Mardiyyah/TAPT_data_V2_split · Datasets at Hugging Face

PMCID stringclasses 24 values	Title stringclasses 24 values	Sentences stringlengths 2 40.7k
PMC10287567	An integrated cell atlas of the lung in health and disease.	g, Composition of the clusters shown in f by study, with cells from control samples colored in gray.
PMC10287567	An integrated cell atlas of the lung in health and disease.	h, Expression of marker genes for IPF-enriched cluster 0 per alveolar fibroblast cluster.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Cluster 5 was excluded as 96% of its cells were from a single donor.
PMC10287567	An integrated cell atlas of the lung in health and disease.	i, UMAP of all MDMs in the HLCA, colored by Leiden cluster.
PMC10287567	An integrated cell atlas of the lung in health and disease.	j, Composition of the MDM clusters from i by disease.
PMC10287567	An integrated cell atlas of the lung in health and disease.	k, Expression of cluster marker genes among all MDM clusters excluding donor-specific clusters 5 and 6.
PMC10287567	An integrated cell atlas of the lung in health and disease.	For h and k, mean counts were normalized such that the highest group mean was set to 1 for each gene.
PMC10287567	An integrated cell atlas of the lung in health and disease.	For b, c and e, the boxes show the median and interquartile range.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Data points more than 1.5 times the interquartile range outside the low and high quartile are considered outliers.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Whiskers extend to the furthest nonoutlier point.
PMC10287567	An integrated cell atlas of the lung in health and disease.	BALF, bronchoalveolar lavage fluid; CF, cystic fibrosis; Drop-Seq, droplet sequencing; ILD, interstitial lung disease; Mph, macrophages; SM, smooth muscle; uncert.,
PMC10287567	An integrated cell atlas of the lung in health and disease.	uncertainty.
PMC10287567	An integrated cell atlas of the lung in health and disease.	a, UMAP of the extended HLCA colored by coarse annotation (HLCA core) or in gray (cells mapped to the core).
PMC10287567	An integrated cell atlas of the lung in health and disease.	b, Uncertainty of label transfer from the HLCA core to newly mapped datasets, categorized by several experimental or biological features.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Categories with fewer than two instances are not shown.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The numbers of datasets per category were as follows: 30 cells, 7 nuclei, 23 healthy, 5 IPF, 3 CF, 3 carcinoma, 4 ILD, 8 surgical resection, 7 donor lung, 12 lung explant, 6 bronchoalveolar lavage fluid, 4 autopsy, 9 10x 5′, 31 10x 3′, 4 Drop-Seq and 3 Seq-Well.
PMC10287567	An integrated cell atlas of the lung in health and disease.	c, Bottom, mean label transfer uncertainty per mapped healthy lung sample in the HLCA extension, grouped into age bins and colored by study.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The numbers of mapped samples per age bin were as follows: 43 for 0–10 years, 33 for 10–20 years, 31 for 20–30 years, 23 for 30–40 years, 19 for 40–50 years, 12 for 50–60 years, 9 for 60–70 years, 8 for 70–80 years and 2 for 80–90 years.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Top, bar plot showing the number of donors per age group in the HLCA core.
PMC10287567	An integrated cell atlas of the lung in health and disease.	d, Violin plot of label transfer uncertainty per transferred cell type label for a single mapped IPF dataset, split into cells from healthy donors (blue) and donors with IPF (orange).
PMC10287567	An integrated cell atlas of the lung in health and disease.	e, Uncertainty-based disease signature scores among alveolar fibroblasts and alveolar macrophages, split into cells from control donors (n = 10,453 and 1,812, respectively), and low-uncertainty cells (n = 1,419 and 200, respectively) and high-uncertainty cells (n = 1,172 and 162, respectively) from donors with IPF.
PMC10287567	An integrated cell atlas of the lung in health and disease.	f, UMAP embedding of alveolar fibroblasts (labeled with manual annotation (core) or label transfer (five IPF datasets)) colored by Leiden cluster.
PMC10287567	An integrated cell atlas of the lung in health and disease.	g, Composition of the clusters shown in f by study, with cells from control samples colored in gray.
PMC10287567	An integrated cell atlas of the lung in health and disease.	h, Expression of marker genes for IPF-enriched cluster 0 per alveolar fibroblast cluster.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Cluster 5 was excluded as 96% of its cells were from a single donor.
PMC10287567	An integrated cell atlas of the lung in health and disease.	i, UMAP of all MDMs in the HLCA, colored by Leiden cluster.
PMC10287567	An integrated cell atlas of the lung in health and disease.	j, Composition of the MDM clusters from i by disease.
PMC10287567	An integrated cell atlas of the lung in health and disease.	k, Expression of cluster marker genes among all MDM clusters excluding donor-specific clusters 5 and 6.
PMC10287567	An integrated cell atlas of the lung in health and disease.	For h and k, mean counts were normalized such that the highest group mean was set to 1 for each gene.
PMC10287567	An integrated cell atlas of the lung in health and disease.	For b, c and e, the boxes show the median and interquartile range.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Data points more than 1.5 times the interquartile range outside the low and high quartile are considered outliers.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Whiskers extend to the furthest nonoutlier point.
PMC10287567	An integrated cell atlas of the lung in health and disease.	BALF, bronchoalveolar lavage fluid; CF, cystic fibrosis; Drop-Seq, droplet sequencing; ILD, interstitial lung disease; Mph, macrophages; SM, smooth muscle; uncert.,
PMC10287567	An integrated cell atlas of the lung in health and disease.	uncertainty.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Out of 37 new datasets, 27 were observed to map well to the HLCA, as evaluated by the mean label transfer uncertainty score (Fig. 6b, Supplementary Fig. 10a and Methods).
PMC10287567	An integrated cell atlas of the lung in health and disease.	The remaining ten datasets were often from coronavirus disease 2019 (COVID-19) studies or, unlike the HLCA core, contained pediatric samples (Fig. 6b,c and Supplementary Fig. 10b).
PMC10287567	An integrated cell atlas of the lung in health and disease.	In these datasets, higher uncertainty values may be attributable to true biological differences between the mapped data and the HLCA core adult, healthy lung samples.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Overall, the successfully mapped datasets include disease samples, as well as single-nucleus and single-cell data from multiple chemistries (Fig. 6b), demonstrating the potential of the HLCA core as a universal reference.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Pulmonary diseases are characterized by the emergence of unique disease-associated transcriptional phenotypes.
PMC10287567	An integrated cell atlas of the lung in health and disease.	We observed higher levels of label transfer uncertainty in datasets from diseased lungs (Fig. 6b, condition), possibly flagging cell types changed in response to disease.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Specifically, labels of alveolar fibroblasts and alveolar macrophages, which interact to form a dysregulated cellular circuit in idiopathic pulmonary fibrosis (IPFs), are transferred with higher uncertainty in IPF samples than in samples from healthy controls from the same dataset (Fig. 6d and Extended Data Fig. 9a,b).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Furthermore, uncertainty scores separate cells—derived from donors with IPF—within these cell types into more and less affected subsets: the genes more highly expressed in the high-uncertainty subset are also lowly expressed in healthy samples (Fig. 6e).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Genes downregulated in high-uncertainty IPF macrophages are associated with homeostatic functions of tissue-resident alveolar macrophages and lipid metabolism (PPARG, FABP4 and others), while upregulated genes are associated with extracellular matrix remodeling and scar formation in the context of lung fibrosis (SPP1, PLA2G7 and CCL2; Supplementary Tables 12 and 13 and Extended Data Fig. 9b,c).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Thus, the HLCA core can be used to annotate new data, identify previously unreported populations, and—using label transfer uncertainty scores—help to detect disease-affected cell states and corresponding gene expression programs.
PMC10287567	An integrated cell atlas of the lung in health and disease.	This vastly speeds up analysis and interpretation of new data, automatically prioritizing the most relevant populations.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Automated mapping of new data to the HLCA core can be done by any user via an interactive web portal (https://github.com/LungCellAtlas/HLCA) or using code tutorials as provided online.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Similar to healthy cellular states, the HLCA can provide insight into disease-specific states that are consistent across demographics and experimental protocols.
PMC10287567	An integrated cell atlas of the lung in health and disease.	To demonstrate this, we determined which cell types are consistently affected by IPF across datasets, extending the previous IPF analysis to five independent datasets.
PMC10287567	An integrated cell atlas of the lung in health and disease.	We found that cells labeled as alveolar fibroblasts consistently show high uncertainty levels in IPF samples compared with controls across all mapped IPF datasets that include controls (Extended Data Fig. 10a).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Clustering of alveolar fibroblasts from the HLCA core and all IPF datasets shows that cells from patients with IPF predominantly cluster together in a single cluster (Fig. 6f,g and Extended Data Fig. 10b) characterized by high expression of genes previously associated with IPF (CCL2, COL1A1, CTHRC1 and MMP19), as well as further fibrosis-associated markers (SERPINE1, an inhibitor of extracellular matrix breakdown, and HIF1A, a chronic hypoxia response gene; Fig. 6h and Supplementary Table 14).
PMC10287567	An integrated cell atlas of the lung in health and disease.	These marker genes are consistently expressed across datasets (Extended Data Fig. 10c), confirming that the identification of this IPF-specific alveolar fibroblast state is reproducible.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The HLCA contains data across more than ten lung diseases, providing the unique opportunity to discover cellular states shared across diseases.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Discovering such common diseased cellular states could improve our understanding of lung diseases and accelerate the identification of effective treatments.
PMC10287567	An integrated cell atlas of the lung in health and disease.	For example, profibrotic SPP1 monocyte-derived macrophages (MDMs) have previously been reported in COVID-19, IPF and cancer.
PMC10287567	An integrated cell atlas of the lung in health and disease.	To test whether similar cross-disease MDM states could be discovered in the HLCA, we performed clustering of all MDMs from the HLCA (Fig. 6i).
PMC10287567	An integrated cell atlas of the lung in health and disease.	We identified four main MDM subtypes (Methods and Supplementary Table 15), each showing distinct gene expression and disease enrichment patterns, and representing different stages of monocyte-to-MDM differentiation and adaptation to the disease microenvironment.
PMC10287567	An integrated cell atlas of the lung in health and disease.	First, an early and inflammatory MDM state was observed that was high in the expression of CCL2, a gene involved in the recruitment of immune cells.
PMC10287567	An integrated cell atlas of the lung in health and disease.	This cluster predominantly contained cells from bronchoalveolar lavage fluid samples collected early during the course of COVID-19 pneumonia (cluster 2; IL1RN and S100A12; Fig. 6i–k and Extended Data Fig. 10d–h).
PMC10287567	An integrated cell atlas of the lung in health and disease.	We further observed an MDM subset expressing inflammation and phagocytosis-associated genes (cluster 4; CCL18, IL18, C1QA and TREM2) and enriched for samples from patients with COVID-19 pneumonia, as well as samples from patients with lung carcinoma (Fig. 6i–k and Extended Data Fig. 10d–h).
PMC10287567	An integrated cell atlas of the lung in health and disease.	A third MDM subset represented a more differentiated MDM phenotype, as indicated by the expression of MARCO and MCEMP1, dominated by cells from nondiseased samples (cluster 3; Fig. 6i–k and Extended Data Fig. 10d,f).
PMC10287567	An integrated cell atlas of the lung in health and disease.	The final MDM subset was dominated by IPF samples.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Interestingly, this cluster was also enriched for cells from patients who died late in the course of COVID-19 and developed post-COVID-19 lung fibrosis, as well as cells from patients with lung carcinoma (cluster 0; Fig. 6i–k and Extended Data Fig. 10g–i).
PMC10287567	An integrated cell atlas of the lung in health and disease.	This multidisease cluster is marked by high expression of SPP1, LPL and CHIT1—markers that have been shown to play a causal role in the development of lung fibrosis (Fig. 6k), one of which (CHIT1) is currently being investigated as a therapeutic target for IPF.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The expression of these markers is consistent across diseases and studies (Extended Data Fig. 10f), suggesting that also in cancer and late-stage COVID-19 samples a subset of MDMs adopt a fibrosis-associated phenotype.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Together, this analysis shows that the HLCA enables a better understanding of cellular states shared between diseases and thereby has the potential to accelerate the discovery of effective disease treatments.
PMC10287567	An integrated cell atlas of the lung in health and disease.	In this study, we built the HLCA: an integrated reference atlas of the human respiratory system.
PMC10287567	An integrated cell atlas of the lung in health and disease.	While previous studies have described the cellular heterogeneity within the human lung, study-specific biases due to experimental design and a limited number of sampled individuals constrain their capacity to capture population variation and serve as a universal reference.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The HLCA integrates data from 49 datasets to produce such a reference of 2.4 million cells, covering all major lung scRNA-seq studies published to date.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The core of this atlas consists of a fully integrated healthy reference of 14 datasets with 61 cell identities, including rare and novel cell types, representing a data-derived consensus annotation of the cellular landscape of the human lung.
PMC10287567	An integrated cell atlas of the lung in health and disease.	We leveraged the unprecedented complexity of the HLCA to recover cell type-specific gene modules associated with covariates such as lung anatomical location, age, sex, BMI and smoking status.
PMC10287567	An integrated cell atlas of the lung in health and disease.	By projecting data onto the HLCA, we showed that the HLCA enables a fast and detailed annotation of new datasets, as well as the identification of unique, disease-associated cell states and cell states common to multiple diseases.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The HLCA is publicly available as a resource for the community, together with an online platform for automated mapping of new data.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Taken together, the HLCA is a universal reference for single-cell lung research that promises to accelerate future studies into pulmonary health and disease.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The ultimate goal of a human lung cell atlas reference is to provide a comprehensive overview of all cells in the healthy human lung, as well as their variation from individual to individual.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Despite its overall diversity, the HLCA is limited by the biological, demographic and experimental diversity in the foundational single-cell studies.
PMC10287567	An integrated cell atlas of the lung in health and disease.	For example, 65% of the HLCA core data are from individuals of European harmonized ethnicity, highlighting the urgent need for diversification of the population sampled in lung studies.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Moreover, ethnicity metadata were based on self-reports and harmonized across datasets, which is an imperfect approach to representing the diversity of the atlas.
PMC10287567	An integrated cell atlas of the lung in health and disease.	SNP-based inference of genetic ancestry constitutes a more objective and therefore preferable approach to the grouping of individuals based on genetic background and would aid in better assessing the genetic diversity captured in the atlas.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Overall, more diverse samples will enrich the atlas, diversify captured cell identities and improve the quality of the HLCA as a reference for new datasets.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Such a reference will also enable comparison with model systems such as mice, cell lines or organoids, although further method development may be required to map across diverse in vitro and clinical datasets.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The constituent datasets of the HLCA vary widely in experimental design, such as the sample handling protocol or single-cell platform used, causing dataset-specific batch effects.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The quality of the HLCA hinges on the choice of data integration method, with methods such as Seurat’s RPCA and Harmony failing to correctly group rare cell identities into separate clusters.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Nevertheless, also in the HLCA, certain subsets of T cells (regulatory T cells and γδ T cells) could not be identified as separate clusters, showing the limitations of the current HLCA in capturing cellular heterogeneity for a subset of immune cell types.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Mapping additional datasets with high-resolution annotations (for example, derived from multimodal data) could provide the power to detect these cell identities in the atlas.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Indeed, the HLCA must be viewed as a live resource that requires continuous updates.
PMC10287567	An integrated cell atlas of the lung in health and disease.	While we showed that mapping new, spatially annotated data to the HLCA core can refine HLCA annotations, this new knowledge must be consolidated by regular updates of the HLCA with new datasets (including epigenomic, spatial and imaging data) and refinements of HLCA annotations based on additional expert opinions.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Thereby, the HLCA can serve as a community- and data-driven platform for open discussion on lung cell identities as the respiratory community progresses in charting the cellular landscape of the lung.
PMC10287567	An integrated cell atlas of the lung in health and disease.	In this process, we envision that the HLCA will be completed in two phases: first on the level of cellular variation (when no new consensus cell types can be found) and then in the description of individual variation (when population diversity is fully represented).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Taken together, the HLCA provides a central single-cell reference of unprecedented size.
PMC10287567	An integrated cell atlas of the lung in health and disease.	It offers a model framework for building integrated, consensus-based, population-scale atlases for other organs within the Human Cell Atlas.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The HLCA is publicly available, and combined with an open-access platform to map new datasets to the atlas, this resource paves the way toward a better and more complete understanding of both health and disease in the human lung.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Ethics approval information per study was as follows.
PMC10287567	An integrated cell atlas of the lung in health and disease.	For the pooled data from refs. ,
PMC10287567	An integrated cell atlas of the lung in health and disease.	approval was given by the Vanderbilt Institutional Review Board (IRB) (numbers 060165 and 171657) and Western IRB (number 20181836).
PMC10287567	An integrated cell atlas of the lung in health and disease.	All samples were collected from declined organ donors who were also consented for research.
PMC10287567	An integrated cell atlas of the lung in health and disease.	For ref. ,
PMC10287567	An integrated cell atlas of the lung in health and disease.	the study was approved by the Comité de Protection des Personnes Sud Est IV (approval number 17/081).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Informed written consent was obtained from all participants involved.
PMC10287567	An integrated cell atlas of the lung in health and disease.	For Jain_Misharin_2021 (A.V.M., M.J. and N.S.M., newly generated dataset), the protocol was approved by the Northwestern University IRB (STU00214826).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Written informed consent was obtained from all study participants.

PMC10287567

An integrated cell atlas of the lung in health and disease.

g, Composition of the clusters shown in f by study, with cells from control samples colored in gray.

PMC10287567

An integrated cell atlas of the lung in health and disease.

h, Expression of marker genes for IPF-enriched cluster 0 per alveolar fibroblast cluster.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Cluster 5 was excluded as 96% of its cells were from a single donor.

PMC10287567

An integrated cell atlas of the lung in health and disease.

i, UMAP of all MDMs in the HLCA, colored by Leiden cluster.

PMC10287567

An integrated cell atlas of the lung in health and disease.

j, Composition of the MDM clusters from i by disease.

PMC10287567

An integrated cell atlas of the lung in health and disease.

k, Expression of cluster marker genes among all MDM clusters excluding donor-specific clusters 5 and 6.

PMC10287567

An integrated cell atlas of the lung in health and disease.

For h and k, mean counts were normalized such that the highest group mean was set to 1 for each gene.

PMC10287567

An integrated cell atlas of the lung in health and disease.

For b, c and e, the boxes show the median and interquartile range.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Data points more than 1.5 times the interquartile range outside the low and high quartile are considered outliers.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Whiskers extend to the furthest nonoutlier point.

PMC10287567

An integrated cell atlas of the lung in health and disease.

BALF, bronchoalveolar lavage fluid; CF, cystic fibrosis; Drop-Seq, droplet sequencing; ILD, interstitial lung disease; Mph, macrophages; SM, smooth muscle; uncert.,

PMC10287567

An integrated cell atlas of the lung in health and disease.

uncertainty.

PMC10287567

An integrated cell atlas of the lung in health and disease.

a, UMAP of the extended HLCA colored by coarse annotation (HLCA core) or in gray (cells mapped to the core).

PMC10287567

An integrated cell atlas of the lung in health and disease.

b, Uncertainty of label transfer from the HLCA core to newly mapped datasets, categorized by several experimental or biological features.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Categories with fewer than two instances are not shown.

PMC10287567

An integrated cell atlas of the lung in health and disease.

The numbers of datasets per category were as follows: 30 cells, 7 nuclei, 23 healthy, 5 IPF, 3 CF, 3 carcinoma, 4 ILD, 8 surgical resection, 7 donor lung, 12 lung explant, 6 bronchoalveolar lavage fluid, 4 autopsy, 9 10x 5′, 31 10x 3′, 4 Drop-Seq and 3 Seq-Well.

PMC10287567

An integrated cell atlas of the lung in health and disease.

c, Bottom, mean label transfer uncertainty per mapped healthy lung sample in the HLCA extension, grouped into age bins and colored by study.

PMC10287567

An integrated cell atlas of the lung in health and disease.

The numbers of mapped samples per age bin were as follows: 43 for 0–10 years, 33 for 10–20 years, 31 for 20–30 years, 23 for 30–40 years, 19 for 40–50 years, 12 for 50–60 years, 9 for 60–70 years, 8 for 70–80 years and 2 for 80–90 years.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Top, bar plot showing the number of donors per age group in the HLCA core.

PMC10287567

An integrated cell atlas of the lung in health and disease.

d, Violin plot of label transfer uncertainty per transferred cell type label for a single mapped IPF dataset, split into cells from healthy donors (blue) and donors with IPF (orange).

PMC10287567

An integrated cell atlas of the lung in health and disease.

e, Uncertainty-based disease signature scores among alveolar fibroblasts and alveolar macrophages, split into cells from control donors (n = 10,453 and 1,812, respectively), and low-uncertainty cells (n = 1,419 and 200, respectively) and high-uncertainty cells (n = 1,172 and 162, respectively) from donors with IPF.

PMC10287567

An integrated cell atlas of the lung in health and disease.

f, UMAP embedding of alveolar fibroblasts (labeled with manual annotation (core) or label transfer (five IPF datasets)) colored by Leiden cluster.

PMC10287567

An integrated cell atlas of the lung in health and disease.

g, Composition of the clusters shown in f by study, with cells from control samples colored in gray.

PMC10287567

An integrated cell atlas of the lung in health and disease.

h, Expression of marker genes for IPF-enriched cluster 0 per alveolar fibroblast cluster.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Cluster 5 was excluded as 96% of its cells were from a single donor.

PMC10287567

An integrated cell atlas of the lung in health and disease.

i, UMAP of all MDMs in the HLCA, colored by Leiden cluster.

PMC10287567

An integrated cell atlas of the lung in health and disease.

j, Composition of the MDM clusters from i by disease.

PMC10287567

An integrated cell atlas of the lung in health and disease.

k, Expression of cluster marker genes among all MDM clusters excluding donor-specific clusters 5 and 6.

PMC10287567

An integrated cell atlas of the lung in health and disease.

For h and k, mean counts were normalized such that the highest group mean was set to 1 for each gene.

PMC10287567

An integrated cell atlas of the lung in health and disease.

For b, c and e, the boxes show the median and interquartile range.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Data points more than 1.5 times the interquartile range outside the low and high quartile are considered outliers.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Whiskers extend to the furthest nonoutlier point.

PMC10287567

An integrated cell atlas of the lung in health and disease.

BALF, bronchoalveolar lavage fluid; CF, cystic fibrosis; Drop-Seq, droplet sequencing; ILD, interstitial lung disease; Mph, macrophages; SM, smooth muscle; uncert.,

PMC10287567

An integrated cell atlas of the lung in health and disease.

uncertainty.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Out of 37 new datasets, 27 were observed to map well to the HLCA, as evaluated by the mean label transfer uncertainty score (Fig. 6b, Supplementary Fig. 10a and Methods).

PMC10287567

An integrated cell atlas of the lung in health and disease.

The remaining ten datasets were often from coronavirus disease 2019 (COVID-19) studies or, unlike the HLCA core, contained pediatric samples (Fig. 6b,c and Supplementary Fig. 10b).

PMC10287567

An integrated cell atlas of the lung in health and disease.

In these datasets, higher uncertainty values may be attributable to true biological differences between the mapped data and the HLCA core adult, healthy lung samples.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Overall, the successfully mapped datasets include disease samples, as well as single-nucleus and single-cell data from multiple chemistries (Fig. 6b), demonstrating the potential of the HLCA core as a universal reference.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Pulmonary diseases are characterized by the emergence of unique disease-associated transcriptional phenotypes.

PMC10287567

An integrated cell atlas of the lung in health and disease.

We observed higher levels of label transfer uncertainty in datasets from diseased lungs (Fig. 6b, condition), possibly flagging cell types changed in response to disease.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Specifically, labels of alveolar fibroblasts and alveolar macrophages, which interact to form a dysregulated cellular circuit in idiopathic pulmonary fibrosis (IPFs), are transferred with higher uncertainty in IPF samples than in samples from healthy controls from the same dataset (Fig. 6d and Extended Data Fig. 9a,b).

PMC10287567

An integrated cell atlas of the lung in health and disease.

Furthermore, uncertainty scores separate cells—derived from donors with IPF—within these cell types into more and less affected subsets: the genes more highly expressed in the high-uncertainty subset are also lowly expressed in healthy samples (Fig. 6e).

PMC10287567

An integrated cell atlas of the lung in health and disease.

Genes downregulated in high-uncertainty IPF macrophages are associated with homeostatic functions of tissue-resident alveolar macrophages and lipid metabolism (PPARG, FABP4 and others), while upregulated genes are associated with extracellular matrix remodeling and scar formation in the context of lung fibrosis (SPP1, PLA2G7 and CCL2; Supplementary Tables 12 and 13 and Extended Data Fig. 9b,c).

PMC10287567

An integrated cell atlas of the lung in health and disease.

Thus, the HLCA core can be used to annotate new data, identify previously unreported populations, and—using label transfer uncertainty scores—help to detect disease-affected cell states and corresponding gene expression programs.

PMC10287567

An integrated cell atlas of the lung in health and disease.

This vastly speeds up analysis and interpretation of new data, automatically prioritizing the most relevant populations.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Automated mapping of new data to the HLCA core can be done by any user via an interactive web portal (https://github.com/LungCellAtlas/HLCA) or using code tutorials as provided online.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Similar to healthy cellular states, the HLCA can provide insight into disease-specific states that are consistent across demographics and experimental protocols.

PMC10287567

An integrated cell atlas of the lung in health and disease.

To demonstrate this, we determined which cell types are consistently affected by IPF across datasets, extending the previous IPF analysis to five independent datasets.

PMC10287567

An integrated cell atlas of the lung in health and disease.

We found that cells labeled as alveolar fibroblasts consistently show high uncertainty levels in IPF samples compared with controls across all mapped IPF datasets that include controls (Extended Data Fig. 10a).

PMC10287567

An integrated cell atlas of the lung in health and disease.

Clustering of alveolar fibroblasts from the HLCA core and all IPF datasets shows that cells from patients with IPF predominantly cluster together in a single cluster (Fig. 6f,g and Extended Data Fig. 10b) characterized by high expression of genes previously associated with IPF (CCL2, COL1A1, CTHRC1 and MMP19), as well as further fibrosis-associated markers (SERPINE1, an inhibitor of extracellular matrix breakdown, and HIF1A, a chronic hypoxia response gene; Fig. 6h and Supplementary Table 14).

PMC10287567

An integrated cell atlas of the lung in health and disease.

These marker genes are consistently expressed across datasets (Extended Data Fig. 10c), confirming that the identification of this IPF-specific alveolar fibroblast state is reproducible.

PMC10287567

An integrated cell atlas of the lung in health and disease.

The HLCA contains data across more than ten lung diseases, providing the unique opportunity to discover cellular states shared across diseases.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Discovering such common diseased cellular states could improve our understanding of lung diseases and accelerate the identification of effective treatments.

PMC10287567

An integrated cell atlas of the lung in health and disease.

For example, profibrotic SPP1 monocyte-derived macrophages (MDMs) have previously been reported in COVID-19, IPF and cancer.

PMC10287567

An integrated cell atlas of the lung in health and disease.

To test whether similar cross-disease MDM states could be discovered in the HLCA, we performed clustering of all MDMs from the HLCA (Fig. 6i).

PMC10287567

An integrated cell atlas of the lung in health and disease.

We identified four main MDM subtypes (Methods and Supplementary Table 15), each showing distinct gene expression and disease enrichment patterns, and representing different stages of monocyte-to-MDM differentiation and adaptation to the disease microenvironment.

PMC10287567

An integrated cell atlas of the lung in health and disease.

First, an early and inflammatory MDM state was observed that was high in the expression of CCL2, a gene involved in the recruitment of immune cells.

PMC10287567

An integrated cell atlas of the lung in health and disease.

This cluster predominantly contained cells from bronchoalveolar lavage fluid samples collected early during the course of COVID-19 pneumonia (cluster 2; IL1RN and S100A12; Fig. 6i–k and Extended Data Fig. 10d–h).

PMC10287567

An integrated cell atlas of the lung in health and disease.

We further observed an MDM subset expressing inflammation and phagocytosis-associated genes (cluster 4; CCL18, IL18, C1QA and TREM2) and enriched for samples from patients with COVID-19 pneumonia, as well as samples from patients with lung carcinoma (Fig. 6i–k and Extended Data Fig. 10d–h).

PMC10287567

An integrated cell atlas of the lung in health and disease.

A third MDM subset represented a more differentiated MDM phenotype, as indicated by the expression of MARCO and MCEMP1, dominated by cells from nondiseased samples (cluster 3; Fig. 6i–k and Extended Data Fig. 10d,f).

PMC10287567

An integrated cell atlas of the lung in health and disease.

The final MDM subset was dominated by IPF samples.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Interestingly, this cluster was also enriched for cells from patients who died late in the course of COVID-19 and developed post-COVID-19 lung fibrosis, as well as cells from patients with lung carcinoma (cluster 0; Fig. 6i–k and Extended Data Fig. 10g–i).

PMC10287567

An integrated cell atlas of the lung in health and disease.

This multidisease cluster is marked by high expression of SPP1, LPL and CHIT1—markers that have been shown to play a causal role in the development of lung fibrosis (Fig. 6k), one of which (CHIT1) is currently being investigated as a therapeutic target for IPF.

PMC10287567

An integrated cell atlas of the lung in health and disease.

The expression of these markers is consistent across diseases and studies (Extended Data Fig. 10f), suggesting that also in cancer and late-stage COVID-19 samples a subset of MDMs adopt a fibrosis-associated phenotype.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Together, this analysis shows that the HLCA enables a better understanding of cellular states shared between diseases and thereby has the potential to accelerate the discovery of effective disease treatments.

PMC10287567

An integrated cell atlas of the lung in health and disease.

In this study, we built the HLCA: an integrated reference atlas of the human respiratory system.

PMC10287567

An integrated cell atlas of the lung in health and disease.

While previous studies have described the cellular heterogeneity within the human lung, study-specific biases due to experimental design and a limited number of sampled individuals constrain their capacity to capture population variation and serve as a universal reference.

PMC10287567

An integrated cell atlas of the lung in health and disease.

The HLCA integrates data from 49 datasets to produce such a reference of 2.4 million cells, covering all major lung scRNA-seq studies published to date.

PMC10287567

An integrated cell atlas of the lung in health and disease.

The core of this atlas consists of a fully integrated healthy reference of 14 datasets with 61 cell identities, including rare and novel cell types, representing a data-derived consensus annotation of the cellular landscape of the human lung.

PMC10287567

An integrated cell atlas of the lung in health and disease.

We leveraged the unprecedented complexity of the HLCA to recover cell type-specific gene modules associated with covariates such as lung anatomical location, age, sex, BMI and smoking status.

PMC10287567

An integrated cell atlas of the lung in health and disease.

By projecting data onto the HLCA, we showed that the HLCA enables a fast and detailed annotation of new datasets, as well as the identification of unique, disease-associated cell states and cell states common to multiple diseases.

PMC10287567

An integrated cell atlas of the lung in health and disease.

The HLCA is publicly available as a resource for the community, together with an online platform for automated mapping of new data.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Taken together, the HLCA is a universal reference for single-cell lung research that promises to accelerate future studies into pulmonary health and disease.

PMC10287567

An integrated cell atlas of the lung in health and disease.

The ultimate goal of a human lung cell atlas reference is to provide a comprehensive overview of all cells in the healthy human lung, as well as their variation from individual to individual.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Despite its overall diversity, the HLCA is limited by the biological, demographic and experimental diversity in the foundational single-cell studies.

PMC10287567

An integrated cell atlas of the lung in health and disease.

For example, 65% of the HLCA core data are from individuals of European harmonized ethnicity, highlighting the urgent need for diversification of the population sampled in lung studies.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Moreover, ethnicity metadata were based on self-reports and harmonized across datasets, which is an imperfect approach to representing the diversity of the atlas.

PMC10287567

An integrated cell atlas of the lung in health and disease.

SNP-based inference of genetic ancestry constitutes a more objective and therefore preferable approach to the grouping of individuals based on genetic background and would aid in better assessing the genetic diversity captured in the atlas.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Overall, more diverse samples will enrich the atlas, diversify captured cell identities and improve the quality of the HLCA as a reference for new datasets.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Such a reference will also enable comparison with model systems such as mice, cell lines or organoids, although further method development may be required to map across diverse in vitro and clinical datasets.

PMC10287567

An integrated cell atlas of the lung in health and disease.

The constituent datasets of the HLCA vary widely in experimental design, such as the sample handling protocol or single-cell platform used, causing dataset-specific batch effects.

PMC10287567

An integrated cell atlas of the lung in health and disease.

The quality of the HLCA hinges on the choice of data integration method, with methods such as Seurat’s RPCA and Harmony failing to correctly group rare cell identities into separate clusters.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Nevertheless, also in the HLCA, certain subsets of T cells (regulatory T cells and γδ T cells) could not be identified as separate clusters, showing the limitations of the current HLCA in capturing cellular heterogeneity for a subset of immune cell types.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Mapping additional datasets with high-resolution annotations (for example, derived from multimodal data) could provide the power to detect these cell identities in the atlas.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Indeed, the HLCA must be viewed as a live resource that requires continuous updates.

PMC10287567

An integrated cell atlas of the lung in health and disease.

While we showed that mapping new, spatially annotated data to the HLCA core can refine HLCA annotations, this new knowledge must be consolidated by regular updates of the HLCA with new datasets (including epigenomic, spatial and imaging data) and refinements of HLCA annotations based on additional expert opinions.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Thereby, the HLCA can serve as a community- and data-driven platform for open discussion on lung cell identities as the respiratory community progresses in charting the cellular landscape of the lung.

PMC10287567

An integrated cell atlas of the lung in health and disease.

In this process, we envision that the HLCA will be completed in two phases: first on the level of cellular variation (when no new consensus cell types can be found) and then in the description of individual variation (when population diversity is fully represented).

PMC10287567

An integrated cell atlas of the lung in health and disease.

Taken together, the HLCA provides a central single-cell reference of unprecedented size.

PMC10287567

An integrated cell atlas of the lung in health and disease.

It offers a model framework for building integrated, consensus-based, population-scale atlases for other organs within the Human Cell Atlas.

PMC10287567

An integrated cell atlas of the lung in health and disease.

The HLCA is publicly available, and combined with an open-access platform to map new datasets to the atlas, this resource paves the way toward a better and more complete understanding of both health and disease in the human lung.

PMC10287567

An integrated cell atlas of the lung in health and disease.

Ethics approval information per study was as follows.

PMC10287567

An integrated cell atlas of the lung in health and disease.

For the pooled data from refs. ,

PMC10287567

An integrated cell atlas of the lung in health and disease.

approval was given by the Vanderbilt Institutional Review Board (IRB) (numbers 060165 and 171657) and Western IRB (number 20181836).

PMC10287567

An integrated cell atlas of the lung in health and disease.

All samples were collected from declined organ donors who were also consented for research.

PMC10287567

An integrated cell atlas of the lung in health and disease.

For ref. ,

PMC10287567

An integrated cell atlas of the lung in health and disease.

the study was approved by the Comité de Protection des Personnes Sud Est IV (approval number 17/081).

PMC10287567

An integrated cell atlas of the lung in health and disease.

Informed written consent was obtained from all participants involved.

PMC10287567

An integrated cell atlas of the lung in health and disease.

For Jain_Misharin_2021 (A.V.M., M.J. and N.S.M., newly generated dataset), the protocol was approved by the Northwestern University IRB (STU00214826).

PMC10287567

An integrated cell atlas of the lung in health and disease.

Written informed consent was obtained from all study participants.