Mardiyyah/TAPT_data_V2_split · Datasets at Hugging Face

PMCID stringclasses 24 values	Title stringclasses 24 values	Sentences stringlengths 2 40.7k
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	d, day; mLTo, mesenchymal lymphoid tissue organizer.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	To assess intestinal organoid fidelity and maturation, we integrated time series scRNA-seq data from duodenal development (59 to 132 days post fertilization) with adult intestinal epithelium (Fig. 3e).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	These data revealed distinct fetal and adult stem cell-to-enterocyte differentiation trajectories, while other epithelial cell types, such as goblet, tuft, M and enteroendocrine cells, showed similar states across both stages (Fig. 3f,g and Extended Data Fig. 7a–f).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Comparing organoids with the primary reference revealed that PSC-derived organoids resembled fetal tissue, whereas FSC- and ASC-derived organoids aligned with adult tissues (Fig. 3h), consistent with reports that FSC-derived organoids lose fetal traits during extended culture.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Metrics such as cell-type proportion, projection probability and similarity to fetal and adult cell types highlighted substantial variation across samples (Fig. 3i–l and Extended Data Fig. 7g,h).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	For example, PSC-derived organoids increase in complexity and reference similarity over time in culture, and after xenografting into a mouse host for maturation, the organoids obtain higher cellular diversity and similarity to primary tissue differentiated enterocytes.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Altogether, these results reveal the diversity of cell composition and cell maturation in intestinal organoids from different sources, time points and protocols.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	We performed a detailed analysis of lung organoid cells, consisting of 221,425 cells obtained from 52 samples and 13 publications, comprising PSC-, FSC- and ASC-derived sources (Fig. 4a).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	We integrated, clustered and annotated these data to generate a human lung organoid cell atlas (HLOCA) (Fig. 4b,c).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The Uniform Manifold Approximation and Projection (UMAP) representation showed integration of data from different publications and samples with undifferentiated stem cells positioned centrally surrounded by more differentiated cell types (Fig. 4b).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Organoids from PSCs displayed a higher proportion of lowly differentiated early endoderm development marker genes such as FABP1 and AFP-defined progenitor cells, which were largely absent in the ASC-derived organoids (Fig. 4d).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	In turn, organoids obtained via ASC-protocols frequently contained a relevant proportion of club cells, whereas a high incidence of goblet and neuroendocrine cells was primarily observed in samples produced using FSC protocols (Fig. 4b–d).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Overall, the differences in cell-type composition suggest effects from stem cell source as well as details of the protocol, including media and growth factors.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	We provide a structured account of the publicly available metadata on lung organoid datasets in the atlas including information on all available protocol components, concentrations and intervals, which can be linked to the samples in the shared HLOCA object.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Fig. 4Human lung organoids from different stem cell origins generate developing and adult cell states.a, Schematic of the analyses performed on the lung organoid subatlas (HLOCA) and comparison with the primary reference tissue.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	b,c, UMAP of the integrated object of all lung organoid samples colored by cell type (b) and stem cell source (c).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	d, Dot plot showing lung marker gene expression across organoid cell types.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	e, Analytical design of the lung organoid subatlas and comparison with the primary reference tissue.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	f,g, UMAP of the integrated lung fetal and adult primary tissue single-cell object colored by adult sample or fetal cell type (f) and age of sample (g).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	h, Projection of lung organoid cells onto fetal and adult primary epithelial single-cell objects categorized by PSC-, FSC- and ASC-derived organoid samples.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	i, Bar plot illustrating the predicted cell proportions of each organoid sample mapped to the primary tissue objects.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The samples are divided by PSC-, FSC- and ASC-derived organoid samples from left to right.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	j, Box plot showing the predicted probability of cell mapping to adult samples.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The cell numbers range from 395 to 13,017, with samples containing fewer than 500 cells marked by an asterisk.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The center represents the median; bounds show the 25% and 75% percentiles; and whiskers indicate values within 1.5× the interquartile range.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	k, Bar plots illustrating the predicted tissue (fetal in gray and adult in blue) proportions.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The order of organoid samples in j and k is consistent with that in i. a, Schematic of the analyses performed on the lung organoid subatlas (HLOCA) and comparison with the primary reference tissue.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	b,c, UMAP of the integrated object of all lung organoid samples colored by cell type (b) and stem cell source (c).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	d, Dot plot showing lung marker gene expression across organoid cell types.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	e, Analytical design of the lung organoid subatlas and comparison with the primary reference tissue.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	f,g, UMAP of the integrated lung fetal and adult primary tissue single-cell object colored by adult sample or fetal cell type (f) and age of sample (g).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	h, Projection of lung organoid cells onto fetal and adult primary epithelial single-cell objects categorized by PSC-, FSC- and ASC-derived organoid samples.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	i, Bar plot illustrating the predicted cell proportions of each organoid sample mapped to the primary tissue objects.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The samples are divided by PSC-, FSC- and ASC-derived organoid samples from left to right.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	j, Box plot showing the predicted probability of cell mapping to adult samples.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The cell numbers range from 395 to 13,017, with samples containing fewer than 500 cells marked by an asterisk.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The center represents the median; bounds show the 25% and 75% percentiles; and whiskers indicate values within 1.5× the interquartile range.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	k, Bar plots illustrating the predicted tissue (fetal in gray and adult in blue) proportions.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The order of organoid samples in j and k is consistent with that in i. To gain insights into how the lung organoid datasets correspond with primary tissue, we integrated a unified reference of primary adult and fetal lung tissues (Fig. 4e–k).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The query to reference mapping of the lung organoid data showed that PSC-derived organoid cells preferentially integrated with fetal counterparts, ASC-derived organoid cells integrated with adult counterparts and FSC-derived organoid cells projected to both fetal and adult references (Fig. 4h).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	This finding is consistent with previous observations from intestine reference mapping analysis in which PSC-derived organoids model fetal biology, ASC-derived organoids model adult biology and FSC-derived organoids have intermediate or unclear mappings.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Metrics such as cell-type proportion, projection probability and similarity to fetal and adult cell types also highlighted substantial variation across samples (Fig. 4i–k).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Interestingly, the results show that most PSC-derived and some FSC-derived organoids contain a large proportion of cells resembling early fetal epithelial cells.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	This observation is consistent with our previous finding of undifferentiated cells in PSC- and FSC-derived organoids.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	In summary, these data offer an integrated atlas for lung organoids (HLOCA) to complement the HEOCA for the study of lung 3D cultures at a single tissue level, providing insight into differences in cell-type composition, maturation state and resemblances to primary tissue from multiple stem cell sources.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	We developed a toolkit to incorporate organoid datasets and compare data with cell states in the integrated HEOCA (Fig. 5a).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	This toolkit (sc2heoca) offers functions to compare samples with tissue references and assess ‘on or off’ target status and cell state maturation.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	In addition, it enables sample projection onto the integrated HEOCA through nearest neighbor analysis and cell annotation through label transfer.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The mean expression of the nearest neighbors serves as paired reference cells for differential expression analysis and mean distance to nearest neighbors provides an estimate for the level of difference between sample and reference states.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	We applied this toolkit to assess organoid protocols, perturbations and disease models (Fig. 5a).Fig.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	5The integrated atlas enables protocol assessment and can be extended via dataset projection.a, Schematic representation showing the analytical pipelines and varied interfaces to facilitate analyzing scRNA-seq data of organoid samples for the atlas.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	b, Experimental design of the ileum organoid sample with TNF treatment to generate M cells.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The bar plot shows the cell proportions of predicted level 2 cell types across control and TNF treatment scRNA-seq data.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	c, Experimental design of the colon organoid sample using a scaffold-guided hydrogel chip model.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types and time points, with a bar plot depicting the cell proportions of predicted level 2 cell types across the time course scRNA-seq data.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	d, Experimental design of the lung alveolar organoid samples.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types and time points, with a bar plot depicting the cell proportions of predicted level 2 cell types across the time course scRNA-seq data.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	e, Experimental design of the lung airway organoid samples.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types and time points, with a bar plot depicting the cell proportions of predicted level 2 cell types across the time course scRNA-seq data.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Ctrl, control; DE, differential expression; Neuroendo.,
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	neuroendocrine.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	a, Schematic representation showing the analytical pipelines and varied interfaces to facilitate analyzing scRNA-seq data of organoid samples for the atlas.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	b, Experimental design of the ileum organoid sample with TNF treatment to generate M cells.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The bar plot shows the cell proportions of predicted level 2 cell types across control and TNF treatment scRNA-seq data.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	c, Experimental design of the colon organoid sample using a scaffold-guided hydrogel chip model.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types and time points, with a bar plot depicting the cell proportions of predicted level 2 cell types across the time course scRNA-seq data.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	d, Experimental design of the lung alveolar organoid samples.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types and time points, with a bar plot depicting the cell proportions of predicted level 2 cell types across the time course scRNA-seq data.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	e, Experimental design of the lung airway organoid samples.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types and time points, with a bar plot depicting the cell proportions of predicted level 2 cell types across the time course scRNA-seq data.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Ctrl, control; DE, differential expression; Neuroendo.,
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	neuroendocrine.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	We provide several examples of how the HEOCA can be used to evaluate single-cell transcriptome datasets from recent organoid protocols (Fig. 5b–e).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	First, we validate a finding that modulation of the TNF pathway promotes M cell abundance in intestinal organoids (Extended Data Fig. 6m).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	We generated ASC-derived ileal organoids in control media or media supplemented with TNF and receptor activator of nuclear factor-κB ligand (RANKL), and performed scRNA-seq after 6 days of treatment.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Reference comparison revealed that the majority of cells from both the control and TNF treatment samples accurately matched the intended intestinal tissue cell types (control, 98.26%; TNF, 95.16%) (Extended Data Fig. 8a).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Projection onto the HEOCA confirmed a notable increase in M cells in the TNF treatment versus control samples, rising from 0% to 34.92%, with corresponding differential expression profiles (Fig. 5b and Extended Data Fig. 8a).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Second, we assessed colonic epithelial tissue generated by seeding human colon ASC-derived organoids on a scaffolded hydrogel in a fluidic chip (Fig. 5c).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Projection analysis demonstrated that this protocol led to colonocyte differentiation and maturation, as indicated by a substantially higher proportion of colonocytes compared with the control samples (day 4, 20.45%; day 14, 54.03%; day 21, 66.97%) (Fig. 5c and Extended Data Fig. 8b).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	This on-chip protocol offers advantages over conventional organoid protocols by providing access to the apical and basal sides of the epithelium and allowing the culture to be maintained for many weeks while sustaining both stem and differentiated cell types.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Third, we analyzed two lung datasets consisting of time courses of lung progenitor organoids differentiated into alveolar or airway organoids (Fig. 5d,e).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	In the alveolar dataset, cells showed increased mapping to alveolar epithelial identities (AT1 and AT2) over the course of differentiation (Fig. 5d).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	This increase was accompanied by a decrease in cells mapping to undifferentiated identities in the reference atlas (Extended Data Fig. 8c).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Similarly, lung progenitor organoids differentiated toward the airway were accurately mapped to airway-specific cell identities, including SCGB3A2 airway progenitors, basal cells and secretory cells, consistent with previous descriptions of these organoids (Fig. 5e and Extended Data Fig. 8d).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Notably, these cells were minimally mapped to alveolar epithelial identities, further validating the accuracy of the reference atlas in distinguishing different lung cell types (Fig. 5d,e).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Finally, we incorporated four additional ASC-derived intestinal organoid datasets (two published and two unpublished) including condition versus control ileum organoids treated with IL-4 and IL-13 and colon organoids treated with IL-22, and time course data of ileum and colon organoids in a medium to promote differentiation.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	For each dataset we projected to the HEOCA, annotated cell types, assessed cell-type proportion, mapped to adult and fetal references, and performed differential expression analysis (Extended Data Fig. 8e–h).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Taken altogether, these data provide a framework for protocol assessment and dataset incorporation into an integrated organoid cell atlas.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	We next sought to use the HEOCA as a cohort to assess organoid perturbations.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	We conducted two perturbation experiments aimed at modeling response to viral infection (interferon (IFN)α, IFNβ and IFNɣ) and acute pathogenic inflammation (TNF, Oncostatin M (OSM), IFNɣ, stem cell factor (SCF), IL-6, IL-17A and IL-18) (Fig. 6a).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	We treated ASC-derived ileum organoids with these cytokines for 24 h and performed scRNA-seq on control (4,191 cells) and treated samples from the same batch (viral response, 3,305 cells; inflammation, 2,158 cells).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	HEOCA projection and annotation revealed diverse cell types including stem cells, enterocytes, goblet cells and enteroendocrine cells (Fig. 6b,c).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Distance-to-atlas analysis revealed that, compared with the control sample, both viral response and inflammation samples had higher distances in all cell types (Fig. 6d,e).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Differential expression analysis between perturbation samples and the paired nearest neighbor cells in the HEOCA cohort revealed 618 genes specific to viral response (for example, ISG15, OAS1-3), 259 specific to inflammation (LCN2, IL32, TNFAIP2), 717 shared (STAT1, WARS1) and 996 genes upregulated in the atlas (Fig. 6f,g).
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Gene Ontology (GO) enrichment analysis showed that viral response-specific upregulated genes were enriched in functions related to the defense response to viruses, response to type I IFN and IFNβ, and regulation of autophagy.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Inflammation-specific differentially expressed genes (DEGs) were associated with the inflammatory responses and cellular responses to chemokines.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	Genes commonly upregulated in both viral response and inflammation samples were involved in regulating epithelial cell proliferation, chromosome organization, epithelial cell migration, intracellular signal transduction and response to cytokines.
PMC12081310	An integrated transcriptomic cell atlas of human endoderm-derived organoids.	By contrast, genes with higher expression in the atlas cohort were enriched in ATP biosynthetic processes, messenger RNA processing and cellular respiration (Fig. 6h).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

d, day; mLTo, mesenchymal lymphoid tissue organizer.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

To assess intestinal organoid fidelity and maturation, we integrated time series scRNA-seq data from duodenal development (59 to 132 days post fertilization) with adult intestinal epithelium (Fig. 3e).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

These data revealed distinct fetal and adult stem cell-to-enterocyte differentiation trajectories, while other epithelial cell types, such as goblet, tuft, M and enteroendocrine cells, showed similar states across both stages (Fig. 3f,g and Extended Data Fig. 7a–f).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Comparing organoids with the primary reference revealed that PSC-derived organoids resembled fetal tissue, whereas FSC- and ASC-derived organoids aligned with adult tissues (Fig. 3h), consistent with reports that FSC-derived organoids lose fetal traits during extended culture.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Metrics such as cell-type proportion, projection probability and similarity to fetal and adult cell types highlighted substantial variation across samples (Fig. 3i–l and Extended Data Fig. 7g,h).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

For example, PSC-derived organoids increase in complexity and reference similarity over time in culture, and after xenografting into a mouse host for maturation, the organoids obtain higher cellular diversity and similarity to primary tissue differentiated enterocytes.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Altogether, these results reveal the diversity of cell composition and cell maturation in intestinal organoids from different sources, time points and protocols.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

We performed a detailed analysis of lung organoid cells, consisting of 221,425 cells obtained from 52 samples and 13 publications, comprising PSC-, FSC- and ASC-derived sources (Fig. 4a).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

We integrated, clustered and annotated these data to generate a human lung organoid cell atlas (HLOCA) (Fig. 4b,c).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The Uniform Manifold Approximation and Projection (UMAP) representation showed integration of data from different publications and samples with undifferentiated stem cells positioned centrally surrounded by more differentiated cell types (Fig. 4b).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Organoids from PSCs displayed a higher proportion of lowly differentiated early endoderm development marker genes such as FABP1 and AFP-defined progenitor cells, which were largely absent in the ASC-derived organoids (Fig. 4d).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

In turn, organoids obtained via ASC-protocols frequently contained a relevant proportion of club cells, whereas a high incidence of goblet and neuroendocrine cells was primarily observed in samples produced using FSC protocols (Fig. 4b–d).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Overall, the differences in cell-type composition suggest effects from stem cell source as well as details of the protocol, including media and growth factors.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

We provide a structured account of the publicly available metadata on lung organoid datasets in the atlas including information on all available protocol components, concentrations and intervals, which can be linked to the samples in the shared HLOCA object.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Fig. 4Human lung organoids from different stem cell origins generate developing and adult cell states.a, Schematic of the analyses performed on the lung organoid subatlas (HLOCA) and comparison with the primary reference tissue.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

b,c, UMAP of the integrated object of all lung organoid samples colored by cell type (b) and stem cell source (c).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

d, Dot plot showing lung marker gene expression across organoid cell types.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

e, Analytical design of the lung organoid subatlas and comparison with the primary reference tissue.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

f,g, UMAP of the integrated lung fetal and adult primary tissue single-cell object colored by adult sample or fetal cell type (f) and age of sample (g).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

h, Projection of lung organoid cells onto fetal and adult primary epithelial single-cell objects categorized by PSC-, FSC- and ASC-derived organoid samples.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

i, Bar plot illustrating the predicted cell proportions of each organoid sample mapped to the primary tissue objects.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The samples are divided by PSC-, FSC- and ASC-derived organoid samples from left to right.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

j, Box plot showing the predicted probability of cell mapping to adult samples.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The cell numbers range from 395 to 13,017, with samples containing fewer than 500 cells marked by an asterisk.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The center represents the median; bounds show the 25% and 75% percentiles; and whiskers indicate values within 1.5× the interquartile range.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

k, Bar plots illustrating the predicted tissue (fetal in gray and adult in blue) proportions.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The order of organoid samples in j and k is consistent with that in i. a, Schematic of the analyses performed on the lung organoid subatlas (HLOCA) and comparison with the primary reference tissue.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

b,c, UMAP of the integrated object of all lung organoid samples colored by cell type (b) and stem cell source (c).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

d, Dot plot showing lung marker gene expression across organoid cell types.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

e, Analytical design of the lung organoid subatlas and comparison with the primary reference tissue.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

f,g, UMAP of the integrated lung fetal and adult primary tissue single-cell object colored by adult sample or fetal cell type (f) and age of sample (g).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

h, Projection of lung organoid cells onto fetal and adult primary epithelial single-cell objects categorized by PSC-, FSC- and ASC-derived organoid samples.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

i, Bar plot illustrating the predicted cell proportions of each organoid sample mapped to the primary tissue objects.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The samples are divided by PSC-, FSC- and ASC-derived organoid samples from left to right.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

j, Box plot showing the predicted probability of cell mapping to adult samples.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The cell numbers range from 395 to 13,017, with samples containing fewer than 500 cells marked by an asterisk.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The center represents the median; bounds show the 25% and 75% percentiles; and whiskers indicate values within 1.5× the interquartile range.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

k, Bar plots illustrating the predicted tissue (fetal in gray and adult in blue) proportions.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The order of organoid samples in j and k is consistent with that in i. To gain insights into how the lung organoid datasets correspond with primary tissue, we integrated a unified reference of primary adult and fetal lung tissues (Fig. 4e–k).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The query to reference mapping of the lung organoid data showed that PSC-derived organoid cells preferentially integrated with fetal counterparts, ASC-derived organoid cells integrated with adult counterparts and FSC-derived organoid cells projected to both fetal and adult references (Fig. 4h).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

This finding is consistent with previous observations from intestine reference mapping analysis in which PSC-derived organoids model fetal biology, ASC-derived organoids model adult biology and FSC-derived organoids have intermediate or unclear mappings.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Metrics such as cell-type proportion, projection probability and similarity to fetal and adult cell types also highlighted substantial variation across samples (Fig. 4i–k).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Interestingly, the results show that most PSC-derived and some FSC-derived organoids contain a large proportion of cells resembling early fetal epithelial cells.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

This observation is consistent with our previous finding of undifferentiated cells in PSC- and FSC-derived organoids.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

In summary, these data offer an integrated atlas for lung organoids (HLOCA) to complement the HEOCA for the study of lung 3D cultures at a single tissue level, providing insight into differences in cell-type composition, maturation state and resemblances to primary tissue from multiple stem cell sources.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

We developed a toolkit to incorporate organoid datasets and compare data with cell states in the integrated HEOCA (Fig. 5a).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

This toolkit (sc2heoca) offers functions to compare samples with tissue references and assess ‘on or off’ target status and cell state maturation.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

In addition, it enables sample projection onto the integrated HEOCA through nearest neighbor analysis and cell annotation through label transfer.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The mean expression of the nearest neighbors serves as paired reference cells for differential expression analysis and mean distance to nearest neighbors provides an estimate for the level of difference between sample and reference states.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

We applied this toolkit to assess organoid protocols, perturbations and disease models (Fig. 5a).Fig.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

5The integrated atlas enables protocol assessment and can be extended via dataset projection.a, Schematic representation showing the analytical pipelines and varied interfaces to facilitate analyzing scRNA-seq data of organoid samples for the atlas.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

b, Experimental design of the ileum organoid sample with TNF treatment to generate M cells.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The bar plot shows the cell proportions of predicted level 2 cell types across control and TNF treatment scRNA-seq data.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

c, Experimental design of the colon organoid sample using a scaffold-guided hydrogel chip model.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types and time points, with a bar plot depicting the cell proportions of predicted level 2 cell types across the time course scRNA-seq data.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

d, Experimental design of the lung alveolar organoid samples.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types and time points, with a bar plot depicting the cell proportions of predicted level 2 cell types across the time course scRNA-seq data.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

e, Experimental design of the lung airway organoid samples.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types and time points, with a bar plot depicting the cell proportions of predicted level 2 cell types across the time course scRNA-seq data.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Ctrl, control; DE, differential expression; Neuroendo.,

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

neuroendocrine.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

a, Schematic representation showing the analytical pipelines and varied interfaces to facilitate analyzing scRNA-seq data of organoid samples for the atlas.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

b, Experimental design of the ileum organoid sample with TNF treatment to generate M cells.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The bar plot shows the cell proportions of predicted level 2 cell types across control and TNF treatment scRNA-seq data.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

c, Experimental design of the colon organoid sample using a scaffold-guided hydrogel chip model.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types and time points, with a bar plot depicting the cell proportions of predicted level 2 cell types across the time course scRNA-seq data.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

d, Experimental design of the lung alveolar organoid samples.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types and time points, with a bar plot depicting the cell proportions of predicted level 2 cell types across the time course scRNA-seq data.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

e, Experimental design of the lung airway organoid samples.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

The UMAP of sample scRNA-seq data mapped to the organoid atlas is colored by predicted level 2 cell types and time points, with a bar plot depicting the cell proportions of predicted level 2 cell types across the time course scRNA-seq data.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Ctrl, control; DE, differential expression; Neuroendo.,

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

neuroendocrine.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

We provide several examples of how the HEOCA can be used to evaluate single-cell transcriptome datasets from recent organoid protocols (Fig. 5b–e).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

First, we validate a finding that modulation of the TNF pathway promotes M cell abundance in intestinal organoids (Extended Data Fig. 6m).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

We generated ASC-derived ileal organoids in control media or media supplemented with TNF and receptor activator of nuclear factor-κB ligand (RANKL), and performed scRNA-seq after 6 days of treatment.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Reference comparison revealed that the majority of cells from both the control and TNF treatment samples accurately matched the intended intestinal tissue cell types (control, 98.26%; TNF, 95.16%) (Extended Data Fig. 8a).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Projection onto the HEOCA confirmed a notable increase in M cells in the TNF treatment versus control samples, rising from 0% to 34.92%, with corresponding differential expression profiles (Fig. 5b and Extended Data Fig. 8a).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Second, we assessed colonic epithelial tissue generated by seeding human colon ASC-derived organoids on a scaffolded hydrogel in a fluidic chip (Fig. 5c).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Projection analysis demonstrated that this protocol led to colonocyte differentiation and maturation, as indicated by a substantially higher proportion of colonocytes compared with the control samples (day 4, 20.45%; day 14, 54.03%; day 21, 66.97%) (Fig. 5c and Extended Data Fig. 8b).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

This on-chip protocol offers advantages over conventional organoid protocols by providing access to the apical and basal sides of the epithelium and allowing the culture to be maintained for many weeks while sustaining both stem and differentiated cell types.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Third, we analyzed two lung datasets consisting of time courses of lung progenitor organoids differentiated into alveolar or airway organoids (Fig. 5d,e).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

In the alveolar dataset, cells showed increased mapping to alveolar epithelial identities (AT1 and AT2) over the course of differentiation (Fig. 5d).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

This increase was accompanied by a decrease in cells mapping to undifferentiated identities in the reference atlas (Extended Data Fig. 8c).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Similarly, lung progenitor organoids differentiated toward the airway were accurately mapped to airway-specific cell identities, including SCGB3A2 airway progenitors, basal cells and secretory cells, consistent with previous descriptions of these organoids (Fig. 5e and Extended Data Fig. 8d).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Notably, these cells were minimally mapped to alveolar epithelial identities, further validating the accuracy of the reference atlas in distinguishing different lung cell types (Fig. 5d,e).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Finally, we incorporated four additional ASC-derived intestinal organoid datasets (two published and two unpublished) including condition versus control ileum organoids treated with IL-4 and IL-13 and colon organoids treated with IL-22, and time course data of ileum and colon organoids in a medium to promote differentiation.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

For each dataset we projected to the HEOCA, annotated cell types, assessed cell-type proportion, mapped to adult and fetal references, and performed differential expression analysis (Extended Data Fig. 8e–h).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Taken altogether, these data provide a framework for protocol assessment and dataset incorporation into an integrated organoid cell atlas.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

We next sought to use the HEOCA as a cohort to assess organoid perturbations.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

We conducted two perturbation experiments aimed at modeling response to viral infection (interferon (IFN)α, IFNβ and IFNɣ) and acute pathogenic inflammation (TNF, Oncostatin M (OSM), IFNɣ, stem cell factor (SCF), IL-6, IL-17A and IL-18) (Fig. 6a).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

We treated ASC-derived ileum organoids with these cytokines for 24 h and performed scRNA-seq on control (4,191 cells) and treated samples from the same batch (viral response, 3,305 cells; inflammation, 2,158 cells).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

HEOCA projection and annotation revealed diverse cell types including stem cells, enterocytes, goblet cells and enteroendocrine cells (Fig. 6b,c).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Distance-to-atlas analysis revealed that, compared with the control sample, both viral response and inflammation samples had higher distances in all cell types (Fig. 6d,e).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Differential expression analysis between perturbation samples and the paired nearest neighbor cells in the HEOCA cohort revealed 618 genes specific to viral response (for example, ISG15, OAS1-3), 259 specific to inflammation (LCN2, IL32, TNFAIP2), 717 shared (STAT1, WARS1) and 996 genes upregulated in the atlas (Fig. 6f,g).

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Gene Ontology (GO) enrichment analysis showed that viral response-specific upregulated genes were enriched in functions related to the defense response to viruses, response to type I IFN and IFNβ, and regulation of autophagy.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Inflammation-specific differentially expressed genes (DEGs) were associated with the inflammatory responses and cellular responses to chemokines.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

Genes commonly upregulated in both viral response and inflammation samples were involved in regulating epithelial cell proliferation, chromosome organization, epithelial cell migration, intracellular signal transduction and response to cytokines.

PMC12081310

An integrated transcriptomic cell atlas of human endoderm-derived organoids.

By contrast, genes with higher expression in the atlas cohort were enriched in ATP biosynthetic processes, messenger RNA processing and cellular respiration (Fig. 6h).