LungMAP: The Molecular Atlas of Lung Development Program
Abstract
The National Heart, Lung, and Blood Institute is funding an effort to create a molecular atlas of the developing lung (LungMAP) to serve as a research resource and public education tool. The lung is a complex organ with lengthy development time driven by interactive gene networks and dynamic cross talk among multiple cell types to control and coordinate lineage specification, cell proliferation, differentiation, migration, morphogenesis, and injury repair. A better understanding of the processes that regulate lung development, particularly alveologenesis, will have a significant impact on survival rates for premature infants born with incomplete lung development and will facilitate lung injury repair and regeneration in adults. A consortium of four research centers, a data coordinating center, and a human tissue repository provides high-quality molecular data of developing human and mouse lungs. LungMAP includes mouse and human data for cross correlation of developmental processes across species. LungMAP is generating foundational data and analysis, creating a web portal for presentation of results and public sharing of data sets, establishing a repository of young human lung tissues obtained through organ donor organizations, and developing a comprehensive lung ontology that incorporates the latest findings of the consortium. The LungMAP website (www.lungmap.net) currently contains moremore »
- Authors:
-
- RTI International, Research Triangle Park, NC (United States)
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Texas Advanced Computing Center, Austin, TX (United States)
- Univ. of Washington, Seattle, WA (United States)
- Univ. of California, San Diego, CA (United States)
- Yale Univ., New Haven, CT (United States). School of Medicine
- Univ. of Rochester, NY (United States). Medical Center
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH (United States)
- Children’s Hospital of Los Angeles, Los Angeles, CA (United States)
- Duke Univ., Durham, NC (United States). School of Medicine
- Univ. of Alabama, Birmingham, AL (United States)
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- USDOE
- Contributing Org.:
- The LungMAP Consortium
- OSTI Identifier:
- 1503219
- Report Number(s):
- PNNL-SA-136379
Journal ID: ISSN 1040-0605
- Grant/Contract Number:
- AC05-76RL01830
- Resource Type:
- Accepted Manuscript
- Journal Name:
- The American Journal of Physiology-Lung Cellular and Molecular Physiology
- Additional Journal Information:
- Journal Volume: 313; Journal Issue: 5; Journal ID: ISSN 1040-0605
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES
Citation Formats
Ardini-Poleske, Maryanne E., Clark, Robert F., Ansong, Charles, Carson, James P., Corley, Richard A., Deutsch, Gail H., Hagood, James S., Kaminski, Naftali, Mariani, Thomas J., Potter, Steven S., Pryhuber, Gloria S., Warburton, David, Whitsett, Jeffrey A., Palmer, Scott M., and Ambalavanan, Namasivayam. LungMAP: The Molecular Atlas of Lung Development Program. United States: N. p., 2017.
Web. doi:10.1152/ajplung.00139.2017.
Ardini-Poleske, Maryanne E., Clark, Robert F., Ansong, Charles, Carson, James P., Corley, Richard A., Deutsch, Gail H., Hagood, James S., Kaminski, Naftali, Mariani, Thomas J., Potter, Steven S., Pryhuber, Gloria S., Warburton, David, Whitsett, Jeffrey A., Palmer, Scott M., & Ambalavanan, Namasivayam. LungMAP: The Molecular Atlas of Lung Development Program. United States. https://doi.org/10.1152/ajplung.00139.2017
Ardini-Poleske, Maryanne E., Clark, Robert F., Ansong, Charles, Carson, James P., Corley, Richard A., Deutsch, Gail H., Hagood, James S., Kaminski, Naftali, Mariani, Thomas J., Potter, Steven S., Pryhuber, Gloria S., Warburton, David, Whitsett, Jeffrey A., Palmer, Scott M., and Ambalavanan, Namasivayam. Wed .
"LungMAP: The Molecular Atlas of Lung Development Program". United States. https://doi.org/10.1152/ajplung.00139.2017. https://www.osti.gov/servlets/purl/1503219.
@article{osti_1503219,
title = {LungMAP: The Molecular Atlas of Lung Development Program},
author = {Ardini-Poleske, Maryanne E. and Clark, Robert F. and Ansong, Charles and Carson, James P. and Corley, Richard A. and Deutsch, Gail H. and Hagood, James S. and Kaminski, Naftali and Mariani, Thomas J. and Potter, Steven S. and Pryhuber, Gloria S. and Warburton, David and Whitsett, Jeffrey A. and Palmer, Scott M. and Ambalavanan, Namasivayam},
abstractNote = {The National Heart, Lung, and Blood Institute is funding an effort to create a molecular atlas of the developing lung (LungMAP) to serve as a research resource and public education tool. The lung is a complex organ with lengthy development time driven by interactive gene networks and dynamic cross talk among multiple cell types to control and coordinate lineage specification, cell proliferation, differentiation, migration, morphogenesis, and injury repair. A better understanding of the processes that regulate lung development, particularly alveologenesis, will have a significant impact on survival rates for premature infants born with incomplete lung development and will facilitate lung injury repair and regeneration in adults. A consortium of four research centers, a data coordinating center, and a human tissue repository provides high-quality molecular data of developing human and mouse lungs. LungMAP includes mouse and human data for cross correlation of developmental processes across species. LungMAP is generating foundational data and analysis, creating a web portal for presentation of results and public sharing of data sets, establishing a repository of young human lung tissues obtained through organ donor organizations, and developing a comprehensive lung ontology that incorporates the latest findings of the consortium. The LungMAP website (www.lungmap.net) currently contains more than 6,000 high-resolution lung images and transcriptomic, proteomic, and lipidomic human and mouse data and provides scientific information to stimulate interest in research careers for young audiences. This paper presents a brief description of research conducted by the consortium, database, and portal development and upcoming features that will enhance the LungMAP experience for a community of users.},
doi = {10.1152/ajplung.00139.2017},
journal = {The American Journal of Physiology-Lung Cellular and Molecular Physiology},
number = 5,
volume = 313,
place = {United States},
year = {Wed Nov 01 00:00:00 EDT 2017},
month = {Wed Nov 01 00:00:00 EDT 2017}
}
Web of Science
Figures / Tables:
Works referenced in this record:
SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis
journal, November 2015
- Guo, Minzhe; Wang, Hui; Potter, S. Steven
- PLOS Computational Biology, Vol. 11, Issue 11
Gene Regulatory Networks Governing Lung Specification: Lung Specification GRN
journal, June 2014
- Rankin, Scott A.; Zorn, Aaron M.
- Journal of Cellular Biochemistry, Vol. 115, Issue 8
The Extracellular Matrix in Bronchopulmonary Dysplasia: Target and Source
journal, December 2015
- Mižíková, Ivana; Morty, Rory E.
- Frontiers in Medicine, Vol. 2
Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples
journal, December 2016
- Clair, Geremy; Piehowski, Paul D.; Nicola, Teodora
- Scientific Reports, Vol. 6, Issue 1
Lung Gene Expression Analysis (LGEA): an integrative web portal for comprehensive gene expression data analysis in lung development
journal, January 2017
- Du, Yina; Kitzmiller, Joseph A.; Sridharan, Anusha
- Thorax, Vol. 72, Issue 5
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
journal, April 2014
- Treutlein, Barbara; Brownfield, Doug G.; Wu, Angela R.
- Nature, Vol. 509, Issue 7500
‘LungGENS’: a web-based tool for mapping single-cell gene expression in the developing lung: Figure 1
journal, June 2015
- Du, Yina; Guo, Minzhe; Whitsett, Jeffrey A.
- Thorax, Vol. 70, Issue 11
An Official American Thoracic Society Clinical Practice Guideline: Classification, Evaluation, and Management of Childhood Interstitial Lung Disease in Infancy
journal, August 2013
- Kurland, Geoffrey; Deterding, Robin R.; Hagood, James S.
- American Journal of Respiratory and Critical Care Medicine, Vol. 188, Issue 3
SLICE: determining cell differentiation and lineage based on single cell entropy
journal, December 2016
- Guo, Minzhe; Bao, Erik L.; Wagner, Michael
- Nucleic Acids Research
Shotgun Approach for Quantitative Imaging of Phospholipids Using Nanospray Desorption Electrospray Ionization Mass Spectrometry
journal, January 2014
- Lanekoff, Ingela; Thomas, Mathew; Laskin, Julia
- Analytical Chemistry, Vol. 86, Issue 3
Tissue Imaging Using Nanospray Desorption Electrospray Ionization Mass Spectrometry
journal, December 2011
- Laskin, Julia; Heath, Brandi S.; Roach, Patrick J.
- Analytical Chemistry, Vol. 84, Issue 1
Altered breathing mechanics and ventilatory response during exercise in children born extremely preterm
journal, June 2016
- MacLean, J. E.; DeHaan, K.; Fuhr, D.
- Thorax, Vol. 71, Issue 11
A method for automated detection of gene expression required for the establishment of a digital transcriptome-wide gene expression atlas
journal, March 2005
- Carson, J. P.; Eichele, G.; Chiu, W.
- Journal of Microscopy, Vol. 217, Issue 3
Deregulation of the lysyl hydroxylase matrix cross-linking system in experimental and clinical bronchopulmonary dysplasia
journal, February 2014
- Witsch, Thilo J.; Turowski, Paweł; Sakkas, Elpidoforos
- American Journal of Physiology-Lung Cellular and Molecular Physiology, Vol. 306, Issue 3
Lung function following very preterm birth in the era of ‘new’ bronchopulmonary dysplasia: Lung function and preterm birth
journal, February 2015
- Simpson, Shannon J.; Hall, Graham L.; Wilson, Andrew C.
- Respirology, Vol. 20, Issue 4
Lung Endoderm Morphogenesis: Gasping for Form and Function
journal, November 2015
- Swarr, Daniel T.; Morrisey, Edward E.
- Annual Review of Cell and Developmental Biology, Vol. 31, Issue 1
Overview of Lung Development in the Newborn Human
journal, January 2017
- Warburton, David
- Neonatology, Vol. 111, Issue 4
Statistical search on the Semantic Web
journal, February 2008
- Kobayashi, Norio; Toyoda, Tetsuro
- Bioinformatics, Vol. 24, Issue 7
Lipidomics reveals dramatic lipid compositional changes in the maturing postnatal lung
journal, February 2017
- Dautel, Sydney E.; Kyle, Jennifer E.; Clair, Geremy
- Scientific Reports, Vol. 7, Issue 1
The Molecular Era of Surfactant Biology
journal, January 2014
- Whitsett, Jeffrey A.
- Neonatology, Vol. 105, Issue 4
Transcriptional Control of Lung Morphogenesis
journal, January 2007
- Maeda, Yutaka; Davé, Vrushank; Whitsett, Jeffrey A.
- Physiological Reviews, Vol. 87, Issue 1
Gene Regulatory Networks Governing Lung Specification: Lung Specification GRN
journal, June 2014
- Rankin, Scott A.; Zorn, Aaron M.
- Journal of Cellular Biochemistry, Vol. 115, Issue 8
A transcriptome atlas of the mouse brain at cellular resolution
journal, October 2002
- Carson, James P.; Thaller, Christina; Eichele, Gregor
- Current Opinion in Neurobiology, Vol. 12, Issue 5
Tissue Imaging Using Nanospray Desorption Electrospray Ionization Mass Spectrometry
journal, December 2011
- Laskin, Julia; Heath, Brandi S.; Roach, Patrick J.
- Analytical Chemistry, Vol. 84, Issue 1
Shotgun Approach for Quantitative Imaging of Phospholipids Using Nanospray Desorption Electrospray Ionization Mass Spectrometry
journal, January 2014
- Lanekoff, Ingela; Thomas, Mathew; Laskin, Julia
- Analytical Chemistry, Vol. 86, Issue 3
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
journal, April 2014
- Treutlein, Barbara; Brownfield, Doug G.; Wu, Angela R.
- Nature, Vol. 509, Issue 7500
Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples
journal, December 2016
- Clair, Geremy; Piehowski, Paul D.; Nicola, Teodora
- Scientific Reports, Vol. 6, Issue 1
Statistical search on the Semantic Web
journal, February 2008
- Kobayashi, Norio; Toyoda, Tetsuro
- Bioinformatics, Vol. 24, Issue 7
SLICE: determining cell differentiation and lineage based on single cell entropy
journal, December 2016
- Guo, Minzhe; Bao, Erik L.; Wagner, Michael
- Nucleic Acids Research
Visualization of high resolution spatial mass spectrometric data during acquisition
conference, August 2012
- Thomas, M.; Heath, B. S.; Laskin, J.
- 2012 34th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society
A method for automated detection of gene expression required for the establishment of a digital transcriptome-wide gene expression atlas
journal, March 2005
- Carson, J. P.; Eichele, G.; Chiu, W.
- Journal of Microscopy, Vol. 217, Issue 3
Altered breathing mechanics and ventilatory response during exercise in children born extremely preterm
journal, June 2016
- MacLean, J. E.; DeHaan, K.; Fuhr, D.
- Thorax, Vol. 71, Issue 11
Deregulation of the lysyl hydroxylase matrix cross-linking system in experimental and clinical bronchopulmonary dysplasia
journal, February 2014
- Witsch, Thilo J.; Turowski, Paweł; Sakkas, Elpidoforos
- American Journal of Physiology-Lung Cellular and Molecular Physiology, Vol. 306, Issue 3
The Molecular Era of Surfactant Biology
journal, January 2014
- Whitsett, Jeffrey A.
- Neonatology, Vol. 105, Issue 4
Overview of Lung Development in the Newborn Human
journal, January 2017
- Warburton, David
- Neonatology, Vol. 111, Issue 4
Gauging triple stores with actual biological data
journal, January 2011
- Mironov, Vladimir; Seethappan, Nirmala; Blondé, Ward
- BMC Bioinformatics, Vol. 13, Issue Suppl 1
Selecting the most appropriate time points to profile in high-throughput studies
journal, January 2017
- Kleyman, Michael; Sefer, Emre; Nicola, Teodora
- eLife, Vol. 6
Works referencing / citing this record:
Cellular crosstalk in the development and regeneration of the respiratory system
journal, June 2019
- Zepp, Jarod A.; Morrisey, Edward E.
- Nature Reviews Molecular Cell Biology, Vol. 20, Issue 9
Single-cell RNA sequencing for the study of development, physiology and disease
journal, May 2018
- Potter, S. Steven
- Nature Reviews Nephrology, Vol. 14, Issue 8
A revised airway epithelial hierarchy includes CFTR-expressing ionocytes
journal, August 2018
- Montoro, Daniel T.; Haber, Adam L.; Biton, Moshe
- Nature, Vol. 560, Issue 7718
Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations
journal, February 2019
- Sakornsakolpat, Phuwanat; Prokopenko, Dmitry; Lamontagne, Maxime
- Nature Genetics, Vol. 51, Issue 3
Transcriptomic and epigenetic mechanisms underlying myeloid diversity in the lung
journal, January 2020
- Sajti, Eniko; Link, Verena M.; Ouyang, Zhengyu
- Nature Immunology, Vol. 21, Issue 2
Dissociation, cellular isolation, and initial molecular characterization of neonatal and pediatric human lung tissues
journal, October 2018
- Bandyopadhyay, Gautam; Huyck, Heidie L.; Misra, Ravi S.
- American Journal of Physiology-Lung Cellular and Molecular Physiology, Vol. 315, Issue 4
The lipofibroblast: more than a lipid-storage depot
journal, May 2019
- McGowan, Stephen E.
- American Journal of Physiology-Lung Cellular and Molecular Physiology, Vol. 316, Issue 5
Recent advances in our understanding of the mechanisms of late lung development and bronchopulmonary dysplasia
journal, December 2017
- Surate Solaligue, David E.; Rodríguez-Castillo, José Alberto; Ahlbrecht, Katrin
- American Journal of Physiology-Lung Cellular and Molecular Physiology, Vol. 313, Issue 6
A multiomics focusing towards the molecular networks of lung development
journal, November 2019
- Clair, Geremy
- American Journal of Physiology-Lung Cellular and Molecular Physiology, Vol. 317, Issue 5
Recent advances in our understanding of the mechanisms of lung alveolarization and bronchopulmonary dysplasia
journal, December 2019
- Lignelli, Ettore; Palumbo, Francesco; Myti, Despoina
- American Journal of Physiology-Lung Cellular and Molecular Physiology, Vol. 317, Issue 6
Cellular senescence in the lung across the age spectrum
journal, May 2019
- Parikh, Pavan; Wicher, Sarah; Khandalavala, Karl
- American Journal of Physiology-Lung Cellular and Molecular Physiology, Vol. 316, Issue 5
Integration of transcriptomic and proteomic data identifies biological functions in cell populations from human infant lung
journal, September 2019
- Du, Yina; Clair, Geremy C.; Al Alam, Denise
- American Journal of Physiology-Lung Cellular and Molecular Physiology, Vol. 317, Issue 3
Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis
journal, June 2019
- Reyfman, Paul A.; Walter, James M.; Joshi, Nikita
- American Journal of Respiratory and Critical Care Medicine, Vol. 199, Issue 12
The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease
journal, July 2019
- Schiller, Herbert B.; Montoro, Daniel T.; Simon, Lukas M.
- American Journal of Respiratory Cell and Molecular Biology, Vol. 61, Issue 1
It’s about time: clocks in the developing lung
journal, January 2020
- Bartman, Colleen M.; Matveyenko, Aleksey; Prakash, Y. S.
- Journal of Clinical Investigation, Vol. 130, Issue 1
NITPicker: selecting time points for follow-up experiments
journal, April 2019
- Ezer, Daphne; Keir, Joseph
- BMC Bioinformatics, Vol. 20, Issue 1
Comprehensive anatomic ontologies for lung development: A comparison of alveolar formation and maturation within mouse and human lung
journal, October 2019
- Pan, Huaqin; Deutsch, Gail H.; Wert, Susan E.
- Journal of Biomedical Semantics, Vol. 10, Issue 1
Human lung development: recent progress and new challenges
journal, August 2018
- Nikolić, Marko Z.; Sun, Dawei; Rawlins, Emma L.
- Development, Vol. 145, Issue 16
High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report
journal, January 2019
- Hersh, Craig P.; Adcock, Ian M.; Celedón, Juan C.
- Annals of the American Thoracic Society, Vol. 16, Issue 1
Genetic Anomalies of the Respiratory Tract
journal, January 2020
- Cuppari, Caterina; Cutrupi, Maria Concetta; Salpietro, Annamaria
- Current Respiratory Medicine Reviews, Vol. 15, Issue 3
Human lung development: recent progress and new challenges
text, January 2018
- Rawlins, Emma; Nikolic, Marko; Sun, Dawei
- Apollo - University of Cambridge Repository
Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations.
text, January 2019
- Sakornsakolpat, Phuwanat; Prokopenko, Dmitry; Lamontagne, Maxime
- Apollo - University of Cambridge Repository
Constructing and optimizing 3D atlases from 2D data with application to the developing mouse brain
journal, February 2021
- Young, David M.; Fazel Darbandi, Siavash; Schwartz, Grace
- eLife, Vol. 10
The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease.
text, January 2019
- Schiller, Herbert B.; Montoro, Daniel T.; Simon, Lukas M.
- Apollo - University of Cambridge Repository
Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations
text, January 2019
- Sakornsakolpat, Phuwanat; Prokopenko, Dmitry; Lamontagne, Maxime
- Nature Publishing Group
Spatial distribution of marker gene activity in the mouse lung during alveolarization
journal, February 2019
- Ljungberg, M. Cecilia; Sadi, Mayce; Wang, Yunguan
- Data in Brief, Vol. 22
A revised airway epithelial hierarchy includes CFTR-expressing ionocytes
journal, August 2018
- Montoro, Daniel T.; Haber, Adam L.; Biton, Moshe
- Nature, Vol. 560, Issue 7718
Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations
journal, February 2019
- Sakornsakolpat, Phuwanat; Prokopenko, Dmitry; Lamontagne, Maxime
- Nature Genetics, Vol. 51, Issue 3
Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis
journal, June 2019
- Reyfman, Paul A.; Walter, James M.; Joshi, Nikita
- American Journal of Respiratory and Critical Care Medicine, Vol. 199, Issue 12
High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report
journal, January 2019
- Hersh, Craig P.; Adcock, Ian M.; Celedón, Juan C.
- Annals of the American Thoracic Society, Vol. 16, Issue 1
Impact of Transcriptomics on Our Understanding of Pulmonary Fibrosis
journal, April 2018
- Vukmirovic, Milica; Kaminski, Naftali
- Frontiers in Medicine, Vol. 5
Figures / Tables found in this record: