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 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.

Keywords: 3D imaging; lung development; lung imaging; lung omics; single cell analysis; web resource.

Fig. 1.

The LungMAP Consortium. Organizations funded by the National Heart, Lung, and Blood Institute for the Molecular Atlas of Lung Development Program. NIH, National Institutes of Health.

Fig. 2.

The LungMAP data. From top, clockwise: reference hematoxylin and eosin histology; multiplex fluorescent in situ hybridization with overlaying feature annotations; high-throughput in situ hybridization; proteomics and lipidomics; imaging mass spectrometry; Vibra-SIMM; 3-dimensional (3D) confocal imaging; profiling mRNA, miR, and methylation during development and maturation; single-cell RNA-seq and related methods; quantitative multicolor immunohistochemistry.

Fig. 3.

The LungMAP resources. LungMAP project resources include public data, specialized analytic tools at complementary consortium websites, educational resources, and opportunities for involvement.

Fig. 4.

The LungMAP home page. Home page for www.lungmap.net, the official website for the LungMAP project.

Fig. 5.

Annotated LungMAP image. Hematoxylin and eosin-stained whole lung from P07 C57BL6 male mouse. Annotated features are shown on the right side of the screen (top to bottom): central bronchiole, lateral bronchiole, left lung alveolar, parenchyma, and pulmonary artery. Multiple instances of these features are noted on the image.

Fig. 6.

Automated LungMAP image annotation. Screenshot of interactive web application for automated identification of anatomic structures within bounding boxes drawn by user. Multiple regions of interest can be identified simultaneously. Right: posterior probability for each label for currently selected bounding box.