Human Lung Cell Atlas 1.0

This network will create the first version of the Human Lung Cell Atlas by developing and extending computational methods to allow the integration of single cell and spatial transcriptomics, microscopy, and other data types.

Creating a lung atlas that will be broadly useful as a reference for understanding diseases such as asthma will require integrating samples from varying ages and ethnicities. This project will build upon the existing collection of pediatric airway and lung samples to include additional Black and Asian pediatric samples from across five age groups and multiple locations in the lung.

This Network was awarded the CZI Seed Networks Incentive to Support Diversity for the Human Cell Atlas.

This group developed techniques for single-cell dissociation, single-nuclear dissociation, PLISH, a multiplexed in situ hybridization platform, and created crucial benchmarking and query mapping tools for single-cell RNA-sequencing data. With this data, they developed an integrated human lung endothelial cell atlas using an inclusive and harmonized set of cell-type annotations proving beneficial in both SARS-CoV-2 research and the greater research community. This work supported numerous publications spanning computational, pulmonary research, and SARS-CoV-2 research, eight softwares and platforms, and nine foundational Human Cell Atlas datasets.

Papers:

• Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease
• A molecular cell atlas of the human lung from single-cell RNA sequencing
• Benchmarking atlas-level data integration in single-cell genomics
• Compositional perturbation autoencoder for single-cell response modeling
• R-SPONDIN2+ Mesenchymal Cells Form the Bud Tip Progenitor Niche During Human Lung Development
• Sfaira accelerates data and model reuse in single-cell genomics
• Connectome: computation and visualization of cell-cell signaling topologies in single-cell systems data
• Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung
• Single-cell RNA sequencing identifies aberrant transcriptional profiles of cellular populations and altered alveolar niche signaling networks in Chronic Obstructive Pulmonary Disease (COPD)
• Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis
• The Idiopathic Pulmonary Fibrosis Cell Atlas. American Journal of Physiology-Lung Cellular and Molecular Physiology
• A Versatile Oblique Plane Microscope for Large-Scale and High-Resolution Imaging of Subcellular Dynamics
• Query to reference single-cell integration with transfer learning
• Lung transplantation for patients with severe COVID-19

Datasets:

• Single-cell RNA-seq mapping of nasal and tracheobronchial airways in human healthy volunteers
• Ischaemic sensitivity of human tissue by single-cell RNA seq
• Tissue Stability Cell Atlas
• Single-cell atlas of the airway epithelium
• Idiopathic Pulmonary Fibrosis Cell Atlas
• Lung Endothelial Cell Atlas
• Pediatric human and mouse lung scTHS-seq
• The local and systemic response to SARS-CoV-2 infection in children and adults
• Lung transplantation for patients with severe COVID-19

Software:

• FastCAR, SCIB, Single-Cell RNA-Sequencing Pipelines, Lung Cell Atlas Platform, OPM (Oblique Plane Microscopy), scArches