PMCID: PMC10970229 DOI: 10.3390/genes15030298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 05/01/2024] Open
Abstract
While animal model studies have extensively defined the mechanisms controlling cell diversity in the developing mammalian lung, there exists a significant knowledge gap with regards to late-stage human lung development. The NHLBI Molecular Atlas of Lung Development Program (LungMAP) seeks to fill this gap by creating a structural, cellular and molecular atlas of the human and mouse lung. Transcriptomic profiling at the single-cell level created a cellular atlas of newborn human lungs. Frozen single-cell isolates obtained from two newborn human lungs from the LungMAP Human Tissue Core Biorepository, were captured, and library preparation was completed on the Chromium 10X system. Data was analyzed in Seurat, and cellular annotation was performed using the ToppGene functional analysis tool. Transcriptional interrogation of 5500 newborn human lung cells identified distinct clusters representing multiple populations of epithelial, endothelial, fibroblasts, pericytes, smooth muscle, immune cells and their gene signatures. Computational integration of data from newborn human cells and with 32,000 cells from postnatal days 1 through 10 mouse lungs generated by the LungMAP Cincinnati Research Center facilitated the identification of distinct cellular lineages among all the major cell types. Integration of the newborn human and mouse cellular transcriptomes also demonstrated cell type-specific differences in maturation states of newborn human lung cells. Specifically, newborn human lung matrix fibroblasts could be separated into those representative of younger cells (n = 393), or older cells (n = 158). Cells with each molecular profile were spatially resolved within newborn human lung tissue. This is the first comprehensive molecular map of the cellular landscape of neonatal human lung, including biomarkers for cells at distinct states of maturity.
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Affiliation(s)
- Soumyaroop Bhattacharya
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Jacquelyn A. Myers
- Genomic Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA; (J.A.M.); (C.B.); (J.R.M.); (J.M.A.)
| | - Cameron Baker
- Genomic Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA; (J.A.M.); (C.B.); (J.R.M.); (J.M.A.)
| | - Minzhe Guo
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA; (M.G.); (S.S.P.); (J.A.W.); (Y.X.)
| | - Soula Danopoulos
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, University of California Los Angeles, Los Angeles, CA 90024, USA; (S.D.)
| | - Jason R. Myers
- Genomic Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA; (J.A.M.); (C.B.); (J.R.M.); (J.M.A.)
| | - Gautam Bandyopadhyay
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Stephen T. Romas
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Heidie L. Huyck
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Ravi S. Misra
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Jennifer Dutra
- Clinical & Translational Science Institute, University of Rochester, Rochester, NY 14642, USA; (J.D.); (J.H.-W.)
| | - Jeanne Holden-Wiltse
- Clinical & Translational Science Institute, University of Rochester, Rochester, NY 14642, USA; (J.D.); (J.H.-W.)
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - Andrew N. McDavid
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - John M. Ashton
- Genomic Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA; (J.A.M.); (C.B.); (J.R.M.); (J.M.A.)
| | - Denise Al Alam
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, University of California Los Angeles, Los Angeles, CA 90024, USA; (S.D.)
| | - S. Steven Potter
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA; (M.G.); (S.S.P.); (J.A.W.); (Y.X.)
| | - Jeffrey A. Whitsett
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA; (M.G.); (S.S.P.); (J.A.W.); (Y.X.)
| | - Yan Xu
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA; (M.G.); (S.S.P.); (J.A.W.); (Y.X.)
| | - Gloria S. Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Thomas J. Mariani
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
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3
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Goldschagg MGE, Hockman D. FGF18. Differentiation 2023:100735. [PMID: 38007374 DOI: 10.1016/j.diff.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/25/2023] [Accepted: 10/25/2023] [Indexed: 11/27/2023]
Abstract
FGF18 was discovered in 1998. It is a pleiotropic growth factor that stimulates major signalling pathways involved in cell proliferation and growth, and is involved in the development and homeostasis of many tissues such as bone, lung, and central nervous system. The gene consists of five exons that code for a 207 amino acid glycosylated protein. FGF18 is widely expressed in developing and adult chickens, mice, and humans, being seen in the mesenchyme, brain, skeleton, heart, and lungs. Knockout studies of FGF18 in mice lead to perinatal death, characterised by distinct phenotypes such as cleft palate, smaller body size, curved long bones, deformed ribs, and reduced crania. As can be expected from a protein involved in so many functions FGF18 is associated with various diseases such as idiopathic pulmonary fibrosis, congenital diaphragmatic hernia, and most notably various types of cancer such as breast, lung, and ovarian cancer.
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Affiliation(s)
- Michael G E Goldschagg
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Dorit Hockman
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
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4
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Loddo F, Nauleau S, Lapalus D, Tardieu S, Bernard O, Boubred F. Association of Maternal Gestational Vitamin D Supplementation with Respiratory Health of Young Children. Nutrients 2023; 15:nu15102380. [PMID: 37242263 DOI: 10.3390/nu15102380] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
This study aimed to evaluate the association between maternal gestational Vitamin D3 supplementation and early respiratory health in offspring. This was a population-based record-linkage study which used data from the French National Health Database System. Maternal Vitamin D3 supplementation consisted of a single high oral dose of cholecalciferol, (100,000 IU) from the seventh month of pregnancy, according to national guidelines. In total, 125,756 term-born singleton children were included, of which 37% had respiratory illness defined as hospital admission due to respiratory causes or inhalation treatment up to 24 months of age. Infants prenatally exposed to maternal Vitamin D3 supplementation (n = 54,596) were more likely to have a longer gestational age (GA) at birth (GA 36-38 weeks, 22% vs. 20%, p < 0.001 in exposed vs. non-exposed infants, respectively). After adjusting for the main risk factors (maternal age, socioeconomic level, mode of delivery, obstetrical and neonatal pathology, birth weight appropriateness, sex, and birth season), the risk of RD was found to be 3% lower than their counterparts (aOR [IC 95%], 0.97 [0.95-0.99], p = 0.01). In conclusion, this study provides evidence for the association between maternal gestational Vitamin D3 supplementation and improved early respiratory outcomes in young children.
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Affiliation(s)
- Fanny Loddo
- APHM, Neonatal Unit, Hospital University la Conception, 13005 Marseille, France
| | - Steve Nauleau
- Regional Health Agency, Provence-Alpes-Côte d'Azur, 13005 Marseille, France
| | - David Lapalus
- Regional Health Agency, Provence-Alpes-Côte d'Azur, 13005 Marseille, France
| | - Sophie Tardieu
- APHM, Public Health and Medical Information Department, EA 3279, CEReSS-Health Service Research and Quality of Life Centre, 13005 Marseille, France
| | - Olivier Bernard
- Regional Health Agency, Provence-Alpes-Côte d'Azur, 13005 Marseille, France
| | - Farid Boubred
- APHM, Neonatal Unit, Hospital University la Conception, 13005 Marseille, France
- Aix-Marseille Université, C2VN, INRAe, INSERM, 13005 Marseille, France
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5
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Danopoulos S, Belgacemi R, Hein RFC, Miller AJ, Deutsch GH, Glass I, Spence JR, Al Alam D. FGF18 promotes human lung branching morphogenesis through regulating mesenchymal progenitor cells. Am J Physiol Lung Cell Mol Physiol 2023; 324:L433-L444. [PMID: 36791060 PMCID: PMC10027085 DOI: 10.1152/ajplung.00316.2022] [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: 09/23/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/16/2023] Open
Abstract
Fibroblast growth factor (FGF) signaling is known to play an important role in lung organogenesis. However, we recently demonstrated that FGF10 fails to induce branching in human fetal lungs as is observed in mouse. Our previous human fetal lung RNA sequencing data exhibited increased FGF18 during the pseudoglandular stage of development, suggestive of its importance in human lung branching morphogenesis. Whereas it has been previously reported that FGF18 is critical during alveologenesis, few studies have described its implication in lung branching, specifically in human. Therefore, we aimed to determine the role of FGF18 in human lung branching morphogenesis. Human fetal lung explants within the pseudoglandular stage of development were treated with recombinant human FGF18 in air-liquid interface culture. Explants were analyzed grossly to assess differences in branching pattern, as well as at the cellular and molecular levels. FGF18 treatment promoted branching in explant cultures and demonstrated increased epithelial proliferation as well as maintenance of the double positive SOX2/SOX9 distal bud progenitor cells, confirming its role in human lung branching morphogenesis. In addition, FGF18 treated explants displayed increased expression of SOX9, FN1, and COL2A1 within the mesenchyme, all factors that are important to chondrocyte differentiation. In humans, cartilaginous airways extend deep into the lung up to the 12th generation of branching whereas in mouse these are restricted to the trachea and main bronchi. Therefore, our data suggest that FGF18 promotes human lung branching morphogenesis through regulating mesenchymal progenitor cells.
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Affiliation(s)
- Soula Danopoulos
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, California, United States
- Division of Neonatology, Department of Pediatrics, David Geffen School of Medicine at University of California, Los Angeles, California, United States
| | - Randa Belgacemi
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, California, United States
| | - Renee F C Hein
- Department of Cell and Developmental biology, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Alyssa J Miller
- Department of Cell and Developmental biology, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Gail H Deutsch
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine and Seattle Children's Research Institute, Seattle, Washington, United States
| | - Ian Glass
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, United States
| | - Jason R Spence
- Department of Cell and Developmental biology, University of Michigan Medical School, Ann Arbor, Michigan, United States
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Denise Al Alam
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, California, United States
- Division of Neonatology, Department of Pediatrics, David Geffen School of Medicine at University of California, Los Angeles, California, United States
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Noël A, Yilmaz S, Farrow T, Schexnayder M, Eickelberg O, Jelesijevic T. Sex-Specific Alterations of the Lung Transcriptome at Birth in Mouse Offspring Prenatally Exposed to Vanilla-Flavored E-Cigarette Aerosols and Enhanced Susceptibility to Asthma. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:3710. [PMID: 36834405 PMCID: PMC9967225 DOI: 10.3390/ijerph20043710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/07/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Currently, approximately 8 million adult Americans use electronic cigarettes (e-cigs) daily, including women of childbearing age. It is known that more than 10% of women smoke during their pregnancy, and recent surveys show that rates of maternal vaping are similar to rates of maternal cigarette smoking. However, the effects of inhaling e-cig aerosol on the health of fetuses remain unknown. The objective of the present study was to increase our understanding of the molecular effects caused by in utero exposures to e-cig aerosols on developing mouse lungs and, later in life, on the offspring's susceptibility to developing asthma. METHODS Pregnant mice were exposed throughout gestation to either filtered air or vanilla-flavored e-cig aerosols containing 18 mg/mL of nicotine. Male and female exposed mouse offspring were sacrificed at birth, and then the lung transcriptome was evaluated. Additionally, once sub-groups of male offspring mice reached 4 weeks of age, they were challenged with house dust mites (HDMs) for 3 weeks to assess asthmatic responses. RESULTS The lung transcriptomic responses of the mouse offspring at birth showed that in utero vanilla-flavored e-cig aerosol exposure significantly regulated 88 genes in males (62 genes were up-regulated and 26 genes were down-regulated), and 65 genes were significantly regulated in females (17 genes were up-regulated and 48 genes were down-regulated). Gene network analyses revealed that in utero e-cig aerosol exposure affected canonical pathways associated with CD28 signaling in T helper cells, the role of NFAT in the regulation of immune responses, and phospholipase C signaling in males, whereas the dysregulated genes in the female offspring were associated with NRF2-mediated oxidative stress responses. Moreover, we found that in utero exposures to vanilla-flavored e-cig aerosol exacerbated HDM-induced asthma in 7-week-old male mouse offspring compared to respective in utero air + HDM controls. CONCLUSIONS Overall, these data demonstrate that in utero e-cig aerosol exposure alters the developing mouse lung transcriptome at birth in a sex-specific manner and provide evidence that the inhalation of e-cig aerosols is detrimental to the respiratory health of offspring by increasing the offspring' susceptibility to developing lung diseases later in life.
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Affiliation(s)
- Alexandra Noël
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Sultan Yilmaz
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Tori Farrow
- Department of Environmental Toxicology, Southern University and A & M College, Baton Rouge, LA 70813, USA
| | | | - Oliver Eickelberg
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Tomislav Jelesijevic
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
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7
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Lun Y, Hu J, Zuming Y. Circular RNAs expression profiles and bioinformatics analysis in bronchopulmonary dysplasia. J Clin Lab Anal 2022; 37:e24805. [PMID: 36514862 PMCID: PMC9833990 DOI: 10.1002/jcla.24805] [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: 06/07/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bronchopulmonary dysplasia (BPD) has long been considered the most challenging chronic lung disease for neonatologists and researchers due to its complex pathological mechanisms and difficulty in prediction. Growing evidence indicates that BPD is associated with the dysregulation of circular RNAs (circRNAs). Therefore, we aimed to explore the expression profiles of circRNAs and investigate the underlying molecular network associated with BPD. METHODS Peripheral blood was collected from very-low-birth-weight (VLBW) infants at 5-8 days of life to extract PBMCs. Microarray analysis and qRT-PCR tests were performed to determine the differentially expressed circRNAs (DEcircRNAs) between BPD and non-BPD VLBW infants. Simultaneous analysis of GSE32472 was conducted to obtain differentially expressed mRNAs (DEmRNA) from BPD infants. The miRNAs were predicted by DEcircRNAs and DEmRNAs of upregulated, respectively, and then screened for overlapping ones. GO and KEGG analysis was performed following construction of the competing endogenous RNA regulatory network (ceRNA) for further investigation. RESULTS A total of 65 circRNAs (52 upregulated and 13 downregulated) were identified as DEcircRNAs between the two groups (FC >2.0 and p.adj <0.05). As a result, the ceRNA network was constructed based on three upregulated DEcircRNAs validated by qRT-PCR (hsa_circ_0007054, hsa_circ_0057950, and hsa_circ_0120151). Bioinformatics analysis indicated these DEcircRNAs participated in response to stimulus, IL-1 receptor activation, neutrophil activation, and metabolic pathways. CONCLUSIONS In VLBW infants with a high risk for developing BPD, the circRNA expression profiles in PBMCs were significantly altered in the early post-birth period, suggesting immune dysregulation caused by infection and inflammatory response already existed.
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Affiliation(s)
- Yu Lun
- Department of Neonatal Intensive Care UnitSuzhou Municipal HospitalJiangsu ProvinceChina
| | - Junlong Hu
- Department of Neonatal Intensive Care UnitSuzhou Municipal HospitalJiangsu ProvinceChina
| | - Yang Zuming
- Department of Neonatal Intensive Care UnitSuzhou Municipal HospitalJiangsu ProvinceChina
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8
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Humbert MV, Spalluto CM, Bell J, Blume C, Conforti F, Davies ER, Dean LSN, Elkington P, Haitchi HM, Jackson C, Jones MG, Loxham M, Lucas JS, Morgan H, Polak M, Staples KJ, Swindle EJ, Tezera L, Watson A, Wilkinson TMA. Towards an artificial human lung: modelling organ-like complexity to aid mechanistic understanding. Eur Respir J 2022; 60:2200455. [PMID: 35777774 DOI: 10.1183/13993003.00455-2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/11/2022] [Indexed: 11/05/2022]
Abstract
Respiratory diseases account for over 5 million deaths yearly and are a huge burden to healthcare systems worldwide. Murine models have been of paramount importance to decode human lung biology in vivo, but their genetic, anatomical, physiological and immunological differences with humans significantly hamper successful translation of research into clinical practice. Thus, to clearly understand human lung physiology, development, homeostasis and mechanistic dysregulation that may lead to disease, it is essential to develop models that accurately recreate the extraordinary complexity of the human pulmonary architecture and biology. Recent advances in micro-engineering technology and tissue engineering have allowed the development of more sophisticated models intending to bridge the gap between the native lung and its replicates in vitro Alongside advanced culture techniques, remarkable technological growth in downstream analyses has significantly increased the predictive power of human biology-based in vitro models by allowing capture and quantification of complex signals. Refined integrated multi-omics readouts could lead to an acceleration of the translational pipeline from in vitro experimental settings to drug development and clinical testing in the future. This review highlights the range and complexity of state-of-the-art lung models for different areas of the respiratory system, from nasal to large airways, small airways and alveoli, with consideration of various aspects of disease states and their potential applications, including pre-clinical drug testing. We explore how development of optimised physiologically relevant in vitro human lung models could accelerate the identification of novel therapeutics with increased potential to translate successfully from the bench to the patient's bedside.
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Affiliation(s)
- Maria Victoria Humbert
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Cosma Mirella Spalluto
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
- M.V. Humbert and C.M. Spalluto are co-first authors and contributed equally to this work
| | - Joseph Bell
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - Cornelia Blume
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Franco Conforti
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - Elizabeth R Davies
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Lareb S N Dean
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - Paul Elkington
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Hans Michael Haitchi
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Claire Jackson
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - Mark G Jones
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - Matthew Loxham
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Jane S Lucas
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - Hywel Morgan
- Institute for Life Sciences, University of Southampton, Southampton, UK
- Electronics and Computer Science, Faculty of Physical Sciences and Engineering, University of Southampton, Southampton, UK
| | - Marta Polak
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Karl J Staples
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - Emily J Swindle
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Liku Tezera
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Department of Infection and Immunity, Faculty of Medicine, University College London, London, UK
| | - Alastair Watson
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Tom M A Wilkinson
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
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9
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Chen H, Chen X, Hu L, Ye C, Zhang J, Cheng G, Yang L, Lu Y, Dong X, Zhou W. Rare-variant Collapsing Analyses Identified Risk Genes for Neonatal Acute Respiratory Distress Syndrome. Comput Struct Biotechnol J 2022; 20:5047-5053. [PMID: 36187926 PMCID: PMC9486038 DOI: 10.1016/j.csbj.2022.08.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/18/2022] [Accepted: 08/27/2022] [Indexed: 11/03/2022] Open
Abstract
Background Results Conclusions
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10
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Orzabal MR, Naik VD, Lee J, Hillhouse AE, Brashear WA, Threadgill DW, Ramadoss J. Impact of E-cig aerosol vaping on fetal and neonatal respiratory development and function. Transl Res 2022; 246:102-114. [PMID: 35351623 PMCID: PMC9197928 DOI: 10.1016/j.trsl.2022.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/09/2022] [Accepted: 03/23/2022] [Indexed: 11/15/2022]
Abstract
Electronic cigarette (e-cig) use has increased over the past decade, and exposure to e-cig aerosols during pregnancy raises concern for maternal and fetal health. The developing fetal lung is known to be sensitive to prenatal tobacco product exposure. Utilizing a 3-pronged approach, we examined the effects of prenatal e-cig aerosols with, and without nicotine on respiratory development in a murine model. RNAseq analysis of fetal lungs revealed extensive dysregulation in gene expression. Morphologic assessment of distal airspaces in neonatal lungs display an emphysematic phenotype. Respiratory mechanics of neonates display signs of increased respiratory workload, with increased resistance and decreased compliance. These data are novel and provide evidence that prenatal e-cig exposure may result in altered lung function or development of disease.
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Affiliation(s)
- Marcus R Orzabal
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Vishal D Naik
- Department of Obstetrics & Gynecology, C.S. Mott Center for Human growth and Development, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Jehoon Lee
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Andrew E Hillhouse
- Institute for Genome Sciences and Society, Texas A&M University, College Station, Texas, USA
| | - Wesley A Brashear
- Institute for Genome Sciences and Society, Texas A&M University, College Station, Texas, USA
| | - David W Threadgill
- Institute for Genome Sciences and Society, Texas A&M University, College Station, Texas, USA
| | - Jayanth Ramadoss
- Department of Obstetrics & Gynecology, C.S. Mott Center for Human growth and Development, School of Medicine, Wayne State University, Detroit, Michigan, USA; Department of Physiology, School of Medicine, Wayne State University, Detroit, Michigan, USA.
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11
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Matta Reddy A, Iqbal M, Chopra H, Urmi S, Junapudi S, Bibi S, Kumar Gupta S, Nirmala Pangi V, Singh I, Abdel-Daim MM. Pivotal role of vitamin D in mitochondrial health, cardiac function, and human reproduction. EXCLI JOURNAL 2022; 21:967-990. [PMID: 36110560 PMCID: PMC9441677 DOI: 10.17179/excli2022-4935] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/24/2022] [Indexed: 11/04/2022]
Abstract
Vitamin D, a secosteroid hormone, appears to have significant beneficial effects on various physiological systems, including the musculoskeletal system. Vitamin D assists in the regulation of numerous critical biological functions and physiological processes in humans, including inflammation, oxidative stress, and mitochondrial respiration, and is also linked to cardiac diseases. It is also reported that vitamin D plays a central role in molecular and cellular mechanisms, which reduce oxidative stress, and tissue damage and regulate cellular health. On the other side, hypovitaminosis D reduces mitochondrial activity and increases oxidative stress and inflammation in the body. Hypervitaminosis D increases the prevalence and severity of cellular damage. It has also been reported that vitamin D is involved in many functions of the reproductive system in human and critically play an important role in the reproductive tissues of women and men. Its role is very well defined, starting from female menarche to menopause, pregnancy, and lactation, and finally in male fertility. Hence, the appropriate amount of vitamin D is necessary to maintain the normal function of cell organelles. Based on recent studies, it is understood that vitamin D is involved in the biological activities of mitochondria in cells, especially in cardiomyocytes. In this review, we emphasized the role of vitamin D in mitochondrial respiration, which could significantly influence heart health and human reproduction.
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Affiliation(s)
- Alavala Matta Reddy
- Department of Zoology, School of Life and Health Sciences, Adikavi Nannaya University, Rajahmundry 533296, Andhra Pradesh, India
| | - Mumtaz Iqbal
- College of Arts and Science, University of South Florida, Tampa, FL33620, USA
| | - Hitesh Chopra
- Chitkara College of Pharmacy, Chitkara University, Punjab140401, India
| | - Shaheda Urmi
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL33612, USA
| | - Sunil Junapudi
- Department of Pharmaceutical Chemistry, Geethanjali College of Pharmacy, Cherryal, Keesara, Medchalmalkajgiri District, Telangana, 501301, India
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan,Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China,*To whom correspondence should be addressed: Shabana Bibi, Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan; Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China, E-mail:
| | | | - Viajaya Nirmala Pangi
- School of Life and Health Sciences, Adikavi Nannaya University, Rajahamahendravaram, Andhra Pradesh, India
| | - Inderbir Singh
- Chitkara College of Pharmacy, Chitkara University, Punjab140401, India
| | - Mohamed M. Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231 Jeddah 21442, Saudi Arabia,Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
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12
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Kho AT, McGeachie MJ, Li J, Chase RP, Amr SS, Hastie AT, Hawkins GA, Li X, Chupp GL, Meyers DA, Bleecker ER, Weiss ST, Tantisira KG. Lung function, airway and peripheral basophils and eosinophils are associated with molecular pharmacogenomic endotypes of steroid response in severe asthma. Thorax 2022; 77:452-460. [PMID: 34580195 PMCID: PMC9016241 DOI: 10.1136/thoraxjnl-2020-215523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 06/26/2021] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Asthma is a complex disease with heterogeneous expression/severity. There is growing interest in defining asthma endotypes consistently associated with different responses to therapy, focusing on type 2 inflammation (Th2) as a key pathological mechanism. Current asthma endotypes are defined primarily by clinical/laboratory criteria. Each endotype is likely characterised by distinct molecular mechanisms that identify optimal therapies. METHODS We applied unsupervised (without a priori clinical criteria) principal component analysis on sputum airway cells RNA-sequencing transcriptomic data from 19 asthmatics from the Severe Asthma Research Program at baseline and 6-8 weeks follow-up after a 40 mg dose of intramuscular corticosteroids. We investigated principal components PC1, PC3 for association with 55 clinical variables. RESULTS PC3 was associated with baseline Th2 clinical features including blood (rank-sum p=0.0082) and airway (rank-sum p=0.0024) eosinophilia, FEV1 change (Kendall tau-b R=-0.333 (-0.592 to -0.012)) and follow-up FEV1 albuterol response (Kendall tau-b R=0.392 (0.079 to 0.634)). PC1 with blood basophlia (rank-sum p=0.0191). The top 5% genes contributing to PC1, PC3 were enriched for distinct immune system/inflammation ontologies suggesting distinct subject-specific clusters of transcriptomic response to corticosteroids. PC3 association with FEV1 change was reproduced in silico in a comparable independent 14-subject (baseline, 8 weeks after daily inhaled corticosteroids (ICS)) airway epithelial cells microRNAome dataset. CONCLUSIONS Transcriptomic PCs from this unsupervised methodology define molecular pharmacogenomic endotypes that may yield novel biology underlying different subject-specific responses to corticosteroid therapy in asthma, and optimal personalised asthma care. Top contributing genes to these PCs may suggest new therapeutic targets.
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Affiliation(s)
- Alvin T Kho
- Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Jiang Li
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Scientific Research Centre, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, People's Republic of China
| | - Robert P Chase
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Sami S Amr
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Partners Personalized Medicine, Partners Healthcare, Boston, Massachusetts, USA
| | - Annette T Hastie
- Center for Genomics and Personalized Medicine Research, Wake Forest Health Sciences, Winston Salem, North Carolina, USA
| | - Gregory A Hawkins
- Center for Genomics and Personalized Medicine Research, Wake Forest Health Sciences, Winston Salem, North Carolina, USA
| | - Xingnan Li
- Division of Genetics, Genomics and Precision Medicine, University of Arizona Health Sciences, Tucson, Arizona, USA
| | - Geoffrey L Chupp
- Pulmonary & Critical Care Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Deborah A Meyers
- Division of Genetics, Genomics and Precision Medicine, University of Arizona Health Sciences, Tucson, Arizona, USA
| | - Eugene R Bleecker
- Division of Genetics, Genomics and Precision Medicine, University of Arizona Health Sciences, Tucson, Arizona, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Partners Personalized Medicine, Partners Healthcare, Boston, Massachusetts, USA
| | - Kelan G Tantisira
- Department of Pediatrics, Division of Respiratory Medicine, University of California San Diego, La Jolla, California, USA
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13
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Clair G, Bramer LM, Misra R, McGraw MD, Bhattacharya S, Kitzmiller JA, Feng S, Danna VG, Bandyopadhyay G, Bhotika H, Huyck HL, Deutsch GH, Mariani TJ, Carson JP, Whitsett JA, Pryhuber GS, Adkins JN, Ansong C. Proteomic Analysis of Human Lung Development. Am J Respir Crit Care Med 2022; 205:208-218. [PMID: 34752721 PMCID: PMC8787240 DOI: 10.1164/rccm.202008-3303oc] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Rationale: The current understanding of human lung development derives mostly from animal studies. Although transcript-level studies have analyzed human donor tissue to identify genes expressed during normal human lung development, protein-level analysis that would enable the generation of new hypotheses on the processes involved in pulmonary development are lacking. Objectives: To define the temporal dynamic of protein expression during human lung development. Methods: We performed proteomics analysis of human lungs at 10 distinct times from birth to 8 years to identify the molecular networks mediating postnatal lung maturation. Measurements and Main Results: We identified 8,938 proteins providing a comprehensive view of the developing human lung proteome. The analysis of the data supports the existence of distinct molecular substages of alveolar development and predicted the age of independent human lung samples, and extensive remodeling of the lung proteome occurred during postnatal development. Evidence of post-transcriptional control was identified in early postnatal development. An extensive extracellular matrix remodeling was supported by changes in the proteome during alveologenesis. The concept of maturation of the immune system as an inherent part of normal lung development was substantiated by flow cytometry and transcriptomics. Conclusions: This study provides the first in-depth characterization of the human lung proteome during development, providing a unique proteomic resource freely accessible at Lungmap.net. The data support the extensive remodeling of the lung proteome during development, the existence of molecular substages of alveologenesis, and evidence of post-transcriptional control in early postnatal development.
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Affiliation(s)
| | | | - Ravi Misra
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Matthew D. McGraw
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | | | - Joseph A. Kitzmiller
- Perinatal Institute, Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and University of Cincinnati School of Medicine, Cincinnati, Ohio
| | | | | | - Gautam Bandyopadhyay
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Harsh Bhotika
- Environmental Molecular Science Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Heidie L. Huyck
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Gail H. Deutsch
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington; and
| | - Thomas J. Mariani
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - James P. Carson
- Texas Advanced Computing Center, University of Texas at Austin, Austin, Texas
| | - Jeffrey A. Whitsett
- Perinatal Institute, Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and University of Cincinnati School of Medicine, Cincinnati, Ohio
| | - Gloria S. Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
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14
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Sahni M, Bhandari V. Patho-mechanisms of the origins of bronchopulmonary dysplasia. Mol Cell Pediatr 2021; 8:21. [PMID: 34894313 PMCID: PMC8665964 DOI: 10.1186/s40348-021-00129-5] [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] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/15/2021] [Indexed: 12/17/2022] Open
Abstract
Bronchopulmonary dysplasia (BPD) continues to be one of the most common complications of prematurity, despite significant advancement in neonatology over the last couple of decades. The new BPD is characterized histopathologically by impaired lung alveolarization and dysregulated vascularization. With the increased survival of extremely preterm infants, the risk for the development of BPD remains high, emphasizing the continued need to understand the patho-mechanisms that play a role in the development of this disease. This brief review summarizes recent advances in our understanding of the maldevelopment of the premature lung, highlighting recent research in pathways of oxidative stress-related lung injury, the role of placental insufficiency, growth factor signaling, the extracellular matrix, and microRNAs.
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Affiliation(s)
- Mitali Sahni
- Pediatrix Medical Group, Sunrise Children's Hospital, Las Vegas, NV, USA.,University of Nevada, Las Vegas, NV, USA
| | - Vineet Bhandari
- Neonatology Research Laboratory, Education and Research Building, Cooper University Hospital, One Cooper Plaza, Camden, NJ, 08103, USA.
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15
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Scaffa A, Yao H, Oulhen N, Wallace J, Peterson AL, Rizal S, Ragavendran A, Wessel G, De Paepe ME, Dennery PA. Single-cell transcriptomics reveals lasting changes in the lung cellular landscape into adulthood after neonatal hyperoxic exposure. Redox Biol 2021; 48:102091. [PMID: 34417156 PMCID: PMC8710996 DOI: 10.1016/j.redox.2021.102091] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/22/2021] [Accepted: 07/31/2021] [Indexed: 01/11/2023] Open
Abstract
Ventilatory support, such as supplemental oxygen, used to save premature infants impairs the growth of the pulmonary microvasculature and distal alveoli, leading to bronchopulmonary dysplasia (BPD). Although lung cellular composition changes with exposure to hyperoxia in neonatal mice, most human BPD survivors are weaned off oxygen within the first weeks to months of life, yet they may have persistent lung injury and pulmonary dysfunction as adults. We hypothesized that early-life hyperoxia alters the cellular landscape in later life and predicts long-term lung injury. Using single-cell RNA sequencing, we mapped lung cell subpopulations at postnatal day (pnd)7 and pnd60 in mice exposed to hyperoxia (95% O2) for 3 days as neonates. We interrogated over 10,000 cells and identified a total of 45 clusters within 32 cell states. Neonatal hyperoxia caused persistent compositional changes in later life (pnd60) in all five type II cell states with unique signatures and function. Premature infants requiring mechanical ventilation with different durations also showed similar alterations in these unique signatures of type II cell states. Pathologically, neonatal hyperoxic exposure caused alveolar simplification in adult mice. We conclude that neonatal hyperoxia alters the lung cellular landscape in later life, uncovering neonatal programing of adult lung dysfunction.
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Affiliation(s)
- Alejandro Scaffa
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI, United States
| | - Hongwei Yao
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI, United States
| | - Nathalie Oulhen
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI, United States
| | - Joselynn Wallace
- Center for Computational Biology of Human Disease and Center for Computation and Visualization, Brown University, Providence, RI, United States
| | - Abigail L Peterson
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI, United States
| | - Salu Rizal
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI, United States
| | - Ashok Ragavendran
- Center for Computational Biology of Human Disease and Center for Computation and Visualization, Brown University, Providence, RI, United States
| | - Gary Wessel
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI, United States
| | - Monique E De Paepe
- Department of Pathology, Women and Infants Hospital, Providence, RI, United States
| | - Phyllis A Dennery
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI, United States; Department of Pediatrics, Warren Alpert Medical School of Brown University, Providence, RI, United States.
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16
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Ningappa M, Adenuga M, Ngo KA, Mohamed N, Narayanan T, Prasadan K, Ashokkumar C, Das J, Schmitt L, Hartman H, Sehrawat A, Salgado CM, Reyes-Mugica M, Gittes GK, Lo CW, Subramaniam S, Sindhi R. Mechanisms of Impaired Lung Development and Ciliation in Mannosidase-1-Alpha-2 ( Man1a2) Mutants. Front Physiol 2021; 12:658518. [PMID: 34366878 PMCID: PMC8343402 DOI: 10.3389/fphys.2021.658518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/03/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Ciliary defects cause heterogenous phenotypes related to mutation burden which lead to impaired development. A previously reported homozygous deletion in the Man1a2 gene causes lethal respiratory failure in newborn pups and decreased lung ciliation compared with wild type (WT) pups. The effects of heterozygous mutation, and the potential for rescue are not known. PURPOSE We hypothesized that survival and lung ciliation, (a) would decrease progressively in Man1a2 +/- heterozygous and Man1a2 -/- null newborn pups compared with WT, and (b) could be enhanced by gestational treatment with N-Acetyl-cysteine (NAC), an antioxidant. METHODS Man1a2+/- adult mice were fed NAC or placebo from a week before breeding through gestation. Survival of newborn pups was monitored for 24 h. Lungs, liver and tails were harvested for morphology, genotyping, and transcriptional profiling. RESULTS Survival (p = 0.0001, Kaplan-Meier) and percent lung ciliation (p = 0.0001, ANOVA) measured by frequency of Arl13b+ respiratory epithelial cells decreased progressively, as hypothesized. Compared with placebo, gestational NAC treatment enhanced (a) lung ciliation in pups with each genotype, (b) survival in heterozygous pups (p = 0.017) but not in WT or null pups. Whole transcriptome of lung but not liver demonstrated patterns of up- and down-regulated genes that were identical in living heterozygous and WT pups, and completely opposite to those in dead heterozygous and null pups. Systems biology analysis enabled reconstruction of protein interaction networks that yielded functionally relevant modules and their interactions. In these networks, the mutant Man1a2 enzyme contributes to abnormal synthesis of proteins essential for lung development. The associated unfolded protein, hypoxic and oxidative stress responses can be mitigated with NAC. Comparisons with the developing human fetal lung transcriptome show that NAC likely restores normal vascular and epithelial tube morphogenesis in Man1a2 mutant mice. CONCLUSION Survival and lung ciliation in the Man1a2 mutant mouse, and its improvement with N-Acetyl cysteine is genotype-dependent. NAC-mediated rescue depends on the central role for oxidative and hypoxic stress in regulating ciliary function and organogenesis during development.
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Affiliation(s)
- Mylarappa Ningappa
- Hillman Center for Pediatric Transplantation, Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, United States
| | - Morayooluwa Adenuga
- Hillman Center for Pediatric Transplantation, Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, United States
| | - Kim A. Ngo
- Department of Bioengineering, University of California, San Diego, San Diego, La Jolla, CA, United States
| | - Nada Mohamed
- Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Tejaswini Narayanan
- Department of Bioengineering, University of California, San Diego, San Diego, La Jolla, CA, United States
| | - Krishna Prasadan
- Rangos Research Center Animal Imaging Core, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Chethan Ashokkumar
- Hillman Center for Pediatric Transplantation, Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, United States
| | - Jishnu Das
- Hillman Center for Pediatric Transplantation, Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, United States
- Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Lori Schmitt
- Histology Core Laboratory Manager, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Hannah Hartman
- Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Anuradha Sehrawat
- Division of Pediatric General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Claudia M. Salgado
- Division of Pediatric Pathology, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Miguel Reyes-Mugica
- Division of Pediatric Pathology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - George K. Gittes
- Surgeon-in-Chief Emeritus, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Cecilia W. Lo
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, San Diego, La Jolla, CA, United States
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, La Jolla, CA, United States
- Department of Computer Science and Engineering, and Nanoengineering, University of California, San Diego, San Diego, La Jolla, CA, United States
| | - Rakesh Sindhi
- Hillman Center for Pediatric Transplantation, Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, United States
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17
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Zhang X, Luo K, He X, Chen P. Association of vitamin D status at birth with pulmonary disease morbidity in very preterm infants. Pediatr Pulmonol 2021; 56:1215-1220. [PMID: 33331677 DOI: 10.1002/ppul.25233] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/17/2020] [Accepted: 12/12/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVE We aimed to assess whether serum 25-hydroxyvitamin D (25(OH)D) levels at birth are associated with pulmonary disease morbidities in very preterm infants. METHODS This prospective cohort analysis included 93 infants born before 32 weeks of gestation in the Second Xiangya Hospital of Central South University between March 2016 and February 2017. Participants were classified into three groups according to their 25(OH)D levels at birth. The groups were compared in terms of demographic variables and pulmonary disease morbidities. RESULTS The mean serum 25(OH)D level at birth was 35.7 ± 19.1 nmol/L, and 38 (40.9%), 31 (33.3%), and 24 (25.8%) infants had 25(OH)D levels of less than 25 nmol/L, 25-50 nmol/L, and more than or equal to 50 nmol/L, respectively. There was a statistically significant difference in neonatal respiratory distress syndrome (RDS) rates among the three groups (43.6% vs. 35.9% vs. 20.5%, p = .029). The rates of bronchopulmonary dysplasia, apnea, respiratory failure, persistent pulmonary hypertension, and pulmonary hemorrhage did not differ significantly among the groups. Logistic analysis, adjusted for gestational age and birth weight, showed that a low serum 25(OH)D level (<50 nmol/L) was a risk factor for RDS (odds ratio, 0.195; p = .017). CONCLUSION There was a high prevalence of low 25(OH)D levels (<50 nmol/L) and an association between vitamin D status and RDS in very preterm infants. However, more research on this association is required.
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Affiliation(s)
- Xuefei Zhang
- Division of Neonatology, Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Laboratory of Neonatal Disease, Institute of Pediatrics, Central South University, Changsha, Hunan, China
| | - Kaiju Luo
- Division of Neonatology, Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Laboratory of Neonatal Disease, Institute of Pediatrics, Central South University, Changsha, Hunan, China
| | - Xiaori He
- Division of Neonatology, Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Laboratory of Neonatal Disease, Institute of Pediatrics, Central South University, Changsha, Hunan, China
| | - Pingyang Chen
- Division of Neonatology, Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Laboratory of Neonatal Disease, Institute of Pediatrics, Central South University, Changsha, Hunan, China
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18
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Milanzi EB, Nkoka O, Kanje V, Ntenda PAM. Air pollution and non-communicable diseases in Sub-Saharan Africa. SCIENTIFIC AFRICAN 2021. [DOI: 10.1016/j.sciaf.2021.e00702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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19
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Goh KJ, Tan EK, Lu H, Roy S, Dunn NR. An NKX2-1 GFP and TP63 tdTomato dual fluorescent reporter for the investigation of human lung basal cell biology. Sci Rep 2021; 11:4712. [PMID: 33633173 PMCID: PMC7907081 DOI: 10.1038/s41598-021-83825-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 02/08/2021] [Indexed: 11/09/2022] Open
Abstract
Basal cells are multipotent stem cells responsible for the repair and regeneration of all the epithelial cell types present in the proximal lung. In mice, the elusive origins of basal cells and their contribution to lung development were recently revealed by high-resolution, lineage tracing studies. It however remains unclear if human basal cells originate and participate in lung development in a similar fashion, particularly with mounting evidence for significant species-specific differences in this process. To address this outstanding question, in the last several years differentiation protocols incorporating human pluripotent stem cells (hPSC) have been developed to produce human basal cells in vitro with varying efficiencies. To facilitate this endeavour, we introduced tdTomato into the human TP63 gene, whose expression specifically labels basal cells, in the background of a previously described hPSC line harbouring an NKX2-1GFP reporter allele. The functionality and specificity of the NKX2-1GFP;TP63tdTomato hPSC line was validated by directed differentiation into lung progenitors as well as more specialised lung epithelial subtypes using an organoid platform. This dual fluorescent reporter hPSC line will be useful for tracking, isolating and expanding basal cells from heterogenous differentiation cultures for further study.
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Affiliation(s)
- Kim Jee Goh
- Institute of Medical Biology, Agency for Science Technology and Research (A∗STAR), 8A Biomedical Grove, #06-06 Immunos, Singapore, 138648, Singapore
- Skin Research Institute of Singapore, 11 Mandalay Road #17-01 Clinical Sciences Building, Singapore, 308232, Singapore
| | - Ee Kim Tan
- Institute of Medical Biology, Agency for Science Technology and Research (A∗STAR), 8A Biomedical Grove, #06-06 Immunos, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Hao Lu
- Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Sudipto Roy
- Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore, 138673, Singapore
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, Singapore, 119288, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - N Ray Dunn
- Institute of Medical Biology, Agency for Science Technology and Research (A∗STAR), 8A Biomedical Grove, #06-06 Immunos, Singapore, 138648, Singapore.
- Skin Research Institute of Singapore, 11 Mandalay Road #17-01 Clinical Sciences Building, Singapore, 308232, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, Singapore, 308232, Singapore.
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20
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Bhattacharya S, Mereness JA, Baran AM, Misra RS, Peterson DR, Ryan RM, Reynolds AM, Pryhuber GS, Mariani TJ. Lymphocyte-Specific Biomarkers Associated With Preterm Birth and Bronchopulmonary Dysplasia. Front Immunol 2021; 11:563473. [PMID: 33552042 PMCID: PMC7859626 DOI: 10.3389/fimmu.2020.563473] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/07/2020] [Indexed: 01/11/2023] Open
Abstract
Many premature babies who are born with neonatal respiratory distress syndrome (RDS) go on to develop Bronchopulmonary Dysplasia (BPD) and later Post-Prematurity Respiratory Disease (PRD) at one year corrected age, characterized by persistent or recurrent lower respiratory tract symptoms frequently related to inflammation and viral infection. Transcriptomic profiles were generated from sorted peripheral blood CD8+ T cells of preterm and full-term infants enrolled with consent in the NHLBI Prematurity and Respiratory Outcomes Program (PROP) at the University of Rochester and the University at Buffalo. We identified outcome-related gene expression patterns following standard methods to identify markers for oxygen utilization and BPD as outcomes in extremely premature infants. We further identified predictor gene sets for BPD based on transcriptomic data adjusted for gestational age at birth (GAB). RNA-Seq analysis was completed for CD8+ T cells from 145 subjects. Among the subjects with highest risk for BPD (born at <29 weeks gestational age (GA); n=72), 501 genes were associated with oxygen utilization. In the same set of subjects, 571 genes were differentially expressed in subjects with a diagnosis of BPD and 105 genes were different in BPD subjects as defined by physiologic challenge. A set of 92 genes could predict BPD with a moderately high degree of accuracy. We consistently observed dysregulation of TGFB, NRF2, HIPPO, and CD40-associated pathways in BPD. Using gene expression data from both premature and full-term subjects (n=116), we identified a 28 gene set that predicted the PRD status with a moderately high level of accuracy, which also were involved in TGFB signaling. Transcriptomic data from sort-purified peripheral blood CD8+ T cells from 145 preterm and full-term infants identified sets of molecular markers of inflammation associated with independent development of BPD in extremely premature infants at high risk for the disease and of PRD among the preterm and full-term subjects.
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Affiliation(s)
- Soumyaroop Bhattacharya
- Division of Neonatology, Department of Pediatrics, University of Rochester, Rochester, NY, United States
| | - Jared A Mereness
- Division of Neonatology, Department of Pediatrics, University of Rochester, Rochester, NY, United States
| | - Andrea M Baran
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, United States
| | - Ravi S Misra
- Division of Neonatology, Department of Pediatrics, University of Rochester, Rochester, NY, United States
| | - Derick R Peterson
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, United States
| | - Rita M Ryan
- Department of Pediatrics, University at Buffalo, Buffalo, NY, United States.,Department of Pediatrics, Case Western Reserve University, Cleveland, OH, United States
| | | | - Gloria S Pryhuber
- Division of Neonatology, Department of Pediatrics, University of Rochester, Rochester, NY, United States
| | - Thomas J Mariani
- Division of Neonatology, Department of Pediatrics, University of Rochester, Rochester, NY, United States
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21
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Effect of Intrauterine Smoke Exposure on microRNA-15a Expression in Human Lung Development and Subsequent Asthma Risk. Healthcare (Basel) 2020; 8:healthcare8040536. [PMID: 33291534 PMCID: PMC7761806 DOI: 10.3390/healthcare8040536] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 11/16/2022] Open
Abstract
Background: In utero smoke (IUS) exposure is associated with asthma susceptibility. Objective: We sought to test the hypothesis that changes in miRNA expression by IUS exposure during human lung development is associated with asthma susceptibility. Methods: Gene expression was profiled from 53 IUS unexposed and 51 IUS exposed human fetal lung tissues. We tested for the differential expression of miRNAs across post-conception age and by IUS using linear models with covariate adjustment. We tested the IUS-associated miRNAs for association with their gene expression targets using pair-wise inverse correlation. Using our mouse model, we investigated the persistence of the IUS-associated miRNA signature using RT-PCR from the lungs of mouse pups with and without IUS at postnatal day 14. MiRNAs were then tested for association with asthma and exacerbations using whole blood gene expression profiles from Asthma BRIDGE. Results: Five miRNAs were differentially expressed across post-conception age (adjusted p < 0.0002) including two that were differentially expressed by IUS exposure in human fetal lung (p < 0.05). MiR-15a was differentially expressed by post-conception age (p = 0.00002), IUS exposure in human fetal lung (p = 0.005), and in the post-natal mouse lung (p = 0.01). MiR-15a was also associated with the in utero expression of GSDMB (adjusted p = 0.0002), a known childhood asthma gene and with asthma exacerbations (p = 0.0009) in Asthma BRIDGE. Thus, miR-15a is expressed during human lung development, is impacted by IUS exposure, regulates the intrauterine expression of asthma genes, and is associated with asthma severity. Conclusions: These results provide evidence for the role of miR-15a in the fetal origin of asthma.
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22
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Abstract
There is a wide differential diagnosis of early onset respiratory distress especially in term babies, and interstitial lung disease (chILD) is a rare but important consideration in this context. chILD manifesting immediately after birth is usually related to mutations in surfactant protein genes, or conditions related to the Congenital Acinar Dysplasia -Alveolar capillary dysplasia - Congenital Alveolar Dysplasia (CAD-ACD) spectrum. There is currently no specific treatment for these conditions, and management is supportive. Prognosis is very poor in most of these babies if onset is early, with relentless respiratory deterioration unless transplanted. Ideally, the diagnosis is made on genetic analysis, but this may be time-consuming and complex in CAD-ACD spectrum, so lung biopsy may be needed to avoid prolonged and futile treatment being instituted. Milder forms with prolonged survival have been reported. Early onset, less severe chILD is usually related to neuroendocrine cell hyperplasia of infancy (NEHI), pulmonary interstitial glycogenosis (PIG) and less severe disorders of surfactant proteins. PIG and NEHI are not specific entities, but are pulmonary dysmaturity syndromes, and there may be a number of underlying genetic and other cause. If the child is stable and thriving, many will not be subject to lung biopsy, and slow improvement and weaning of supplemental oxygen can be anticipated. Where possible, a precise genetic diagnosis should be made in early onset cHILD allow for genetic counselling. chILD survivors and their families have complex respiratory and other needs, and co-ordinated, multi-disciplinary support in the community is essential.
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Affiliation(s)
- Andrew Bush
- Imperial College, UK; Royal Brompton and Harefield NHS Foundation Trust, UK.
| | | | - Jo Gregory
- Royal Brompton and Harefield NHS Foundation Trust, UK
| | - Andrew Gordon Nicholson
- Royal Brompton and Harefield NHS Foundation Trust, UK; National Heart and Lung Institute, Imperial College, UK
| | - Thomas Semple
- Imperial College, UK; Royal Brompton and Harefield NHS Foundation Trust, UK
| | - Rishi Pabary
- Imperial College, UK; Royal Brompton and Harefield NHS Foundation Trust, UK
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23
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Kunisaki SM, Jiang G, Biancotti JC, Ho KKY, Dye BR, Liu AP, Spence JR. Human induced pluripotent stem cell-derived lung organoids in an ex vivo model of the congenital diaphragmatic hernia fetal lung. Stem Cells Transl Med 2020; 10:98-114. [PMID: 32949227 PMCID: PMC7780804 DOI: 10.1002/sctm.20-0199] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/03/2020] [Accepted: 08/09/2020] [Indexed: 01/06/2023] Open
Abstract
Three‐dimensional lung organoids (LOs) derived from pluripotent stem cells have the potential to enhance our understanding of disease mechanisms and to enable novel therapeutic approaches in neonates with pulmonary disorders. We established a reproducible ex vivo model of lung development using transgene‐free human induced pluripotent stem cells generated from fetuses and infants with Bochdalek congenital diaphragmatic hernia (CDH), a polygenic disorder associated with fetal lung compression and pulmonary hypoplasia at birth. Molecular and cellular comparisons of CDH LOs revealed impaired generation of NKX2.1+ progenitors, type II alveolar epithelial cells, and PDGFRα+ myofibroblasts. We then subjected these LOs to disease relevant mechanical cues through ex vivo compression and observed significant changes in genes associated with pulmonary progenitors, alveolar epithelial cells, and mesenchymal fibroblasts. Collectively, these data suggest both primary cell‐intrinsic and secondary mechanical causes of CDH lung hypoplasia and support the use of this stem cell‐based approach for disease modeling in CDH.
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Affiliation(s)
- Shaun M Kunisaki
- Department of Surgery, Johns Hopkins University, Baltimore, Maryland, USA.,Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Guihua Jiang
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Juan C Biancotti
- Department of Surgery, Johns Hopkins University, Baltimore, Maryland, USA.,Institute for Cell Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Kenneth K Y Ho
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Briana R Dye
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
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24
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Steiner LA, Getman M, Schiralli Lester GM, Iqbal MA, Katzman P, Szafranski P, Stankiewicz P, Bhattacharya S, Mariani T, Pryhuber G, Lin X, Young JL, Dean DA, Scheible K. Disruption of normal patterns of FOXF1 expression in a lethal disorder of lung development. J Med Genet 2019; 57:296-300. [PMID: 31662342 DOI: 10.1136/jmedgenet-2019-106095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 09/06/2019] [Accepted: 09/13/2019] [Indexed: 01/22/2023]
Abstract
BACKGROUND Alveolar capillary dysplasia with misalignment of the pulmonary veins (ACDMPV) is a lethal disorder of lung development. ACDMPV is associated with haploinsufficiency of the transcription factor FOXF1, which plays an important role in the development of the lung and intestine. CNVs upstream of the FOXF1 gene have also been associated with an ACDMPV phenotype, but mechanism(s) by which these deletions disrupt lung development are not well understood. The objective of our study is to gain insights into the mechanisms by which CNVs contribute to an ACDMPV phenotype. METHODS We analysed primary lung tissue from an infant with classic clinical and histological findings of ACDMPV and harboured a 340 kb deletion on chromosome 16q24.1 located 250 kb upstream of FOXF1. RESULTS In RNA generated from paraffin-fixed lung sections, our patient had lower expression of FOXF1 than age-matched controls. He also had an abnormal pattern of FOXF1 protein expression, with a dramatic loss of FOXF1 expression in the lung. To gain insights into the mechanisms underlying these changes, we assessed the epigenetic landscape using chromatin immunoprecipitation, which demonstrated loss of histone H3 lysine 27 acetylation (H3K27Ac), an epigenetic mark of active enhancers, in the region of the deletion. CONCLUSIONS Together, these data suggest that the deletion disrupts an enhancer responsible for directing FOXF1 expression in the developing lung and provide novel insights into the mechanisms underlying a fatal developmental lung disorder.
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Affiliation(s)
| | - Michael Getman
- Pediatrics, University of Rochester, Rochester, New York, USA
| | | | - M Anwar Iqbal
- Pediatrics, University of Rochester, Rochester, New York, USA
| | - Philip Katzman
- Pathology, University of Rochester, Rochester, New York, USA
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Thomas Mariani
- Division of Neonatology and Center for Pediatric Biomedical Research, University of Rochester, Rochester, New York, USA
| | - Gloria Pryhuber
- Pediatrics, University of Rochester, Rochester, New York, USA
| | - Xin Lin
- Pediatrics, University of Rochester, Rochester, New York, USA
| | | | - David A Dean
- Pediatrics, University of Rochester, Rochester, New York, USA
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25
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Spadafora R, Lu J, Khetani RS, Zhang C, Iberg A, Li H, Shi Y, Lerou PH. Lung-Resident Mesenchymal Stromal Cells Reveal Transcriptional Dynamics of Lung Development in Preterm Infants. Am J Respir Crit Care Med 2019; 198:961-964. [PMID: 29757681 DOI: 10.1164/rccm.201801-0024le] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
| | - Junjie Lu
- 2 Massachusetts General Hospital Boston, Massachusetts
| | | | | | - Aimee Iberg
- 5 Boston Children's Hospital Boston, Massachusetts
| | - Hu Li
- 4 Mayo Clinic Rochester, Minnesota and
| | - Yang Shi
- 5 Boston Children's Hospital Boston, Massachusetts
| | - Paul H Lerou
- 2 Massachusetts General Hospital Boston, Massachusetts
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26
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Preventing bronchopulmonary dysplasia: new tools for an old challenge. Pediatr Res 2019; 85:432-441. [PMID: 30464331 DOI: 10.1038/s41390-018-0228-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 09/12/2018] [Accepted: 09/25/2018] [Indexed: 12/12/2022]
Abstract
Bronchopulmonary dysplasia (BPD) is the most prevalent chronic lung disease in infants and presents as a consequence of preterm birth. Due to the lack of effective preventive and treatment strategies, BPD currently represents a major therapeutic challenge that requires continued research efforts at the basic, translational, and clinical levels. However, not all very low birth weight premature babies develop BPD, which suggests that in addition to known gestational age and intrauterine and extrauterine risk factors, other unknown factors must be involved in this disease's development. One of the main goals in BPD research is the early prediction of very low birth weight infants who are at risk of developing BPD in order to initiate the adequate preventive strategies. Other benefits of determining the risk of BPD include providing prognostic information and stratifying infants for clinical trial enrollment. In this article, we describe new opportunities to address BPD's complex pathophysiology by identifying prognostic biomarkers and develop novel, complex in vitro human lung models in order to develop effective therapies. These therapies for protecting the immature lung from injury can be developed by taking advantage of recent scientific progress in -omics, 3D organoids, and regenerative medicine.
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27
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Ustun N, Eyerci N, Karadag N, Yesilyurt A, Zenciroglu A, Okumus N. Association of vitamin D receptor gene FokI and TaqI polymorphisms and risk of RDS. J Matern Fetal Neonatal Med 2019; 33:3640-3646. [PMID: 30760068 DOI: 10.1080/14767058.2019.1582629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Background: Vitamin D and its receptor (VDR) have important roles in perinatal lung development. The objective of this study was to investigate the possible association between VDR FokI and TaqI polymorphism and development of respiratory distress syndrome (RDS) in preterm infants.Method: A total of 173 premature infants <34 weeks: 82 with RDS and 91 without RDS were enrolled. Genotyping of VDR polymorphisms was assayed by real-time PCR. Serum 25-hydroxyvitamin D (25-OHD) levels were measured by ELISA in blood samples that were obtained at the time of admission to the neonatal intensive care unit.Results: Gestational age (GA) was significantly lower in the RDS group compared with the controls. In univariate analysis, VDR TaqI CT and CC genotypes were associated with the increased risk of RDS (OR = 3.264, p = .001, 95% CI = 1.597-6.672 and OR = 5.222, p < .001, 95% CI = 2.165-12.597, respectively); while VDR FokI showed no association with RDS. In multivariate logistic regression analysis, variant TaqI genotype increased risk of RDS (p = 0.001, OR = 3.464, 95% CI = 1.655-7.251) independent of gestational age, birth weight and gender. 25-OHD levels in the RDS group were significantly lower compared with those in without the RDS group (p = .002). Serum 25-OHD levels were not significantly different among the different FokI and TaqI genotypes in RDS group.Conclusions: This is the first report of association of VDR polymorphism with RDS development in preterm neonates. Current study suggests that VDR TaqI polymorphism may be involved in predisposition to RDS in premature neonates. Further studies are needed to assess the contribution of vitamin D and VDR signaling to the pathogenesis RDS.
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Affiliation(s)
- Nuran Ustun
- Department of Neonatology, Dr Sami Ulus Maternity and Children's Training and Research Hospital, Ankara, Turkey
| | - Nilnur Eyerci
- Department of Genetics, Dıskapı Yıldırım Beyazıt Education and Training Hospital, Ankara, Turkey
| | - Nilgun Karadag
- Department of Neonatology, Dr Sami Ulus Maternity and Children's Training and Research Hospital, Ankara, Turkey
| | - Ahmet Yesilyurt
- Department of Genetics, Dıskapı Yıldırım Beyazıt Education and Training Hospital, Ankara, Turkey
| | - Aysegul Zenciroglu
- Department of Neonatology, Dr Sami Ulus Maternity and Children's Training and Research Hospital, Ankara, Turkey
| | - Nurullah Okumus
- Department of Neonatology, Dr Sami Ulus Maternity and Children's Training and Research Hospital, Ankara, Turkey
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28
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Frey U, Usemann J. Addressing the complexity of prenatal and postnatal environmental exposures affecting childhood lung function. Lancet Planet Health 2019; 3:e51-e52. [PMID: 30737193 DOI: 10.1016/s2542-5196(19)30011-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Urs Frey
- University Children's Hospital Basel (UKBB), 4056 Basel, Switzerland.
| | - Jakob Usemann
- University Children's Hospital Basel (UKBB), 4056 Basel, Switzerland; Division of Respiratory Medicine, University Children's Hospital Zurich, Zurich, Switzerland; University of Basel, Basel, Switzerland
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29
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Single cell RNA analysis identifies cellular heterogeneity and adaptive responses of the lung at birth. Nat Commun 2019; 10:37. [PMID: 30604742 PMCID: PMC6318311 DOI: 10.1038/s41467-018-07770-1] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 11/19/2018] [Indexed: 12/12/2022] Open
Abstract
The respiratory system undergoes a diversity of structural, biochemical, and functional changes necessary for adaptation to air breathing at birth. To identify the heterogeneity of pulmonary cell types and dynamic changes in gene expression mediating adaptation to respiration, here we perform single cell RNA analyses of mouse lung on postnatal day 1. Using an iterative cell type identification strategy we unbiasedly identify the heterogeneity of murine pulmonary cell types. We identify distinct populations of epithelial, endothelial, mesenchymal, and immune cells, each containing distinct subpopulations. Furthermore we compare temporal changes in RNA expression patterns before and after birth to identify signaling pathways selectively activated in specific pulmonary cell types, including activation of cell stress and the unfolded protein response during perinatal adaptation of the lung. The present data provide a single cell view of the adaptation to air breathing after birth. The respiratory system is transformed in terms of functional change at birth to adapt to breathing air. Here, the authors examine the molecular changes behind the first breath in the mouse by Drop-seq based RNA sequencing, identifying activation of the unfolded protein response as a perinatal adaptation of the lung.
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30
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Danopoulos S, Thornton ME, Grubbs BH, Frey MR, Warburton D, Bellusci S, Al Alam D. Discordant roles for FGF ligands in lung branching morphogenesis between human and mouse. J Pathol 2018; 247:254-265. [PMID: 30357827 DOI: 10.1002/path.5188] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/26/2018] [Accepted: 10/18/2018] [Indexed: 01/08/2023]
Abstract
Fibroblast growth factor (FGF) signaling plays an important role in lung organogenesis. Over recent decades, FGF signaling in lung development has been extensively studied in animal models. However, little is known about the expression, localization, and functional roles of FGF ligands during human fetal lung development. Therefore, we aimed to determine the expression and function of several FGF ligands and receptors in human lung development. Using in situ hybridization (ISH) and RNA sequencing, we assessed their expression and distribution in native human fetal lung. Human fetal lung explants were treated with recombinant FGF7, FGF9, or FGF10 in air-liquid interface culture. Explants were analyzed grossly to observe differences in branching pattern as well as at the cellular and molecular level. ISH demonstrated that FGF7 is expressed in both the epithelium and mesenchyme; FGF9 is mainly localized in the distal epithelium, whereas FGF10 demonstrated diffuse expression throughout the parenchyma, with some expression in the smooth muscle cells (SMCs). FGFR2 expression was high in both proximal and distal epithelial cells as well as the SMCs. FGFR3 was expressed mostly in the epithelial cells, with lower expression in the mesenchyme, while FGFR4 was highly expressed throughout the mesenchyme and in the distal epithelium. Using recombinant FGFs, we demonstrated that FGF7 and FGF9 had similar effects on human fetal lung as on mouse fetal lung; however, FGF10 caused the human explants to expand and form cysts as opposed to inducing epithelial branching as seen in the mouse. In conjunction with decreased branching, treatment with recombinant FGF7, FGF9, and FGF10 also resulted in decreased double-positive SOX2/SOX9 progenitor cells, which are exclusively present in the distal epithelial tips in early human fetal lung. Although FGF ligand localization may be somewhat comparable between developing mouse and human lungs, their functional roles may differ substantially. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Soula Danopoulos
- Department of Pediatric Surgery, Developmental Biology and Regenerative Medicine Program, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA.,Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Matthew E Thornton
- Department of Obstetrics and Gynecology, Maternal Fetal Medicine Division, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Brendan H Grubbs
- Department of Pediatric Surgery, Developmental Biology and Regenerative Medicine Program, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA.,Department of Obstetrics and Gynecology, Maternal Fetal Medicine Division, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Mark R Frey
- Department of Pediatric Surgery, Developmental Biology and Regenerative Medicine Program, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA.,Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David Warburton
- Department of Pediatric Surgery, Developmental Biology and Regenerative Medicine Program, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA.,Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Saverio Bellusci
- Department of Pediatric Surgery, Developmental Biology and Regenerative Medicine Program, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA.,Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Excellence Cluster Cardio-Pulmonary System (ECCPS), Universities of Giessen and Marburg Lung Center (UGMLC), Justus-Liebig-University Giessen, German Center for Lung Research (DZL), Giessen, Germany
| | - Denise Al Alam
- Department of Pediatric Surgery, Developmental Biology and Regenerative Medicine Program, The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA.,Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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31
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Hamvas A, Feng R, Bi Y, Wang F, Bhattacharya S, Mereness J, Kaushal M, Cotten CM, Ballard PL, Mariani TJ. Exome sequencing identifies gene variants and networks associated with extreme respiratory outcomes following preterm birth. BMC Genet 2018; 19:94. [PMID: 30342483 PMCID: PMC6195962 DOI: 10.1186/s12863-018-0679-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 10/01/2018] [Indexed: 12/28/2022] Open
Abstract
Background Previous studies have identified genetic variants associated with bronchopulmonary dysplasia (BPD) in extremely preterm infants. However, findings with genome-wide significance have been rare, and not replicated. We hypothesized that whole exome sequencing (WES) of premature subjects with extremely divergent phenotypic outcomes could facilitate the identification of genetic variants or gene networks contributing disease risk. Results The Prematurity and Respiratory Outcomes Program (PROP) recruited a cohort of > 765 extremely preterm infants for the identification of markers of respiratory morbidity. We completed WES on 146 PROP subjects (85 affected, 61 unaffected) representing extreme phenotypes of early respiratory morbidity. We tested for association between disease status and individual common variants, screened for rare variants exclusive to either affected or unaffected subjects, and tested the combined association of variants across gene loci. Pathway analysis was performed and disease-related expression patterns were assessed. Marginal association with BPD was observed for numerous common and rare variants. We identified 345 genes with variants unique to BPD-affected preterm subjects, and 292 genes with variants unique to our unaffected preterm subjects. Of these unique variants, 28 (19 in the affected cohort and 9 in unaffected cohort) replicate a prior WES study of BPD-associated variants. Pathway analysis of sets of variants, informed by disease-related gene expression, implicated protein kinase A, MAPK and Neuregulin/epidermal growth factor receptor signaling. Conclusions We identified novel genes and associated pathways that may play an important role in susceptibility/resilience for the development of lung disease in preterm infants. Electronic supplementary material The online version of this article (10.1186/s12863-018-0679-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aaron Hamvas
- Department of Pediatrics, Northwestern University, Chicago, IL, USA. .,Ann and Robert H. Lurie Children's Hospital of Chicago and Northwestern University, Chicago, IL, USA.
| | - Rui Feng
- Department of Biostatistics, University of Pennsylvania, Philadelphia, PA, USA
| | - Yingtao Bi
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Fan Wang
- Department of Biostatistics, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jared Mereness
- Department of Pediatrics, University of Rochester, Rochester, NY, USA
| | - Madhurima Kaushal
- Center for Biomedical Informatics, Washington University, St. Louis, MO, USA
| | | | - Philip L Ballard
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Thomas J Mariani
- Department of Pediatrics, University of Rochester, Rochester, NY, USA. .,Division of Neonatology and Pediatric Molecular and Personalized Medicine Program University of Rochester Medical Center, 601 Elmwood Ave, Box 850, Rochester, NY, 14642, USA.
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Modepalli V, Kumar A, Sharp JA, Saunders NR, Nicholas KR, Lefèvre C. Gene expression profiling of postnatal lung development in the marsupial gray short-tailed opossum (Monodelphis domestica) highlights conserved developmental pathways and specific characteristics during lung organogenesis. BMC Genomics 2018; 19:732. [PMID: 30290757 PMCID: PMC6173930 DOI: 10.1186/s12864-018-5102-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 09/21/2018] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND After a short gestation, marsupials give birth to immature neonates with lungs that are not fully developed and in early life the neonate partially relies on gas exchange through the skin. Therefore, significant lung development occurs after birth in marsupials in contrast to eutherian mammals such as humans and mice where lung development occurs predominantly in the embryo. To explore the mechanisms of marsupial lung development in comparison to eutherians, morphological and gene expression analysis were conducted in the gray short-tailed opossum (Monodelphis domestica). RESULTS Postnatal lung development of Monodelphis involves three key stages of development: (i) transition from late canalicular to early saccular stages, (ii) saccular and (iii) alveolar stages, similar to developmental stages overlapping the embryonic and perinatal period in eutherians. Differentially expressed genes were identified and correlated with developmental stages. Functional categories included growth factors, extracellular matrix protein (ECMs), transcriptional factors and signalling pathways related to branching morphogenesis, alveologenesis and vascularisation. Comparison with published data on mice highlighted the conserved importance of extracellular matrix remodelling and signalling pathways such as Wnt, Notch, IGF, TGFβ, retinoic acid and angiopoietin. The comparison also revealed changes in the mammalian gene expression program associated with the initiation of alveologenesis and birth, pointing to subtle differences between the non-functional embryonic lung of the eutherian mouse and the partially functional developing lung of the marsupial Monodelphis neonates. The data also highlighted a subset of contractile proteins specifically expressed in Monodelphis during and after alveologenesis. CONCLUSION The results provide insights into marsupial lung development and support the potential of the marsupial model of postnatal development towards better understanding of the evolution of the mammalian bronchioalveolar lung.
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Affiliation(s)
| | - Amit Kumar
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Julie A Sharp
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Australia.,Institute of Frontiers Materials, Deakin University, Pigdons Road, Geelong, VIC, Australia
| | - Norman R Saunders
- Department of Pharmacology and Therapeutics, The University of Melbourne, Melbourne, Australia
| | - Kevin R Nicholas
- School of Medicine, Deakin University, Pigdons Road, Geelong, VIC, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, Australia.,Monash Institute of Pharmaceutical Science, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Christophe Lefèvre
- School of Medicine, Deakin University, Pigdons Road, Geelong, VIC, Australia. .,Division of Bioinformatics, Walter and Eliza Hall Medical Research Institute, Melbourne, Australia. .,Department of Pharmacology and Therapeutics, The University of Melbourne, Melbourne, Australia. .,Peter MacCallum Cancer Centre, Melbourne, Australia.
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Kyle JE, Clair G, Bandyopadhyay G, Misra RS, Zink EM, Bloodsworth KJ, Shukla AK, Du Y, Lillis J, Myers JR, Ashton J, Bushnell T, Cochran M, Deutsch G, Baker ES, Carson JP, Mariani TJ, Xu Y, Whitsett JA, Pryhuber G, Ansong C. Cell type-resolved human lung lipidome reveals cellular cooperation in lung function. Sci Rep 2018; 8:13455. [PMID: 30194354 PMCID: PMC6128932 DOI: 10.1038/s41598-018-31640-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/26/2018] [Indexed: 12/21/2022] Open
Abstract
Cell type-resolved proteome analyses of the brain, heart and liver have been reported, however a similar effort on the lipidome is currently lacking. Here we applied liquid chromatography-tandem mass spectrometry to characterize the lipidome of major lung cell types isolated from human donors, representing the first lipidome map of any organ. We coupled this with cell type-resolved proteomics of the same samples (available at Lungmap.net). Complementary proteomics analyses substantiated the functional identity of the isolated cells. Lipidomics analyses showed significant variations in the lipidome across major human lung cell types, with differences most evident at the subclass and intra-subclass (i.e. total carbon length of the fatty acid chains) level. Further, lipidomic signatures revealed an overarching posture of high cellular cooperation within the human lung to support critical functions. Our complementary cell type-resolved lipid and protein datasets serve as a rich resource for analyses of human lung function.
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Affiliation(s)
- Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Geremy Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Gautam Bandyopadhyay
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Ravi S Misra
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Erika M Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kent J Bloodsworth
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Anil K Shukla
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yina Du
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Jacquelyn Lillis
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Jason R Myers
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - John Ashton
- Genomics Research Center, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Timothy Bushnell
- Flow Cytometry Core Facility, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Matthew Cochran
- Flow Cytometry Core Facility, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Gail Deutsch
- Department of Pathology, Seattle Children's Hospital, Seattle, WA, 98105, USA
| | - Erin S Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - James P Carson
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, 78712, USA
| | - Thomas J Mariani
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Yan Xu
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Jeffrey A Whitsett
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Gloria Pryhuber
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Rochester, NY, 14642, USA
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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Nikolić MZ, Sun D, Rawlins EL. Human lung development: recent progress and new challenges. Development 2018; 145:145/16/dev163485. [PMID: 30111617 PMCID: PMC6124546 DOI: 10.1242/dev.163485] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recent studies have revealed biologically significant differences between human and mouse lung development, and have reported new in vitro systems that allow experimental manipulation of human lung models. At the same time, emerging clinical data suggest that the origins of some adult lung diseases are found in embryonic development and childhood. The convergence of these research themes has fuelled a resurgence of interest in human lung developmental biology. In this Review, we discuss our current understanding of human lung development, which has been profoundly influenced by studies in mice and, more recently, by experiments using in vitro human lung developmental models and RNA sequencing of human foetal lung tissue. Together, these approaches are helping to shed light on the mechanisms underlying human lung development and disease, and may help pave the way for new therapies. Summary: This Review describes how recent technological advances have shed light on the mechanisms underlying human lung development and disease, and outlines the future challenges in this field.
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Affiliation(s)
- Marko Z Nikolić
- Wellcome Trust/CRUK Gurdon Institute, Wellcome Trust/MRC Stem Cell Institute, Department of Pathology, University of Cambridge, Cambridge CB2 1QN, UK.,University of Cambridge School of Clinical Medicine, Department of Medicine, Cambridge CB2 0QQ, UK
| | - Dawei Sun
- Wellcome Trust/CRUK Gurdon Institute, Wellcome Trust/MRC Stem Cell Institute, Department of Pathology, University of Cambridge, Cambridge CB2 1QN, UK
| | - Emma L Rawlins
- Wellcome Trust/CRUK Gurdon Institute, Wellcome Trust/MRC Stem Cell Institute, Department of Pathology, University of Cambridge, Cambridge CB2 1QN, UK
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35
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Bandyopadhyay G, Huyck HL, Misra RS, Bhattacharya S, Wang Q, Mereness J, Lillis J, Myers JR, Ashton J, Bushnell T, Cochran M, Holden-Wiltse J, Katzman P, Deutsch G, Whitsett JA, Xu Y, Mariani TJ, Pryhuber GS. Dissociation, cellular isolation, and initial molecular characterization of neonatal and pediatric human lung tissues. Am J Physiol Lung Cell Mol Physiol 2018; 315:L576-L583. [PMID: 29975103 DOI: 10.1152/ajplung.00041.2018] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Human lung morphogenesis begins by embryonic life and continues after birth into early childhood to form a complex organ with numerous morphologically and functionally distinct cell types. Pulmonary organogenesis involves dynamic changes in cell proliferation, differentiation, and migration of specialized cells derived from diverse embryonic lineages. Studying the molecular and cellular processes underlying formation of the fully functional lung requires isolating distinct pulmonary cell populations during development. We now report novel methods to isolate four major pulmonary cell populations from pediatric human lung simultaneously. Cells were dissociated by protease digestion of neonatal and pediatric lung and isolated on the basis of unique cell membrane protein expression patterns. Epithelial, endothelial, nonendothelial mesenchymal, and immune cells were enriched by fluorescence-activated cell sorting. Dead cells and erythrocytes were excluded by 7-aminoactinomycin D uptake and glycophorin-A (CD235a) expression, respectively. Leukocytes were identified by membrane CD45 (protein tyrosine phosphatase, receptor type C), endothelial cells by platelet endothelial cell adhesion molecule-1 (CD31) and vascular endothelial cadherin (CD144), and both were isolated. Thereafter, epithelial cell adhesion molecule (CD326)-expressing cells were isolated from the endothelial- and immune cell-depleted population to enrich epithelial cells. Cells lacking these membrane markers were collected as "nonendothelial mesenchymal" cells. Quantitative RT-PCR and RNA sequencing analyses of population specific transcriptomes demonstrate the purity of the subpopulations of isolated cells. The method efficiently isolates major human lung cell populations that we announce are now available through the National Heart, Lung, and Blood Institute Lung Molecular Atlas Program (LungMAP) for their further study.
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Affiliation(s)
- Gautam Bandyopadhyay
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center , Rochester, New York
| | - Heidie L Huyck
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center , Rochester, New York
| | - Ravi S Misra
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center , Rochester, New York
| | - Soumyaroop Bhattacharya
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center , Rochester, New York.,Program in Pediatric Molecular and Personalized Medicine, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Qian Wang
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center , Rochester, New York.,Program in Pediatric Molecular and Personalized Medicine, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Jared Mereness
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center , Rochester, New York.,Program in Pediatric Molecular and Personalized Medicine, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Jacquelyn Lillis
- University of Rochester Genomics Research Center, University of Rochester Medical Center , Rochester, New York
| | - Jason R Myers
- University of Rochester Genomics Research Center, University of Rochester Medical Center , Rochester, New York
| | - John Ashton
- University of Rochester Genomics Research Center, University of Rochester Medical Center , Rochester, New York
| | - Timothy Bushnell
- University of Rochester Flow Cytometry Core Facility, University of Rochester Medical Center , Rochester, New York
| | - Matthew Cochran
- University of Rochester Flow Cytometry Core Facility, University of Rochester Medical Center , Rochester, New York
| | - Jeanne Holden-Wiltse
- University of Rochester Biocomputational Center, University of Rochester Medical Center , Rochester, New York
| | - Philip Katzman
- Department of Pathology, University of Rochester Medical Center , Rochester, New York
| | - Gail Deutsch
- Department of Pathology, Seattle Children's Hospital, University of Washington , Seattle, Washington
| | - Jeffrey A Whitsett
- Division of Neonatology, Perinatal and Pulmonary Biology Cincinnati Children's Hospital Medical Center , Cincinnati, Ohio
| | - Yan Xu
- Division of Neonatology, Perinatal and Pulmonary Biology Cincinnati Children's Hospital Medical Center , Cincinnati, Ohio
| | - Thomas J Mariani
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center , Rochester, New York.,Program in Pediatric Molecular and Personalized Medicine, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Gloria S Pryhuber
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center , Rochester, New York
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36
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Moghieb A, Clair G, Mitchell HD, Kitzmiller J, Zink EM, Kim YM, Petyuk V, Shukla A, Moore RJ, Metz TO, Carson J, McDermott JE, Corley RA, Whitsett JA, Ansong C. Time-resolved proteome profiling of normal lung development. Am J Physiol Lung Cell Mol Physiol 2018; 315:L11-L24. [PMID: 29516783 PMCID: PMC6087896 DOI: 10.1152/ajplung.00316.2017] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 01/31/2018] [Accepted: 03/01/2018] [Indexed: 12/20/2022] Open
Abstract
Biochemical networks mediating normal lung morphogenesis and function have important implications for ameliorating morbidity and mortality in premature infants. Although several transcript-level studies have examined normal lung development, corresponding protein-level analyses are lacking. Here we performed proteomics analysis of murine lungs from embryonic to early adult ages to identify the molecular networks mediating normal lung development. We identified 8,932 proteins, providing a deep and comprehensive view of the lung proteome. Analysis of the proteomics data revealed discrete modules and the underlying regulatory and signaling network modulating their expression during development. Our data support the cell proliferation that characterizes early lung development and highlight responses of the lung to exposure to a nonsterile oxygen-rich ambient environment and the important role of lipid (surfactant) metabolism in lung development. Comparison of dynamic regulation of proteomic and recent transcriptomic analyses identified biological processes under posttranscriptional control. Our study provides a unique proteomic resource for understanding normal lung formation and function and can be freely accessed at Lungmap.net.
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Affiliation(s)
- Ahmed Moghieb
- Biological Science Division, Pacific Northwest National Laboratory , Richland, Washington
| | - Geremy Clair
- Biological Science Division, Pacific Northwest National Laboratory , Richland, Washington
| | - Hugh D Mitchell
- Biological Science Division, Pacific Northwest National Laboratory , Richland, Washington
| | - Joseph Kitzmiller
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center , Cincinnati, Ohio
| | - Erika M Zink
- Biological Science Division, Pacific Northwest National Laboratory , Richland, Washington
| | - Young-Mo Kim
- Biological Science Division, Pacific Northwest National Laboratory , Richland, Washington
| | - Vladislav Petyuk
- Biological Science Division, Pacific Northwest National Laboratory , Richland, Washington
| | - Anil Shukla
- Biological Science Division, Pacific Northwest National Laboratory , Richland, Washington
| | - Ronald J Moore
- Biological Science Division, Pacific Northwest National Laboratory , Richland, Washington
| | - Thomas O Metz
- Biological Science Division, Pacific Northwest National Laboratory , Richland, Washington
| | - James Carson
- Texas Advanced Computing Center, University of Texas at Austin , Austin, Texas
| | - Jason E McDermott
- Biological Science Division, Pacific Northwest National Laboratory , Richland, Washington
| | - Richard A Corley
- Biological Science Division, Pacific Northwest National Laboratory , Richland, Washington
| | - Jeffrey A Whitsett
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center , Cincinnati, Ohio
| | - Charles Ansong
- Biological Science Division, Pacific Northwest National Laboratory , Richland, Washington
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37
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Zhang FY, Yang N, Rao YF, Du WH, Hao HS, Zhao XM, Zhu HB, Liu Y. Profiling of miRNAs in neonatal cloned bovines with collapsed lungs and respiratory distress. Reprod Domest Anim 2018; 53:550-555. [DOI: 10.1111/rda.13144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 12/28/2017] [Indexed: 01/05/2023]
Affiliation(s)
- FY Zhang
- Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
- College of Biological Sciences; China Agricultural University; Beijing China
| | - N Yang
- Laboratory of Zoonosis of Liaoning Province; College of Animal Science & Veterinary Medicine; Shenyang Agricultural University; Shenyang Liaoning China
| | - YF Rao
- Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - WH Du
- Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - HS Hao
- Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - XM Zhao
- Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - HB Zhu
- Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - Y Liu
- Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
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Abstract
The onset of chronic obstructive pulmonary disease (COPD) can arise either from failure to attain the normal spirometric plateau or from an accelerated decline in lung function. Despite reports from numerous big cohorts, no single adult life factor, including smoking, accounts for this accelerated decline. By contrast, five childhood risk factors (maternal and paternal asthma, maternal smoking, childhood asthma and respiratory infections) are strongly associated with an accelerated rate of lung function decline and COPD. Among adverse effects on lung development are transgenerational (grandmaternal smoking), antenatal (exposure to tobacco and pollution), and early childhood (exposure to tobacco and pollution including pesticides) factors. Antenatal adverse events can operate by causing structural changes in the developing lung, causing low birth weight and prematurity and altered immunological responses. Also important are mode of delivery, early microbiological exposures, and multiple early atopic sensitizations. Early bronchial hyperresponsiveness, before any evidence of airway inflammation, is associated with adverse respiratory outcomes. Overlapping cohort studies established that spirometry tracks from the preschool years to late middle age, and those with COPD in the sixth decade already had the worst spirometry at age 10 years. Alveolar development is now believed to continue throughout somatic growth and is adversely impacted by early tobacco smoke exposure. Genetic factors are also important, with genes important in lung development and early wheezing also being implicated in COPD. The inescapable conclusion is that the roots of COPD are in early life, and COPD is a disease of childhood adverse factors interacting with genetic factors.
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Yu RQ, Chen DZ, Zhou Q, Wang M, Mei YZ, Jiang SY. [Association between serum 25(OH)D levels at birth and bronchopulmonary dysplasia in preterm infants]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2017; 19:1051-1055. [PMID: 29046199 PMCID: PMC7389274 DOI: 10.7499/j.issn.1008-8830.2017.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/18/2017] [Indexed: 06/07/2023]
Abstract
OBJECTIVE To assess the association between serum 25-hydroxyvitamin D [25(OH)D] levels at birth and bronchopulmonary dysplasia (BPD) in preterm infants. METHODS This study recruited preterm infants with gestational age of below 34 weeks who were born between January 2014 and December 2016. These preterm infants were classified into two groups: BPD and control. The association between serum 25(OH)D levels at birth and BPD was analyzed. RESULTS Serum 25(OH)D levels in the BPD group was significantly lower than those in the control group [(37±17 nmol/L vs 47±20 nmol/L; P<0.05), and the rate of vitamin D deficiency was significantly higher than those in the control group (90.2% vs 74.0%; P<0.05). The level of serum 25(OH)D was negatively correlated with the incidence of BPD (r=-0.201, P=0.001). CONCLUSIONS Vitamin D deficiency at birth may be associated with BPD in preterm infants, but need to be further studied by multivariate analysis.
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Affiliation(s)
- Ren-Qiang Yu
- Department of Neonatology, Wuxi Maternity and Child Health Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu 214002, China.
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Mirzakhani H, De Vivo I, Leeder JS, Gaedigk R, Vyhlidal CA, Weiss ST, Tantisira K. Early pregnancy intrauterine fetal exposure to maternal smoking and impact on fetal telomere length. Eur J Obstet Gynecol Reprod Biol 2017; 218:27-32. [PMID: 28926727 DOI: 10.1016/j.ejogrb.2017.09.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/19/2017] [Accepted: 09/13/2017] [Indexed: 11/18/2022]
Abstract
BACKGROUND Reduced telomere length, or its accelerated attrition, has been implicated in aging, mortality, and several human diseases, including respiratory diseases. Age dependent manifestation of telomere-mediated disease during life span indicates the role of developmental stage in these diseases and highlights the importance of fetal developmental process in utero and at earlier life stages. Environmental determinants during developmental and later stages of life could affect telomere length. Smoke exposure as one of these significant determinants have been investigated in association with telomere length in neonates at time of delivery, children and adults. OBJECTIVE We sought to investigate whether intrauterine fetal exposure to tobacco smoking characterized by placenta cotinine levels during early weeks of pregnancy might be associated with shorter relative telomere length (T/S ratio) as compared to fetuses without exposure to tobacco smoking. STUDY DESIGN 207 Human placenta and epithelial lung samples were used for both fetal lung telomere length assessment and measurement of placental cotinine levels. Tissues were obtained from two NICHD-supported tissue retrieval programs with registries for elective abortions, the University of Washington Center for Birth Defects Research (Seattle, WA) and the University of Maryland Brain and Tissue Bank for Developmental Disorders (Baltimore, MD). Cotinine levels (ng/g total placental tissue) were determined in whole cell extracts prepared from human placenta samples to characterize and confirm the cotinine exposure status associated with maternal smoking. Relative telomere length (T/S ratio) in genomic DNA extracted from fetal lung tissue was measured by use of quantitative real-time polymerase chain reaction. Multivariable linear regression was used to investigate the relationship between fetal Telomere-to-Single Copy (T/S) ratio and tobacco exposure. RESULTS The estimated post-conception ages for included samples in the study ranged from 54 to 137days (7-19 weeks of gestation); 47.37% of fetal samples had female sex. Of the samples included in the analysis 96 and 111 fetal samples with and without intrauterine tobacco smoking exposure were distinguished. While T/S ratio was not different between those with and without smoking exposure (1.24±0.41 and 1.27±0.48, respectively; P=0.70), a significant effect modification of post-conception age on the relationship of intrauterine smoke exposure on fetal T/S ratio was observed (adjusted coefficient=-0.008, 95% CI: -0.016, -0.0004). The smoke exposure status was associated with T/S ratio after 93-day post conception (adjusted coefficient=-0.29, 95% CI: -0.53, -0.052). CONCLUSIONS Our results demonstrate a significant association of smoke exposure in utero at early pregnancy with shortened fetal relative telomere length in the developing lung and suggest that the detrimental effect of smoking exposure on future disease sequelae may start at the early stages of pregnancy.
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Affiliation(s)
- Hooman Mirzakhani
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Immaculata De Vivo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Epidemiology, T.H. Chan School of Public Health, Boston, MA, USA
| | - J Steven Leeder
- Division of Pharmacology, Toxicology and Experimental Therapeutics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Roger Gaedigk
- Division of Pharmacology, Toxicology and Experimental Therapeutics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Carrie A Vyhlidal
- Division of Pharmacology, Toxicology and Experimental Therapeutics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kelan Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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41
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Mohamed Hegazy A, Mohamed Shinkar D, Refaat Mohamed N, Abdalla Gaber H. Association between serum 25 (OH) vitamin D level at birth and respiratory morbidities among preterm neonates. J Matern Fetal Neonatal Med 2017; 31:2649-2655. [DOI: 10.1080/14767058.2017.1350162] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Nikolić MZ, Caritg O, Jeng Q, Johnson JA, Sun D, Howell KJ, Brady JL, Laresgoiti U, Allen G, Butler R, Zilbauer M, Giangreco A, Rawlins EL. Human embryonic lung epithelial tips are multipotent progenitors that can be expanded in vitro as long-term self-renewing organoids. eLife 2017; 6. [PMID: 28665271 PMCID: PMC5555721 DOI: 10.7554/elife.26575] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/23/2017] [Indexed: 12/17/2022] Open
Abstract
The embryonic mouse lung is a widely used substitute for human lung development. For example, attempts to differentiate human pluripotent stem cells to lung epithelium rely on passing through progenitor states that have only been described in mouse. The tip epithelium of the branching mouse lung is a multipotent progenitor pool that self-renews and produces differentiating descendants. We hypothesized that the human distal tip epithelium is an analogous progenitor population and tested this by examining morphology, gene expression and in vitro self-renewal and differentiation capacity of human tips. These experiments confirm that human and mouse tips are analogous and identify signalling pathways that are sufficient for long-term self-renewal of human tips as differentiation-competent organoids. Moreover, we identify mouse-human differences, including markers that define progenitor states and signalling requirements for long-term self-renewal. Our organoid system provides a genetically-tractable tool that will allow these human-specific features of lung development to be investigated. DOI:http://dx.doi.org/10.7554/eLife.26575.001 Degenerative lung disease occurs when the structure of the lungs breaks down, which makes it harder to get enough oxygen into the bloodstream. Most, but not all, cases occur in smokers and ex-smokers or people who have been exposed to a lot of air pollution. Currently, there is no way to reverse the damage, and even slowing the progress of the disease is extremely difficult. Some researchers are looking for ways to treat patients with degenerative lung diseases by regenerating the surface of their lungs. However, it is still not clear what the most effective route towards this long-term goal will be. One approach to lung regeneration is to use findings from developmental biology to understand how embryos normally build the gas exchange surfaces in the lungs. This knowledge may allow scientists to trigger a similar process in an adult lung to renew or replace any diseased tissue. Alternatively, cells could be collected from patients, reprogrammed and then coaxed into becoming a gas exchange surface in the laboratory. Such a “lung-in-a-dish” could be used to understand how degenerative diseases develop, to discover and test new drugs, or even to treat the patient directly via a transplant. To date, the embryonic development of lungs has mostly been studied using mouse lungs as a model system. However, it was not clear if human lungs actually develop in similar ways to mouse lungs, and whether using mice is a valid research strategy. Nikolić et al. compared embryonic lungs from humans and mice and showed that they are indeed very similar in terms of the cell types that they contain and how they mature. However, some key differences were identified that can only be explored in human cells and tissue. Nikolić et al. went on to identify conditions that allowed them to grow cells from human embryonic lungs indefinitely in a dish. These cells can now be used to investigate the aspects of lung development that are specific to humans. Together these findings provide a useful guide to allow scientists to coax human cells growing in a laboratory to become lung cells. Further improvements to this process will make the lungs-in-a-dish more true to the real organs, meaning that they could be used to better understand lung disease and identify new medicines. In the longer term, Nikolić et al. hope to gain enough insight from the human lung-in-a-dish model to eventually be able to regenerate the lungs of patients with degenerative lung disease. However, this possibility is still many years away. DOI:http://dx.doi.org/10.7554/eLife.26575.002
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Affiliation(s)
- Marko Z Nikolić
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Oriol Caritg
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Quitz Jeng
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Jo-Anne Johnson
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Dawei Sun
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Kate J Howell
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Jane L Brady
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Usua Laresgoiti
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - George Allen
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Richard Butler
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom.,Department of Paediatric Gastroenterology, University of Cambridge and Addenbrookes Hospital, Cambridge, United Kingdom
| | - Adam Giangreco
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, United Kingdom
| | - Emma L Rawlins
- Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.,Department of Pathology, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust/MRC Stem Cell Institute, Cambridge, United Kingdom
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Kho AT, Chhabra D, Sharma S, Qiu W, Carey VJ, Gaedigk R, Vyhlidal CA, Leeder JS, Tantisira KG, Weiss ST. Age, Sexual Dimorphism, and Disease Associations in the Developing Human Fetal Lung Transcriptome. Am J Respir Cell Mol Biol 2017; 54:814-21. [PMID: 26584061 DOI: 10.1165/rcmb.2015-0326oc] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The fetal origins of disease hypothesis suggests that variations in the course of prenatal lung development may affect life-long pulmonary function growth, decline, and pathobiology. Many studies support the existence of differences in the developing lung trajectory in males and females, and sex-specific differences in the prevalence of chronic lung diseases, such as asthma and bronchopulmonary dysplasia. The objectives of this study were to investigate the early developing fetal lung for transcriptomic correlates of postconception age (maturity) and sex, and their associations with chronic lung diseases. We analyzed whole-lung transcriptome profiles of 61 females and 78 males at 54-127 days postconception (dpc) from nonsmoking mothers using unsupervised principal component analysis and supervised linear regression models. We identified dominant transcriptomic correlates for postconception age and sex with corresponding gene sets that were enriched for developing lung structural and functional ontologies. We observed that the transcriptomic sex difference was not a uniform global time shift/lag, rather, lungs of males appear to be more mature than those of females before 96 dpc, and females appear to be more mature than males after 96 dpc. The age correlate gene set was consistently enriched for asthma and bronchopulmonary dysplasia genes, but the sex correlate gene sets were not. Despite sex differences in the developing fetal lung transcriptome, postconception age appears to be more dominant than sex in the effect of early fetal lung developments on disease risk during this early pseudoglandular phase of development.
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Affiliation(s)
- Alvin T Kho
- 1 Children's Hospital Informatics Program, Boston Children's Hospital, Boston, Massachusetts.,2 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,3 Harvard Medical School, Boston, Massachusetts; and
| | - Divya Chhabra
- 2 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,3 Harvard Medical School, Boston, Massachusetts; and
| | - Sunita Sharma
- 2 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,3 Harvard Medical School, Boston, Massachusetts; and.,4 Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Weiliang Qiu
- 2 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,3 Harvard Medical School, Boston, Massachusetts; and
| | - Vincent J Carey
- 2 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,3 Harvard Medical School, Boston, Massachusetts; and
| | - Roger Gaedigk
- 5 Division of Pediatric Clinical Pharmacology and Medical Toxicology, Children's Mercy Hospital and Clinics, Kansas City, Missouri; and
| | - Carrie A Vyhlidal
- 5 Division of Pediatric Clinical Pharmacology and Medical Toxicology, Children's Mercy Hospital and Clinics, Kansas City, Missouri; and
| | - J Steven Leeder
- 5 Division of Pediatric Clinical Pharmacology and Medical Toxicology, Children's Mercy Hospital and Clinics, Kansas City, Missouri; and
| | - Kelan G Tantisira
- 2 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,3 Harvard Medical School, Boston, Massachusetts; and
| | - Scott T Weiss
- 2 Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,3 Harvard Medical School, Boston, Massachusetts; and
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Qiao D, Lange C, Beaty TH, Crapo JD, Barnes KC, Bamshad M, Hersh CP, Morrow J, Pinto-Plata VM, Marchetti N, Bueno R, Celli BR, Criner GJ, Silverman EK, Cho MH. Exome Sequencing Analysis in Severe, Early-Onset Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2017; 193:1353-63. [PMID: 26736064 DOI: 10.1164/rccm.201506-1223oc] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
RATIONALE Genomic regions identified by genome-wide association studies explain only a small fraction of heritability for chronic obstructive pulmonary disease (COPD). Alpha-1 antitrypsin deficiency shows that rare coding variants of large effect also influence COPD susceptibility. We hypothesized that exome sequencing in families identified through a proband with severe, early-onset COPD would identify additional rare genetic determinants of large effect. OBJECTIVES To identify rare genetic determinants of severe COPD. METHODS We applied filtering approaches to identify potential causal variants for COPD in whole exomes from 347 subjects in 49 extended pedigrees from the Boston Early-Onset COPD Study. We assessed the power of this approach under different levels of genetic heterogeneity using simulations. We tested genes identified in these families using gene-based association tests in exomes of 204 cases with severe COPD and 195 resistant smokers from the COPDGene study. In addition, we examined previously described loci associated with COPD using these datasets. MEASUREMENTS AND MAIN RESULTS We identified 69 genes with predicted deleterious nonsynonymous, stop, or splice variants that segregated with severe COPD in at least two pedigrees. Four genes (DNAH8, ALCAM, RARS, and GBF1) also demonstrated an increase in rare nonsynonymous, stop, and/or splice mutations in cases compared with resistant smokers from the COPDGene study; however, these results were not statistically significant. We demonstrate the limitations of the power of this approach under genetic heterogeneity through simulation. CONCLUSIONS Rare deleterious coding variants may increase risk for COPD, but multiple genes likely contribute to COPD susceptibility.
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Affiliation(s)
| | - Christoph Lange
- 2 Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Terri H Beaty
- 3 Johns Hopkins Bloomberg School of Public Health, and
| | | | - Kathleen C Barnes
- 5 Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Michael Bamshad
- 6 Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, Washington
| | - Craig P Hersh
- 1 Channing Division of Network Medicine.,7 Division of Pulmonary and Critical Care Medicine, and
| | | | - Victor M Pinto-Plata
- 8 Department of Critical Care Medicine and Pulmonary Disease, Baystate Medical Center, Springfield, Massachusetts
| | | | - Raphael Bueno
- 10 Division of Thoracic Surgery, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Gerald J Criner
- 11 Division of Pulmonary and Critical Care Medicine Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Edwin K Silverman
- 1 Channing Division of Network Medicine.,7 Division of Pulmonary and Critical Care Medicine, and
| | - Michael H Cho
- 1 Channing Division of Network Medicine.,7 Division of Pulmonary and Critical Care Medicine, and
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45
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Hawkins F, Kramer P, Jacob A, Driver I, Thomas DC, McCauley KB, Skvir N, Crane AM, Kurmann AA, Hollenberg AN, Nguyen S, Wong BG, Khalil AS, Huang SX, Guttentag S, Rock JR, Shannon JM, Davis BR, Kotton DN. Prospective isolation of NKX2-1-expressing human lung progenitors derived from pluripotent stem cells. J Clin Invest 2017; 127:2277-2294. [PMID: 28463226 DOI: 10.1172/jci89950] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 03/02/2017] [Indexed: 12/12/2022] Open
Abstract
It has been postulated that during human fetal development, all cells of the lung epithelium derive from embryonic, endodermal, NK2 homeobox 1-expressing (NKX2-1+) precursor cells. However, this hypothesis has not been formally tested owing to an inability to purify or track these progenitors for detailed characterization. Here we have engineered and developmentally differentiated NKX2-1GFP reporter pluripotent stem cells (PSCs) in vitro to generate and isolate human primordial lung progenitors that express NKX2-1 but are initially devoid of differentiated lung lineage markers. After sorting to purity, these primordial lung progenitors exhibited lung epithelial maturation. In the absence of mesenchymal coculture support, this NKX2-1+ population was able to generate epithelial-only spheroids in defined 3D cultures. Alternatively, when recombined with fetal mouse lung mesenchyme, the cells recapitulated epithelial-mesenchymal developing lung interactions. We imaged these progenitors in real time and performed time-series global transcriptomic profiling and single-cell RNA sequencing as they moved through the earliest moments of lung lineage specification. The profiles indicated that evolutionarily conserved, stage-dependent gene signatures of early lung development are expressed in primordial human lung progenitors and revealed a CD47hiCD26lo cell surface phenotype that allows their prospective isolation from untargeted, patient-specific PSCs for further in vitro differentiation and future applications in regenerative medicine.
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Affiliation(s)
- Finn Hawkins
- Center for Regenerative Medicine, and.,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Philipp Kramer
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas, USA
| | - Anjali Jacob
- Center for Regenerative Medicine, and.,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Ian Driver
- Department of Anatomy, UCSF, San Francisco, California, USA
| | | | - Katherine B McCauley
- Center for Regenerative Medicine, and.,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | | | - Ana M Crane
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas, USA
| | - Anita A Kurmann
- Center for Regenerative Medicine, and.,Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Anthony N Hollenberg
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Brandon G Wong
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Ahmad S Khalil
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, Massachusetts, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Sarah Xl Huang
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas, USA.,Columbia Center for Translational Immunology & Columbia Center for Human Development, Columbia University Medical Center, New York, New York, USA
| | - Susan Guttentag
- Department of Pediatrics, Monroe Carell Jr. Children's Hospital, Vanderbilt University, Nashville, Tennessee, USA
| | - Jason R Rock
- Department of Anatomy, UCSF, San Francisco, California, USA
| | - John M Shannon
- Division of Pulmonary Biology, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Brian R Davis
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine, and.,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
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46
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Bush A, Bolton CE. Longer Term Sequelae of Prematurity: The Adolescent and Young Adult. RESPIRATORY OUTCOMES IN PRETERM INFANTS 2017. [DOI: 10.1007/978-3-319-48835-6_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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47
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Miller S, Henry AP, Hodge E, Kheirallah AK, Billington CK, Rimington TL, Bhaker SK, Obeidat M, Melén E, Merid SK, Swan C, Gowland C, Nelson CP, Stewart CE, Bolton CE, Kilty I, Malarstig A, Parker SG, Moffatt MF, Wardlaw AJ, Hall IP, Sayers I. The Ser82 RAGE Variant Affects Lung Function and Serum RAGE in Smokers and sRAGE Production In Vitro. PLoS One 2016; 11:e0164041. [PMID: 27755550 PMCID: PMC5068780 DOI: 10.1371/journal.pone.0164041] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/19/2016] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION Genome-Wide Association Studies have identified associations between lung function measures and Chronic Obstructive Pulmonary Disease (COPD) and chromosome region 6p21 containing the gene for the Advanced Glycation End Product Receptor (AGER, encoding RAGE). We aimed to (i) characterise RAGE expression in the lung, (ii) identify AGER transcripts, (iii) ascertain if SNP rs2070600 (Gly82Ser C/T) is associated with lung function and serum sRAGE levels and (iv) identify whether the Gly82Ser variant is functionally important in altering sRAGE levels in an airway epithelial cell model. METHODS Immunohistochemistry was used to identify RAGE protein expression in 26 human tissues and qPCR was used to quantify AGER mRNA in lung cells. Gene expression array data was used to identify AGER expression during lung development in 38 fetal lung samples. RNA-Seq was used to identify AGER transcripts in lung cells. sRAGE levels were assessed in cells and patient serum by ELISA. BEAS2B-R1 cells were transfected to overexpress RAGE protein with either the Gly82 or Ser82 variant and sRAGE levels identified. RESULTS Immunohistochemical assessment of 6 adult lung samples identified high RAGE expression in the alveoli of healthy adults and individuals with COPD. AGER/RAGE expression increased across developmental stages in human fetal lung at both the mRNA (38 samples) and protein levels (20 samples). Extensive AGER splicing was identified. The rs2070600T (Ser82) allele is associated with higher FEV1, FEV1/FVC and lower serum sRAGE levels in UK smokers. Using an airway epithelium model overexpressing the Gly82 or Ser82 variants we found that HMGB1 activation of the RAGE-Ser82 receptor results in lower sRAGE production. CONCLUSIONS This study provides new information regarding the expression profile and potential role of RAGE in the human lung and shows a functional role of the Gly82Ser variant. These findings advance our understanding of the potential mechanisms underlying COPD particularly for carriers of this AGER polymorphism.
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Affiliation(s)
- Suzanne Miller
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
- * E-mail:
| | - Amanda P. Henry
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Emily Hodge
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | | | | | - Tracy L. Rimington
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Sangita K. Bhaker
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Ma’en Obeidat
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Simon K. Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Caroline Swan
- Department of Biology, University of York, York, United Kingdom
| | - Catherine Gowland
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Carl P. Nelson
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Ceri E. Stewart
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Charlotte E. Bolton
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Iain Kilty
- Pfizer Worldwide Research & Development, Cambridge, Massachusetts, United States of America
| | - Anders Malarstig
- Pfizer Worldwide Research & Development, Cambridge, United Kingdom
| | - Stuart G. Parker
- Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, United Kingdom
| | - Miriam F. Moffatt
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Andrew J. Wardlaw
- Institute for Lung Health, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
| | - Ian P. Hall
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Ian Sayers
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
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48
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Al-Garawi A, Carey VJ, Chhabra D, Mirzakhani H, Morrow J, Lasky-Su J, Qiu W, Laranjo N, Litonjua AA, Weiss ST. The Role of Vitamin D in the Transcriptional Program of Human Pregnancy. PLoS One 2016; 11:e0163832. [PMID: 27711190 PMCID: PMC5053446 DOI: 10.1371/journal.pone.0163832] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/12/2016] [Indexed: 11/18/2022] Open
Abstract
Background Patterns of gene expression of human pregnancy are poorly understood. In a trial of vitamin D supplementation in pregnant women, peripheral blood transcriptomes were measured longitudinally on 30 women and used to characterize gene co-expression networks. Objective Studies suggest that increased maternal Vitamin D levels may reduce the risk of asthma in early life, yet the underlying mechanisms have not been examined. In this study, we used a network-based approach to examine changes in gene expression profiles during the course of normal pregnancy and evaluated their association with maternal Vitamin D levels. Design The VDAART study is a randomized clinical trial of vitamin D supplementation in pregnancy for reduction of pediatric asthma risk. The trial enrolled 881 women at 10–18 weeks of gestation. Longitudinal gene expression measures were obtained on thirty pregnant women, using RNA isolated from peripheral blood samples obtained in the first and third trimesters. Differentially expressed genes were identified using significance of analysis of microarrays (SAM), and clustered using a weighted gene co-expression network analysis (WGCNA). Gene-set enrichment was performed to identify major biological pathways. Results Comparison of transcriptional profiles between first and third trimesters of pregnancy identified 5839 significantly differentially expressed genes (FDR<0.05). Weighted gene co-expression network analysis clustered these transcripts into 14 co-expression modules of which two showed significant correlation with maternal vitamin D levels. Pathway analysis of these two modules revealed genes enriched in immune defense pathways and extracellular matrix reorganization as well as genes enriched in notch signaling and transcription factor networks. Conclusion Our data show that gene expression profiles of healthy pregnant women change during the course of pregnancy and suggest that maternal Vitamin D levels influence transcriptional profiles. These alterations of the maternal transcriptome may contribute to fetal immune imprinting and reduce allergic sensitization in early life. Trial Registration clinicaltrials.gov NCT00920621
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Affiliation(s)
- Amal Al-Garawi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Vincent J. Carey
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Divya Chhabra
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Hooman Mirzakhani
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Nancy Laranjo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Augusto A. Litonjua
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- * E-mail:
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49
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Beauchemin KJ, Wells JM, Kho AT, Philip VM, Kamir D, Kohane IS, Graber JH, Bult CJ. Temporal dynamics of the developing lung transcriptome in three common inbred strains of laboratory mice reveals multiple stages of postnatal alveolar development. PeerJ 2016; 4:e2318. [PMID: 27602285 PMCID: PMC4991849 DOI: 10.7717/peerj.2318] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/12/2016] [Indexed: 12/12/2022] Open
Abstract
To characterize temporal patterns of transcriptional activity during normal lung development, we generated genome wide gene expression data for 26 pre- and post-natal time points in three common inbred strains of laboratory mice (C57BL/6J, A/J, and C3H/HeJ). Using Principal Component Analysis and least squares regression modeling, we identified both strain-independent and strain-dependent patterns of gene expression. The 4,683 genes contributing to the strain-independent expression patterns were used to define a murine Developing Lung Characteristic Subtranscriptome (mDLCS). Regression modeling of the Principal Components supported the four canonical stages of mammalian embryonic lung development (embryonic, pseudoglandular, canalicular, saccular) defined previously by morphology and histology. For postnatal alveolar development, the regression model was consistent with four stages of alveolarization characterized by episodic transcriptional activity of genes related to pulmonary vascularization. Genes expressed in a strain-dependent manner were enriched for annotations related to neurogenesis, extracellular matrix organization, and Wnt signaling. Finally, a comparison of mouse and human transcriptomics from pre-natal stages of lung development revealed conservation of pathways associated with cell cycle, axon guidance, immune function, and metabolism as well as organism-specific expression of genes associated with extracellular matrix organization and protein modification. The mouse lung development transcriptome data generated for this study serves as a unique reference set to identify genes and pathways essential for normal mammalian lung development and for investigations into the developmental origins of respiratory disease and cancer. The gene expression data are available from the Gene Expression Omnibus (GEO) archive (GSE74243). Temporal expression patterns of mouse genes can be investigated using a study specific web resource (http://lungdevelopment.jax.org).
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Affiliation(s)
- Kyle J. Beauchemin
- The Jackson Laboratory, Bar Harbor, ME, United States
- Graduate School of Biomedical Sciences and Engineering, The University of Maine, Orono, ME, United States
| | | | - Alvin T. Kho
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA, United States
| | | | - Daniela Kamir
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Isaac S. Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States
| | | | - Carol J. Bult
- The Jackson Laboratory, Bar Harbor, ME, United States
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50
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Miller S, Melén E, Merid SK, Hall IP, Sayers I. Genes associated with polymorphic variants predicting lung function are differentially expressed during human lung development. Respir Res 2016; 17:95. [PMID: 27473260 PMCID: PMC4966770 DOI: 10.1186/s12931-016-0410-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/20/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Recent meta-analyses of genome-wide association studies have identified single nucleotide polymorphisms (SNPs) within/near 54 genes associated with lung function measures. Current understanding of the contribution of these genes to human lung development is limited. We set out to further define i) the expression profile of these genes during human lung development using a unique set of resources to examine both mRNA and protein expression and ii) the link between key polymorphisms and genes using expression quantitative trait loci (eQTL) approaches. METHODS The mRNA expression profile of lung function associated genes across pseudoglandular and canalicular stages of lung development were determined using expression array data of 38 human fetal lungs. eQTLs were investigated for selected genes using blood cell and lung tissue data. Immunohistochemistry of the top 5 candidates was performed in a panel of 24 fetal lung samples. RESULTS Twenty-nine lung function associated genes were differentially expressed during lung development at the mRNA level. The greatest magnitude of effect was observed for 5 genes; TMEM163, FAM13A and HHIP which had increasing expression and CDC123 and PTCH1 with decreased expression across developmental stages. Focussed eQTL analyses investigating SNPs in these five loci identified several cis-eQTL's. Protein expression of TMEM163 increased and CDC123 decreased with fetal lung age in agreement with mRNA data. Protein expression in FAM13A, HHIP and PTCH1 remained relatively constant throughout lung development. CONCLUSIONS We have identified that > 50 % of lung function associated genes show evidence of differential expression during lung development and we show that in particular TMEM163 and CDC123 are differentially expressed at both the mRNA and protein levels. Our data provides a systematic evaluation of lung function associated genes in this context and offers some insight into the potential role of several of these genes in contributing to human lung development.
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Affiliation(s)
- S Miller
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK.
| | - E Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Sachs' Children's Hospital, Stockholm, Sweden
| | - S K Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - I P Hall
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
| | - I Sayers
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
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