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, Log-normalized expression of the migratory dendritic cell marker CCR7 in cells identified during re-annotation as migratory dendritic cells, versus other dendritic cells.
PMC10287567	An integrated cell atlas of the lung in health and disease.	AT, alveolar type; DC, dendritic cell; FB, fibroblast; Mph, macrophage; MT, metallothionein; SM, smooth muscle; SMG, submucosal gland; TB, terminal bronchiole.
PMC10287567	An integrated cell atlas of the lung in health and disease.	a, A UMAP of the integrated HLCA, colored by level 1 annotation.
PMC10287567	An integrated cell atlas of the lung in health and disease.	b, Cluster label disagreement (label entropy) of Leiden 3 clusters of the HLCA.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The HLCA was split into three parts (immune, epithelial and endothelial/stromal) for ease of visualization.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Cells from every cluster are colored by label entropy.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Clusters with less than 20% of cells annotated at level 3 are colored gray.
PMC10287567	An integrated cell atlas of the lung in health and disease.	c, Cell type label composition of the immune cluster with the most label disagreement (left), with original labels (middle left) and matching manual re-annotations (middle right).
PMC10287567	An integrated cell atlas of the lung in health and disease.	A zoom-in on the UMAP from b shows the final re-annotations (right).
PMC10287567	An integrated cell atlas of the lung in health and disease.	d, UMAPs of the immune, epithelial and endothelial/stromal parts of the HLCA core with cell annotations from the expert manual re-annotation.
PMC10287567	An integrated cell atlas of the lung in health and disease.	e, Percentage of cells originally labeled correctly, mislabeled or underlabeled (that is, only labeled at a coarser level) compared with final manual re-annotations.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The percentages were calculated per manual annotation, as well as across all cells (right bar).
PMC10287567	An integrated cell atlas of the lung in health and disease.	f, UMAP of HLCA clusters annotated as rare epithelial cell types (that is, ionocytes, neuroendocrine cells and tuft cells).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Final annotations, original labels and the study of origin are shown (top), as well as the expression of ionocyte marker FOXI1, tuft cell marker LRMP and neuroendocrine marker CALCA (bottom).
PMC10287567	An integrated cell atlas of the lung in health and disease.	g, Log-normalized expression of the migratory dendritic cell marker CCR7 in cells identified during re-annotation as migratory dendritic cells, versus other dendritic cells.
PMC10287567	An integrated cell atlas of the lung in health and disease.	AT, alveolar type; DC, dendritic cell; FB, fibroblast; Mph, macrophage; MT, metallothionein; SM, smooth muscle; SMG, submucosal gland; TB, terminal bronchiole.
PMC10287567	An integrated cell atlas of the lung in health and disease.	A large-scale integrated atlas provides the unique opportunity to systematically investigate the consensus in cell type labeling across datasets.
PMC10287567	An integrated cell atlas of the lung in health and disease.	To identify areas of consensus and disagreement, we iteratively clustered the HLCA core and investigated donor diversity and cell type label agreement in these clusters using entropy scores (see Methods).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Most clusters contained cells from many donors (Extended Data Fig. 1a).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Clusters with low donor diversity (n = 14) were largely immune cell clusters (n = 13), representing donor- or donor group-specific phenotypes.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Similarly, a high diversity of (contradictory) cell type labels (high label entropy) can identify both annotation disagreements between studies and clusters of doublets (Methods).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Most clusters (61 out of 94) showed low label entropy, suggesting overall agreement of coarse cell type labels across datasets (Fig. 3b).
PMC10287567	An integrated cell atlas of the lung in health and disease.	The remaining 33 clusters exhibited high label entropy, highlighting cellular phenotypes that were differently labeled across datasets (Fig. 3b).
PMC10287567	An integrated cell atlas of the lung in health and disease.	For example, the immune cluster with the highest label entropy contained many cells that were originally mislabeled as monocytes and macrophages but were actually type 2 dendritic cells (Fig. 3c and Extended Data Fig. 1b).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Thus, populations with high label entropy identify mislabeled cell types, indicating the need for consensus re-annotation of the integrated atlas.
PMC10287567	An integrated cell atlas of the lung in health and disease.	As a first step to achieve such a consensus on the diversity of cell types present in the HLCA core, we performed a full re-annotation of the integrated data on the basis of the original annotations and six expert opinions (consensus annotation; Methods and Fig. 3d).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Each of the 61 annotated cell types (Supplementary Table 5) was detected in at least four datasets out of 14, often in specific parts of the respiratory system, and different cell types showed varying fractions of proliferating (MKI67) cells (Extended Data Fig. 2a–c).
PMC10287567	An integrated cell atlas of the lung in health and disease.	While our consensus cell type annotations partly correspond to original labels (41% of cells), there were also refinements (28%) and substantial re-annotations (31%; Fig. 3e and Supplementary Fig. 2).
PMC10287567	An integrated cell atlas of the lung in health and disease.	To robustly characterize the cell types, we established a universal set of marker genes that generalizes across individuals and studies (Methods, Extended Data Fig. 3 and Supplementary Table 6).
PMC10287567	An integrated cell atlas of the lung in health and disease.	The fully re-annotated HLCA core thus combines data from a diverse set of studies to provide a carefully curated reference for cell type annotations and marker genes in healthy lung tissue.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Rare cell types, such as ionocytes, tuft cells, neuroendocrine cells and specific immune cell subsets, are often difficult to identify in individual datasets.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Yet, combining datasets in the HLCA core provides better power for identifying these rare cell types.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Ionocytes, tuft and neuroendocrine cells make up only 0.08, 0.01 and 0.02% of the cells in the HLCA core according to the original labels, and were originally identified in only seven, two and four datasets out of 14, respectively.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Despite their low abundance, these cells formed three separate clusters of the HLCA core (Fig. 3f).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Our re-annotation increases the number of datasets in which these cells are detected up to threefold and identifies both cells falsely annotated as monocytes, tuft cells or neuroendocrine cells, as well as originally undetected rare cells (Fig. 3f and Supplementary Fig. 3a).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Importantly, other integration methods tested during our benchmarking, such as Harmony and Seurat’s RPCA, failed to separate these rare cells into distinct clusters (Supplementary Fig. 3b).
PMC10287567	An integrated cell atlas of the lung in health and disease.	We were further able to detect six cell identities that were not previously found in the human lung or were only recently described in individual studies.
PMC10287567	An integrated cell atlas of the lung in health and disease.	These cell types include migratory dendritic cells (n = 312 cells, expressing CCR7, LAD1 and COL19), hematopoietic stem cells (n = 60, expressing SPINK2, STMN, PRSS57 and CD34), highly proliferative hillock-like epithelial cells not previously reported in adult human lung (n = 4,600, expressing KRT6A, KRT13 and KRT14), the recently described alveolar type 0 cells (n = 1,440, expressing STFPB, SCGB3A2, SFTPC and SCGB3A1) and the closely related preterminal bronchiole secretory cells (n = 4,393, expressing SFTPB, SCGB3A2, SFTPC and SCGB3A1, together with alveolar type 0 cells called transitional club-AT2 cells) and a subset of smooth muscle cells (n = 335) that to our knowledge have not previously been described (Fig. 3d,g and Extended Data Fig. 4a–f).
PMC10287567	An integrated cell atlas of the lung in health and disease.	These smooth muscle cells, predominantly found in the airways, express canonical smooth muscle markers (CNN1 and MYH11) and also uniquely and consistently express FAM83D across datasets (Extended Data Fig. 4e,f).
PMC10287567	An integrated cell atlas of the lung in health and disease.	The HLCA core thus enables improved detection and identification of rare cell types, as well as the discovery of unknown cell types.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Demographic and other metadata covariates affect cellular transcriptional phenotypes.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Better insight into the impact of these covariates (for example, sex, BMI and smoking) on cell type gene expression can shed light on the contribution of these factors to progression from healthy to diseased states.
PMC10287567	An integrated cell atlas of the lung in health and disease.	In addition, technical covariates such as ribosomal and mitochondrial genes exhibit batch-specific variation in expression (Methods and Supplementary Table 7).
PMC10287567	An integrated cell atlas of the lung in health and disease.	The diversity in demographics (for example, smoking status, age, harmonized ethnicity and BMI) and experimental protocols represented in the HLCA core enables us to explore the contribution of each technical or biological covariate to cell type-specific gene expression variation (Methods and Supplementary Fig. 4).
PMC10287567	An integrated cell atlas of the lung in health and disease.	For many cell types, anatomical location is the biological variable explaining most of the variance between samples (Fig. 4a).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Furthermore, sex is most associated with transcriptomic variation in lymphatic endothelial cells, whereas BMI is most associated with variation in B and T cells, harmonized ethnicity in transitional club-AT2 cells and smoking status in innate lymphoid/natural killer cells.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Furthermore, for several cell types (for example, mast, AT1 and smooth muscle cells), the tissue dissociation protocol explains most of the variance of all technical as well as biological covariates recorded.
PMC10287567	An integrated cell atlas of the lung in health and disease.	These associations provide a systematic overview of the effects of biological and technical factors on the transcriptional state of lung cell types.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Fig. 4Demographic and technical variables driving interindividual variation.a, Fraction of total inter-sample variance in the HLCA core integrated embedding that correlates with specific covariates.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Covariates are split into technical (left) and biological covariates (right).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Cell types are ordered by the number of samples in which they were detected.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Only cell types present in at least 40 samples are shown.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Tissue sampling method represents the way a sample was obtained (for example, surgical resection or nasal brush).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Donor status represents the state of the donor at the moment of sample collection (for example, organ donor, diseased alive or healthy alive).
PMC10287567	An integrated cell atlas of the lung in health and disease.	The heatmap is masked gray where fewer than 40 samples were annotated for a specific covariate or where only one value was observed for all samples for that cell type.
PMC10287567	An integrated cell atlas of the lung in health and disease.	b, Selection of gene sets that are significantly associated with anatomical location CCF score, in different airway epithelial cell types.
PMC10287567	An integrated cell atlas of the lung in health and disease.	All gene set names are Gene Ontology biological process (GO: BP) terms.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Sets upregulated toward distal lungs are shown in green, whereas sets downregulated are shown in blue.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The full name of the term marked by an asterisk is ‘Antigen processing and presentation of exogenous peptide antigen via MHC-I’.
PMC10287567	An integrated cell atlas of the lung in health and disease.	c, Cell type proportions per sample, along the proximal-to-distal axis of the respiratory system.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The lowest and highest CCF scores shown (0.36 and 0.97) represent the most proximal and most distal sampled parts of the respiratory system, respectively (trachea and parenchyma), excluding the upper airways.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The dots are colored by the tissue dissociation protocol and tissue sampling method used for each sample.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The boxes show the median and interquartile range of the proportions.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Samples with proportions more than 1.5 times the interquartile range away from the high and low 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.	n = 23, 19, 9 and 90 for CCF scores 0.36, 0.72, 0.81 and 0.97, respectively.
PMC10287567	An integrated cell atlas of the lung in health and disease.	d, Selection of gene sets significantly up- (green) or downregulated (blue) with increasing BMI, in four different cell types.
PMC10287567	An integrated cell atlas of the lung in health and disease.	For b and d, P values were calculated using correlation-adjusted mean-rank gene set tests (Methods) and false discovery rate corrected using the Benjamini–Hochberg procedure.
PMC10287567	An integrated cell atlas of the lung in health and disease.	IL-1, interleukin-1; MHC-I, major histocompatibility complex class I; TNF, tumor necrosis factor.
PMC10287567	An integrated cell atlas of the lung in health and disease.	a, Fraction of total inter-sample variance in the HLCA core integrated embedding that correlates with specific covariates.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Covariates are split into technical (left) and biological covariates (right).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Cell types are ordered by the number of samples in which they were detected.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Only cell types present in at least 40 samples are shown.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Tissue sampling method represents the way a sample was obtained (for example, surgical resection or nasal brush).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Donor status represents the state of the donor at the moment of sample collection (for example, organ donor, diseased alive or healthy alive).
PMC10287567	An integrated cell atlas of the lung in health and disease.	The heatmap is masked gray where fewer than 40 samples were annotated for a specific covariate or where only one value was observed for all samples for that cell type.
PMC10287567	An integrated cell atlas of the lung in health and disease.	b, Selection of gene sets that are significantly associated with anatomical location CCF score, in different airway epithelial cell types.
PMC10287567	An integrated cell atlas of the lung in health and disease.	All gene set names are Gene Ontology biological process (GO: BP) terms.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Sets upregulated toward distal lungs are shown in green, whereas sets downregulated are shown in blue.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The full name of the term marked by an asterisk is ‘Antigen processing and presentation of exogenous peptide antigen via MHC-I’.
PMC10287567	An integrated cell atlas of the lung in health and disease.	c, Cell type proportions per sample, along the proximal-to-distal axis of the respiratory system.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The lowest and highest CCF scores shown (0.36 and 0.97) represent the most proximal and most distal sampled parts of the respiratory system, respectively (trachea and parenchyma), excluding the upper airways.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The dots are colored by the tissue dissociation protocol and tissue sampling method used for each sample.
PMC10287567	An integrated cell atlas of the lung in health and disease.	The boxes show the median and interquartile range of the proportions.
PMC10287567	An integrated cell atlas of the lung in health and disease.	Samples with proportions more than 1.5 times the interquartile range away from the high and low 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.	n = 23, 19, 9 and 90 for CCF scores 0.36, 0.72, 0.81 and 0.97, respectively.
PMC10287567	An integrated cell atlas of the lung in health and disease.	d, Selection of gene sets significantly up- (green) or downregulated (blue) with increasing BMI, in four different cell types.
PMC10287567	An integrated cell atlas of the lung in health and disease.	For b and d, P values were calculated using correlation-adjusted mean-rank gene set tests (Methods) and false discovery rate corrected using the Benjamini–Hochberg procedure.
PMC10287567	An integrated cell atlas of the lung in health and disease.	IL-1, interleukin-1; MHC-I, major histocompatibility complex class I; TNF, tumor necrosis factor.
PMC10287567	An integrated cell atlas of the lung in health and disease.	To better characterize how biological variables affect cellular phenotypes, we modeled their cell type-specific effects on the transcriptome at the gene level (Methods).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Sex-related differences in lymphatic endothelial cells are dominated by differential expression of genes located on the X and Y chromosomes, but also include a decrease in IFNAR1 in females (Supplementary Table 8), which may be linked to differential interferon responses between the biological sexes.
PMC10287567	An integrated cell atlas of the lung in health and disease.	We furthermore found cell type-specific programs that change with proximal (low CCF score) to distal (high CCF score) location along the respiratory tract (Supplementary Tables 8 and 9).
PMC10287567	An integrated cell atlas of the lung in health and disease.	For instance, oxidative phosphorylation (including cytochrome c oxidase genes such as COX7A1), antigen presentation by major histocompatibility complex class I molecules (including proteasome and protease subunit genes such as PSMD14 and PSMB4), signaling by interleukin-1 and tumor necrosis factor α, as well as planar cell polarity, were downregulated toward more distal locations in secretory, multiciliated and basal cells (Fig. 4b).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Some gene programs were specific for a subset of airway epithelial cell types (for example, cornification and keratinization, which were programs that were downregulated in distal multiciliated and secretory cells; including genes such as KRT8 and KRT19).
PMC10287567	An integrated cell atlas of the lung in health and disease.	The changes in airway epithelial cell states toward the terminal airways are further illustrated by increased expression of developmental pathway genes such as NKX2-1, NFIB, GATA6, BMP4 and SOX9 in multiciliated cells along the proximal-to-distal axis (Fig. 4b), whereas basal cells decrease in number (Fig. 4c).
PMC10287567	An integrated cell atlas of the lung in health and disease.	Similarly, several cell types display transcriptomic changes in donors with increasing BMI (Fig. 4d and Supplementary Tables 8 and 9).
PMC10287567	An integrated cell atlas of the lung in health and disease.	AT2 cells, secretory cells and alveolar macrophages exhibit downregulation of a range of biological processes (Supplementary Fig. 5), including cellular respiration, differentiation and synthesis of peptides and other molecules.
PMC10287567	An integrated cell atlas of the lung in health and disease.	In secretory cells, a downregulation of the insulin response pathway is also associated with higher BMI, in line with the insulin resistance observed in donors with obesity.
PMC10287567	An integrated cell atlas of the lung in health and disease.	In alveolar macrophages, inflammatory responses involving JAK/STAT signaling (previously associated with obesity-induced chronic systemic inflammation) are associated with higher BMI.

PMC10287567

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

g, Log-normalized expression of the migratory dendritic cell marker CCR7 in cells identified during re-annotation as migratory dendritic cells, versus other dendritic cells.

PMC10287567

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

AT, alveolar type; DC, dendritic cell; FB, fibroblast; Mph, macrophage; MT, metallothionein; SM, smooth muscle; SMG, submucosal gland; TB, terminal bronchiole.

PMC10287567

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

a, A UMAP of the integrated HLCA, colored by level 1 annotation.

PMC10287567

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

b, Cluster label disagreement (label entropy) of Leiden 3 clusters of the HLCA.

PMC10287567

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

The HLCA was split into three parts (immune, epithelial and endothelial/stromal) for ease of visualization.

PMC10287567

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

Cells from every cluster are colored by label entropy.

PMC10287567

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

Clusters with less than 20% of cells annotated at level 3 are colored gray.

PMC10287567

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

c, Cell type label composition of the immune cluster with the most label disagreement (left), with original labels (middle left) and matching manual re-annotations (middle right).

PMC10287567

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

A zoom-in on the UMAP from b shows the final re-annotations (right).

PMC10287567

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

d, UMAPs of the immune, epithelial and endothelial/stromal parts of the HLCA core with cell annotations from the expert manual re-annotation.

PMC10287567

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

e, Percentage of cells originally labeled correctly, mislabeled or underlabeled (that is, only labeled at a coarser level) compared with final manual re-annotations.

PMC10287567

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

The percentages were calculated per manual annotation, as well as across all cells (right bar).

PMC10287567

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

f, UMAP of HLCA clusters annotated as rare epithelial cell types (that is, ionocytes, neuroendocrine cells and tuft cells).

PMC10287567

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

Final annotations, original labels and the study of origin are shown (top), as well as the expression of ionocyte marker FOXI1, tuft cell marker LRMP and neuroendocrine marker CALCA (bottom).

PMC10287567

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

g, Log-normalized expression of the migratory dendritic cell marker CCR7 in cells identified during re-annotation as migratory dendritic cells, versus other dendritic cells.

PMC10287567

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

AT, alveolar type; DC, dendritic cell; FB, fibroblast; Mph, macrophage; MT, metallothionein; SM, smooth muscle; SMG, submucosal gland; TB, terminal bronchiole.

PMC10287567

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

A large-scale integrated atlas provides the unique opportunity to systematically investigate the consensus in cell type labeling across datasets.

PMC10287567

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

To identify areas of consensus and disagreement, we iteratively clustered the HLCA core and investigated donor diversity and cell type label agreement in these clusters using entropy scores (see Methods).

PMC10287567

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

Most clusters contained cells from many donors (Extended Data Fig. 1a).

PMC10287567

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

Clusters with low donor diversity (n = 14) were largely immune cell clusters (n = 13), representing donor- or donor group-specific phenotypes.

PMC10287567

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

Similarly, a high diversity of (contradictory) cell type labels (high label entropy) can identify both annotation disagreements between studies and clusters of doublets (Methods).

PMC10287567

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

Most clusters (61 out of 94) showed low label entropy, suggesting overall agreement of coarse cell type labels across datasets (Fig. 3b).

PMC10287567

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

The remaining 33 clusters exhibited high label entropy, highlighting cellular phenotypes that were differently labeled across datasets (Fig. 3b).

PMC10287567

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

For example, the immune cluster with the highest label entropy contained many cells that were originally mislabeled as monocytes and macrophages but were actually type 2 dendritic cells (Fig. 3c and Extended Data Fig. 1b).

PMC10287567

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

Thus, populations with high label entropy identify mislabeled cell types, indicating the need for consensus re-annotation of the integrated atlas.

PMC10287567

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

As a first step to achieve such a consensus on the diversity of cell types present in the HLCA core, we performed a full re-annotation of the integrated data on the basis of the original annotations and six expert opinions (consensus annotation; Methods and Fig. 3d).

PMC10287567

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

Each of the 61 annotated cell types (Supplementary Table 5) was detected in at least four datasets out of 14, often in specific parts of the respiratory system, and different cell types showed varying fractions of proliferating (MKI67) cells (Extended Data Fig. 2a–c).

PMC10287567

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

While our consensus cell type annotations partly correspond to original labels (41% of cells), there were also refinements (28%) and substantial re-annotations (31%; Fig. 3e and Supplementary Fig. 2).

PMC10287567

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

To robustly characterize the cell types, we established a universal set of marker genes that generalizes across individuals and studies (Methods, Extended Data Fig. 3 and Supplementary Table 6).

PMC10287567

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

The fully re-annotated HLCA core thus combines data from a diverse set of studies to provide a carefully curated reference for cell type annotations and marker genes in healthy lung tissue.

PMC10287567

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

Rare cell types, such as ionocytes, tuft cells, neuroendocrine cells and specific immune cell subsets, are often difficult to identify in individual datasets.

PMC10287567

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

Yet, combining datasets in the HLCA core provides better power for identifying these rare cell types.

PMC10287567

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

Ionocytes, tuft and neuroendocrine cells make up only 0.08, 0.01 and 0.02% of the cells in the HLCA core according to the original labels, and were originally identified in only seven, two and four datasets out of 14, respectively.

PMC10287567

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

Despite their low abundance, these cells formed three separate clusters of the HLCA core (Fig. 3f).

PMC10287567

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

Our re-annotation increases the number of datasets in which these cells are detected up to threefold and identifies both cells falsely annotated as monocytes, tuft cells or neuroendocrine cells, as well as originally undetected rare cells (Fig. 3f and Supplementary Fig. 3a).

PMC10287567

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

Importantly, other integration methods tested during our benchmarking, such as Harmony and Seurat’s RPCA, failed to separate these rare cells into distinct clusters (Supplementary Fig. 3b).

PMC10287567

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

We were further able to detect six cell identities that were not previously found in the human lung or were only recently described in individual studies.

PMC10287567

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

These cell types include migratory dendritic cells (n = 312 cells, expressing CCR7, LAD1 and COL19), hematopoietic stem cells (n = 60, expressing SPINK2, STMN, PRSS57 and CD34), highly proliferative hillock-like epithelial cells not previously reported in adult human lung (n = 4,600, expressing KRT6A, KRT13 and KRT14), the recently described alveolar type 0 cells (n = 1,440, expressing STFPB, SCGB3A2, SFTPC and SCGB3A1) and the closely related preterminal bronchiole secretory cells (n = 4,393, expressing SFTPB, SCGB3A2, SFTPC and SCGB3A1, together with alveolar type 0 cells called transitional club-AT2 cells) and a subset of smooth muscle cells (n = 335) that to our knowledge have not previously been described (Fig. 3d,g and Extended Data Fig. 4a–f).

PMC10287567

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

These smooth muscle cells, predominantly found in the airways, express canonical smooth muscle markers (CNN1 and MYH11) and also uniquely and consistently express FAM83D across datasets (Extended Data Fig. 4e,f).

PMC10287567

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

The HLCA core thus enables improved detection and identification of rare cell types, as well as the discovery of unknown cell types.

PMC10287567

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

Demographic and other metadata covariates affect cellular transcriptional phenotypes.

PMC10287567

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

Better insight into the impact of these covariates (for example, sex, BMI and smoking) on cell type gene expression can shed light on the contribution of these factors to progression from healthy to diseased states.

PMC10287567

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

In addition, technical covariates such as ribosomal and mitochondrial genes exhibit batch-specific variation in expression (Methods and Supplementary Table 7).

PMC10287567

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

The diversity in demographics (for example, smoking status, age, harmonized ethnicity and BMI) and experimental protocols represented in the HLCA core enables us to explore the contribution of each technical or biological covariate to cell type-specific gene expression variation (Methods and Supplementary Fig. 4).

PMC10287567

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

For many cell types, anatomical location is the biological variable explaining most of the variance between samples (Fig. 4a).

PMC10287567

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

Furthermore, sex is most associated with transcriptomic variation in lymphatic endothelial cells, whereas BMI is most associated with variation in B and T cells, harmonized ethnicity in transitional club-AT2 cells and smoking status in innate lymphoid/natural killer cells.

PMC10287567

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

Furthermore, for several cell types (for example, mast, AT1 and smooth muscle cells), the tissue dissociation protocol explains most of the variance of all technical as well as biological covariates recorded.

PMC10287567

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

These associations provide a systematic overview of the effects of biological and technical factors on the transcriptional state of lung cell types.

PMC10287567

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

Fig. 4Demographic and technical variables driving interindividual variation.a, Fraction of total inter-sample variance in the HLCA core integrated embedding that correlates with specific covariates.

PMC10287567

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

Covariates are split into technical (left) and biological covariates (right).

PMC10287567

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

Cell types are ordered by the number of samples in which they were detected.

PMC10287567

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

Only cell types present in at least 40 samples are shown.

PMC10287567

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

Tissue sampling method represents the way a sample was obtained (for example, surgical resection or nasal brush).

PMC10287567

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

Donor status represents the state of the donor at the moment of sample collection (for example, organ donor, diseased alive or healthy alive).

PMC10287567

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

The heatmap is masked gray where fewer than 40 samples were annotated for a specific covariate or where only one value was observed for all samples for that cell type.

PMC10287567

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

b, Selection of gene sets that are significantly associated with anatomical location CCF score, in different airway epithelial cell types.

PMC10287567

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

All gene set names are Gene Ontology biological process (GO: BP) terms.

PMC10287567

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

Sets upregulated toward distal lungs are shown in green, whereas sets downregulated are shown in blue.

PMC10287567

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

The full name of the term marked by an asterisk is ‘Antigen processing and presentation of exogenous peptide antigen via MHC-I’.

PMC10287567

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

c, Cell type proportions per sample, along the proximal-to-distal axis of the respiratory system.

PMC10287567

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

The lowest and highest CCF scores shown (0.36 and 0.97) represent the most proximal and most distal sampled parts of the respiratory system, respectively (trachea and parenchyma), excluding the upper airways.

PMC10287567

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

The dots are colored by the tissue dissociation protocol and tissue sampling method used for each sample.

PMC10287567

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

The boxes show the median and interquartile range of the proportions.

PMC10287567

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

Samples with proportions more than 1.5 times the interquartile range away from the high and low 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.

n = 23, 19, 9 and 90 for CCF scores 0.36, 0.72, 0.81 and 0.97, respectively.

PMC10287567

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

d, Selection of gene sets significantly up- (green) or downregulated (blue) with increasing BMI, in four different cell types.

PMC10287567

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

For b and d, P values were calculated using correlation-adjusted mean-rank gene set tests (Methods) and false discovery rate corrected using the Benjamini–Hochberg procedure.

PMC10287567

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

IL-1, interleukin-1; MHC-I, major histocompatibility complex class I; TNF, tumor necrosis factor.

PMC10287567

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

a, Fraction of total inter-sample variance in the HLCA core integrated embedding that correlates with specific covariates.

PMC10287567

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

Covariates are split into technical (left) and biological covariates (right).

PMC10287567

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

Cell types are ordered by the number of samples in which they were detected.

PMC10287567

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

Only cell types present in at least 40 samples are shown.

PMC10287567

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

Tissue sampling method represents the way a sample was obtained (for example, surgical resection or nasal brush).

PMC10287567

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

Donor status represents the state of the donor at the moment of sample collection (for example, organ donor, diseased alive or healthy alive).

PMC10287567

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

The heatmap is masked gray where fewer than 40 samples were annotated for a specific covariate or where only one value was observed for all samples for that cell type.

PMC10287567

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

b, Selection of gene sets that are significantly associated with anatomical location CCF score, in different airway epithelial cell types.

PMC10287567

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

All gene set names are Gene Ontology biological process (GO: BP) terms.

PMC10287567

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

Sets upregulated toward distal lungs are shown in green, whereas sets downregulated are shown in blue.

PMC10287567

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

The full name of the term marked by an asterisk is ‘Antigen processing and presentation of exogenous peptide antigen via MHC-I’.

PMC10287567

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

c, Cell type proportions per sample, along the proximal-to-distal axis of the respiratory system.

PMC10287567

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

The lowest and highest CCF scores shown (0.36 and 0.97) represent the most proximal and most distal sampled parts of the respiratory system, respectively (trachea and parenchyma), excluding the upper airways.

PMC10287567

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

The dots are colored by the tissue dissociation protocol and tissue sampling method used for each sample.

PMC10287567

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

The boxes show the median and interquartile range of the proportions.

PMC10287567

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

Samples with proportions more than 1.5 times the interquartile range away from the high and low 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.

n = 23, 19, 9 and 90 for CCF scores 0.36, 0.72, 0.81 and 0.97, respectively.

PMC10287567

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

d, Selection of gene sets significantly up- (green) or downregulated (blue) with increasing BMI, in four different cell types.

PMC10287567

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

For b and d, P values were calculated using correlation-adjusted mean-rank gene set tests (Methods) and false discovery rate corrected using the Benjamini–Hochberg procedure.

PMC10287567

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

IL-1, interleukin-1; MHC-I, major histocompatibility complex class I; TNF, tumor necrosis factor.

PMC10287567

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

To better characterize how biological variables affect cellular phenotypes, we modeled their cell type-specific effects on the transcriptome at the gene level (Methods).

PMC10287567

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

Sex-related differences in lymphatic endothelial cells are dominated by differential expression of genes located on the X and Y chromosomes, but also include a decrease in IFNAR1 in females (Supplementary Table 8), which may be linked to differential interferon responses between the biological sexes.

PMC10287567

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

We furthermore found cell type-specific programs that change with proximal (low CCF score) to distal (high CCF score) location along the respiratory tract (Supplementary Tables 8 and 9).

PMC10287567

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

For instance, oxidative phosphorylation (including cytochrome c oxidase genes such as COX7A1), antigen presentation by major histocompatibility complex class I molecules (including proteasome and protease subunit genes such as PSMD14 and PSMB4), signaling by interleukin-1 and tumor necrosis factor α, as well as planar cell polarity, were downregulated toward more distal locations in secretory, multiciliated and basal cells (Fig. 4b).

PMC10287567

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

Some gene programs were specific for a subset of airway epithelial cell types (for example, cornification and keratinization, which were programs that were downregulated in distal multiciliated and secretory cells; including genes such as KRT8 and KRT19).

PMC10287567

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

The changes in airway epithelial cell states toward the terminal airways are further illustrated by increased expression of developmental pathway genes such as NKX2-1, NFIB, GATA6, BMP4 and SOX9 in multiciliated cells along the proximal-to-distal axis (Fig. 4b), whereas basal cells decrease in number (Fig. 4c).

PMC10287567

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

Similarly, several cell types display transcriptomic changes in donors with increasing BMI (Fig. 4d and Supplementary Tables 8 and 9).

PMC10287567

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

AT2 cells, secretory cells and alveolar macrophages exhibit downregulation of a range of biological processes (Supplementary Fig. 5), including cellular respiration, differentiation and synthesis of peptides and other molecules.

PMC10287567

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

In secretory cells, a downregulation of the insulin response pathway is also associated with higher BMI, in line with the insulin resistance observed in donors with obesity.

PMC10287567

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

In alveolar macrophages, inflammatory responses involving JAK/STAT signaling (previously associated with obesity-induced chronic systemic inflammation) are associated with higher BMI.