Mardiyyah/TAPT_data_V2_split · Datasets at Hugging Face

PMCID stringclasses 24 values	Title stringclasses 24 values	Sentences stringlengths 2 40.7k
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	By day 30, F7: myofibroblasts had become the predominant population, consistent with a role in established fibrosis/scarring.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Overall, our results point toward F6: inflammatory myofibroblasts as an intermediate differentiation state toward F7: myofibroblasts in human skin, with potential plasticity in fibroblast origin (Fig. 5d,e and Extended Data Fig. 7e).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	We next investigated if the skin fibroblast subtypes we identified were conserved across other human tissues.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Previous studies have reported fibroblast states that are found across human tissues.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	However, because these studies each defined fibroblast subtypes with different nomenclature and gene markers, it is unclear how these populations relate to each other and to the skin fibroblast populations reported in our study.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	To answer this and perform an overarching analysis across tissues and diseases, we undertook two approaches.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	The first was to assess the expression of marker genes for cross-tissue fibroblast subtypes in our skin data.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	This identified that reported cross-tissue populations from previous studies are likely present in human skin, consistent with F2: universal, F3: FRC-like, F6: inflammatory myofibroblast, and F7: myofibroblast subtypes (Fig. 6a and Extended Data Fig. 8a).Fig.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	6Human cross-tissue disease fibroblast populations.a, Human tissues previously included in cross-tissue fibroblast studies and the fibroblast subtypes they have identified (above heatmap), colored by study (Buechler et al. in green, Korsunsky et al. in orange and Gao et al. in blue).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Heatmap shows gene expression of marker genes previously reported for cross-tissue fibroblast populations in our lesional skin fibroblast subtypes.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Immediately above the heatmap we show the skin fibroblast subtype with most similar gene expression to reported cross-tissue populations.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	b, UMAP visualization for cross-tissue integration (left) and for fibroblasts specifically (right), colored by tissue.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Color bars indicate expression (log1P norm).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	c, UMAP visualization for fibroblasts colored by re-annotated clusters (Methods).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	d, Dotplots of expression of marker genes we previously used for skin fibroblasts in cross-tissue atlas clusters by tissue type.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Note that not all genes were available as the endometrial dataset contained ~17,000 genes.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Illustrations in a were partly created using BioRender.com.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	a, Human tissues previously included in cross-tissue fibroblast studies and the fibroblast subtypes they have identified (above heatmap), colored by study (Buechler et al. in green, Korsunsky et al. in orange and Gao et al. in blue).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Heatmap shows gene expression of marker genes previously reported for cross-tissue fibroblast populations in our lesional skin fibroblast subtypes.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Immediately above the heatmap we show the skin fibroblast subtype with most similar gene expression to reported cross-tissue populations.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	b, UMAP visualization for cross-tissue integration (left) and for fibroblasts specifically (right), colored by tissue.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Color bars indicate expression (log1P norm).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	c, UMAP visualization for fibroblasts colored by re-annotated clusters (Methods).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	d, Dotplots of expression of marker genes we previously used for skin fibroblasts in cross-tissue atlas clusters by tissue type.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Note that not all genes were available as the endometrial dataset contained ~17,000 genes.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Illustrations in a were partly created using BioRender.com.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	The second approach was to integrate published datasets of ~5.8 million cells from human skin, lung, intestine, synovium, endometrium, heart and nasal mucosa (Methods and Fig. 6b).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	This approach uses the whole transcriptome profile, instead of restricted marker genes, and thus more comprehensively defines cell state similarity.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Approximately 1 million fibroblasts were selected for downstream analysis based on expression of canonical marker genes (Fig. 6b).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	In the cross-tissue integrated dataset, we were able to discern shared fibroblast states across tissues, as well as fibroblasts that were unique to certain tissues (Fig. 6b,c and Extended Data Fig. 8b).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	In addition to known cross-tissue populations identified above (Fig. 6a), we found evidence for F2/3: perivascular (CXCL12, APOC1 and PPARG) and F5: NGFR (Schwann-like; SCN7A, NGFR, ITGA6 and EBF2) fibroblasts across human tissues, including in lung, gut and nasal mucosa (Fig. 6c,d and Extended Data Fig. 8b,c).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Further interrogation of labeled intestine and lung datasets supported these results (Supplementary Note 3).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	F1: superficial showed variable gene expression by tissue, which may reflect distinct epithelia patterning across sites (Extended Data Fig. 8d).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Overall, our results point toward the presence of previously reported cross-tissue fibroblast states in skin, despite major differences in the biophysical properties of different human tissues.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	We additionally suggest F2/3: perivascular and F5: NGFR (nerve-associated) fibroblasts as novel cross-tissue populations.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Fibroblast-mediated processes such as fibrosis and maintenance of immune cell niches are observed across multiple human tissues.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	We therefore asked whether disease-associated fibroblast states identified in skin were similarly enriched by disease category in non-skin tissues (Methods).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	We focused on F3: FRC-like and F6: inflammatory myofibroblasts based on their conserved states across tissues and potential immune-interacting roles from pathway enrichment analysis (Extended Data Figs. 2a and 5c).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Then, to predict functional interactions with immune cells, we utilized our skin data to perform cell–cell communication analysis.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Across tissues, we observed that F3: FRC-like fibroblasts were present in both inflammatory disorders and fibrotic processes with immune-mediated pathology, including lung (COVID-19 and interstitial lung disease) and intestine (inflammatory bowel disease (IBD)) (Fig. 7a,b).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	While FRC-like fibroblasts were not reported in the Human Lung Cell Atlas (HLCA), following re-clustering we identified an F3: FRC-like population in lung (Extended Data Fig. 8e,f), consistent with a previous report.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	We also confirmed equivalence of F3: FRC-like fibroblasts to T reticular cells (an FRC subset) in IBD (Supplementary Note 3 and Extended Data Fig. 8g).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Receptor–ligand analysis suggested interactions of skin F3: FRC-like fibroblasts with migrating dendritic cells (MigDCs) (CCL19-CCR7) and T cell subsets (CXCL12-CXCR4) (Extended Data Fig. 9a), suggesting that F3: FRC-like fibroblasts maintain T lymphoid populations and facilitate T cell–dendritic cell interactions analogous to T reticular cells in lymphoid tissue.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	We corroborated these findings using NicheCompass for niche identification in inflamed atopic dermatitis skin, which revealed CCR7 MigDCs and CXCR4 T cells within the F3 superficial perivascular niche (Fig. 7c and Extended Data Fig. 9b).Fig.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	7Cross-tissue F3: FRC-like fibroblasts and F6: inflammatory myofibroblasts regulate skin immune niches.a, Proportion of disease-associated F3: FRC-like fibroblasts, F6: inflammatory myofibroblasts and F7: myofibroblasts in non-skin tissues by disease (left) and disease category (right).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	b, Dotplot of F3: FRC-like expression across diseases (skin and non-skin) (left).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Dotplot of F6: inflammatory myofibroblasts gene expression across diseases (skin and non-skin) (right).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Diseases with a minimum of 50 cells.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	c, H&E slide of lesional atopic dermatitis skin with annotation of perivascular infiltrate regions (top left).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Niche identification and proportion of cells in the perivascular superficial niche (bottom left).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Composition of the perivascular superficial niche in 10x Genomics Xenium.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Insert: zoomed in version of perivascular niche cluster.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	d, Cell–cell communication analysis for F6: inflammatory myofibroblasts and skin immune cells (Methods).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	TCM, T central memory.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	e, Proportion of F6: inflammatory myofibroblasts in IBD by intestinal tissue inflammation status and linear regression of proportion with inflammation scores with 95% CI.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	f, Schematic summary of cell–cell interactions for F3: FRC-like fibroblasts and F6: inflammatory myofibroblasts.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Schematic in f were created using BioRender.com.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	a, Proportion of disease-associated F3: FRC-like fibroblasts, F6: inflammatory myofibroblasts and F7: myofibroblasts in non-skin tissues by disease (left) and disease category (right).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	b, Dotplot of F3: FRC-like expression across diseases (skin and non-skin) (left).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Dotplot of F6: inflammatory myofibroblasts gene expression across diseases (skin and non-skin) (right).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Diseases with a minimum of 50 cells.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	c, H&E slide of lesional atopic dermatitis skin with annotation of perivascular infiltrate regions (top left).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Niche identification and proportion of cells in the perivascular superficial niche (bottom left).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Composition of the perivascular superficial niche in 10x Genomics Xenium.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Insert: zoomed in version of perivascular niche cluster.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	d, Cell–cell communication analysis for F6: inflammatory myofibroblasts and skin immune cells (Methods).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	TCM, T central memory.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	e, Proportion of F6: inflammatory myofibroblasts in IBD by intestinal tissue inflammation status and linear regression of proportion with inflammation scores with 95% CI.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	f, Schematic summary of cell–cell interactions for F3: FRC-like fibroblasts and F6: inflammatory myofibroblasts.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Schematic in f were created using BioRender.com.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	F6: inflammatory myofibroblasts were abundant in cancer and inflammation but relatively uncommon in established fibrosis (Fig. 7a,b), consistent with skin data (Fig. 4b).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Inflammatory myofibroblasts are well described in IBD, and we confirmed equivalence of these cells to skin F6: inflammatory myofibroblasts (Supplementary Note 3 and Extended Data Fig. 8g).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	To further assess the clinical relevance of F6 in IBD, we used an scRNA-seq dataset with clinical metadata.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	F6: inflammatory myofibroblasts were significantly elevated in inflamed tissue, compared to non-inflamed tissue, and their prevalence correlated with clinical inflammation severity scores (Fig. 7e).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Receptor–ligand analysis suggested that F6: inflammatory myofibroblasts recruit and maintain neutrophils (CXCL5/6/8-CXCR2 and CSF3-CSF3R), macrophages/monocytes (CCL5/26-CCR1 and CSF3-CSF3R) and B cells (CXCL13/CXCR5) in the skin (Fig. 7c and Methods).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	These genes were highly expressed in the skin during wound healing, acne and hidradenitis suppurativa, as well as in IBD and lung cancer (Fig. 7b), suggesting a similar mechanism for recruitment of immune cells across tissues.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Overall, our results suggest that F3: FRC-like (CCL19CD74TNFRSF13B and IL33/IL15) and F6: inflammatory myofibroblasts (IL11MMP1CXCL5IL7R) mediate distinct immune niches driving pathology in the skin and other tissues (Fig. 7f).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Given the similar transcriptomic profiles of adult skin F3: FRC-like and intestinal T reticular cells, we hypothesized that these fibroblasts had similar origins in their respective tissues.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Intestinal FRCs are found in the Peyer’s patch and are thought to arise from prenatal lymphoid tissue organizer (LTo) cells; however, the skin does not harbor the equivalent of Peyer’s patch and the origin of F3: FRC-like cells remains unknown.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	To explore F3 ontogeny from a developmental perspective, we first integrated adult and prenatal skin fibroblasts and identified the corresponding fibroblast populations (Supplementary Note 4).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	This identified that adult F3: FRC-like fibroblasts correlated with prenatal skin CCL19 fibroblasts (Fig. 8a,b).Fig.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	8Adult skin F3: FRC-like fibroblasts potentially arise from prenatal skin LTo cells.a, UMAP visualization for prenatal human skin and adult skin colored by cell type and (insert) age group.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	b, Heatmap of adult skin gene module scores applied to prenatal skin fibroblasts.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	c, UMAP visualization for prenatal human skin and intestine.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Insert: cluster of LTo-like cells.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	(m)LTo: (mesenchymal) lymphoid tissue organizer.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Dotplot of marker gene expression for LTo-like cells by tissue.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	d, Dotplot of expression of F3: FRC-like fibroblasts and LTo-associated marker genes in healthy adult skin F3: FRC-like fibroblasts, prenatal skin CCL19 fibroblasts and intestinal mLTo cells.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	e, Dotplot of expression of marker genes for adult skin F3: FRC-like fibroblasts and LTo-associated marker genes in diseased adult skin, by disease, for diseases with a minimum of 100 F3: FRC-like fibroblasts.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	DRESS, drug reaction with eosinophilia and systemic symptoms.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	f, Dotplot of expression of F3: FRC-like fibroblast marker genes in mouse steady-state cross-tissue atlas (Buechler et al.).
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	g, Proportion of Ccl19 fibroblasts (labels from original study) in mouse in different healthy tissues (including mouse flank skin) and of F3: FRC-like fibroblasts in healthy human skin.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Illustrations in f and g were partly created using BioRender.com.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	a, UMAP visualization for prenatal human skin and adult skin colored by cell type and (insert) age group.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	b, Heatmap of adult skin gene module scores applied to prenatal skin fibroblasts.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	c, UMAP visualization for prenatal human skin and intestine.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Insert: cluster of LTo-like cells.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	(m)LTo: (mesenchymal) lymphoid tissue organizer.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	Dotplot of marker gene expression for LTo-like cells by tissue.
PMC12479362	A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.	d, Dotplot of expression of F3: FRC-like fibroblasts and LTo-associated marker genes in healthy adult skin F3: FRC-like fibroblasts, prenatal skin CCL19 fibroblasts and intestinal mLTo cells.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

By day 30, F7: myofibroblasts had become the predominant population, consistent with a role in established fibrosis/scarring.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Overall, our results point toward F6: inflammatory myofibroblasts as an intermediate differentiation state toward F7: myofibroblasts in human skin, with potential plasticity in fibroblast origin (Fig. 5d,e and Extended Data Fig. 7e).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

We next investigated if the skin fibroblast subtypes we identified were conserved across other human tissues.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Previous studies have reported fibroblast states that are found across human tissues.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

However, because these studies each defined fibroblast subtypes with different nomenclature and gene markers, it is unclear how these populations relate to each other and to the skin fibroblast populations reported in our study.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

To answer this and perform an overarching analysis across tissues and diseases, we undertook two approaches.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

The first was to assess the expression of marker genes for cross-tissue fibroblast subtypes in our skin data.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

This identified that reported cross-tissue populations from previous studies are likely present in human skin, consistent with F2: universal, F3: FRC-like, F6: inflammatory myofibroblast, and F7: myofibroblast subtypes (Fig. 6a and Extended Data Fig. 8a).Fig.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

6Human cross-tissue disease fibroblast populations.a, Human tissues previously included in cross-tissue fibroblast studies and the fibroblast subtypes they have identified (above heatmap), colored by study (Buechler et al. in green, Korsunsky et al. in orange and Gao et al. in blue).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Heatmap shows gene expression of marker genes previously reported for cross-tissue fibroblast populations in our lesional skin fibroblast subtypes.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Immediately above the heatmap we show the skin fibroblast subtype with most similar gene expression to reported cross-tissue populations.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

b, UMAP visualization for cross-tissue integration (left) and for fibroblasts specifically (right), colored by tissue.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Color bars indicate expression (log1P norm).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

c, UMAP visualization for fibroblasts colored by re-annotated clusters (Methods).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

d, Dotplots of expression of marker genes we previously used for skin fibroblasts in cross-tissue atlas clusters by tissue type.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Note that not all genes were available as the endometrial dataset contained ~17,000 genes.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Illustrations in a were partly created using BioRender.com.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

a, Human tissues previously included in cross-tissue fibroblast studies and the fibroblast subtypes they have identified (above heatmap), colored by study (Buechler et al. in green, Korsunsky et al. in orange and Gao et al. in blue).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Heatmap shows gene expression of marker genes previously reported for cross-tissue fibroblast populations in our lesional skin fibroblast subtypes.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Immediately above the heatmap we show the skin fibroblast subtype with most similar gene expression to reported cross-tissue populations.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

b, UMAP visualization for cross-tissue integration (left) and for fibroblasts specifically (right), colored by tissue.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Color bars indicate expression (log1P norm).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

c, UMAP visualization for fibroblasts colored by re-annotated clusters (Methods).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

d, Dotplots of expression of marker genes we previously used for skin fibroblasts in cross-tissue atlas clusters by tissue type.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Note that not all genes were available as the endometrial dataset contained ~17,000 genes.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Illustrations in a were partly created using BioRender.com.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

The second approach was to integrate published datasets of ~5.8 million cells from human skin, lung, intestine, synovium, endometrium, heart and nasal mucosa (Methods and Fig. 6b).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

This approach uses the whole transcriptome profile, instead of restricted marker genes, and thus more comprehensively defines cell state similarity.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Approximately 1 million fibroblasts were selected for downstream analysis based on expression of canonical marker genes (Fig. 6b).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

In the cross-tissue integrated dataset, we were able to discern shared fibroblast states across tissues, as well as fibroblasts that were unique to certain tissues (Fig. 6b,c and Extended Data Fig. 8b).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

In addition to known cross-tissue populations identified above (Fig. 6a), we found evidence for F2/3: perivascular (CXCL12, APOC1 and PPARG) and F5: NGFR (Schwann-like; SCN7A, NGFR, ITGA6 and EBF2) fibroblasts across human tissues, including in lung, gut and nasal mucosa (Fig. 6c,d and Extended Data Fig. 8b,c).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Further interrogation of labeled intestine and lung datasets supported these results (Supplementary Note 3).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

F1: superficial showed variable gene expression by tissue, which may reflect distinct epithelia patterning across sites (Extended Data Fig. 8d).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Overall, our results point toward the presence of previously reported cross-tissue fibroblast states in skin, despite major differences in the biophysical properties of different human tissues.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

We additionally suggest F2/3: perivascular and F5: NGFR (nerve-associated) fibroblasts as novel cross-tissue populations.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Fibroblast-mediated processes such as fibrosis and maintenance of immune cell niches are observed across multiple human tissues.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

We therefore asked whether disease-associated fibroblast states identified in skin were similarly enriched by disease category in non-skin tissues (Methods).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

We focused on F3: FRC-like and F6: inflammatory myofibroblasts based on their conserved states across tissues and potential immune-interacting roles from pathway enrichment analysis (Extended Data Figs. 2a and 5c).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Then, to predict functional interactions with immune cells, we utilized our skin data to perform cell–cell communication analysis.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Across tissues, we observed that F3: FRC-like fibroblasts were present in both inflammatory disorders and fibrotic processes with immune-mediated pathology, including lung (COVID-19 and interstitial lung disease) and intestine (inflammatory bowel disease (IBD)) (Fig. 7a,b).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

While FRC-like fibroblasts were not reported in the Human Lung Cell Atlas (HLCA), following re-clustering we identified an F3: FRC-like population in lung (Extended Data Fig. 8e,f), consistent with a previous report.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

We also confirmed equivalence of F3: FRC-like fibroblasts to T reticular cells (an FRC subset) in IBD (Supplementary Note 3 and Extended Data Fig. 8g).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Receptor–ligand analysis suggested interactions of skin F3: FRC-like fibroblasts with migrating dendritic cells (MigDCs) (CCL19-CCR7) and T cell subsets (CXCL12-CXCR4) (Extended Data Fig. 9a), suggesting that F3: FRC-like fibroblasts maintain T lymphoid populations and facilitate T cell–dendritic cell interactions analogous to T reticular cells in lymphoid tissue.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

We corroborated these findings using NicheCompass for niche identification in inflamed atopic dermatitis skin, which revealed CCR7 MigDCs and CXCR4 T cells within the F3 superficial perivascular niche (Fig. 7c and Extended Data Fig. 9b).Fig.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

7Cross-tissue F3: FRC-like fibroblasts and F6: inflammatory myofibroblasts regulate skin immune niches.a, Proportion of disease-associated F3: FRC-like fibroblasts, F6: inflammatory myofibroblasts and F7: myofibroblasts in non-skin tissues by disease (left) and disease category (right).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

b, Dotplot of F3: FRC-like expression across diseases (skin and non-skin) (left).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Dotplot of F6: inflammatory myofibroblasts gene expression across diseases (skin and non-skin) (right).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Diseases with a minimum of 50 cells.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

c, H&E slide of lesional atopic dermatitis skin with annotation of perivascular infiltrate regions (top left).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Niche identification and proportion of cells in the perivascular superficial niche (bottom left).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Composition of the perivascular superficial niche in 10x Genomics Xenium.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Insert: zoomed in version of perivascular niche cluster.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

d, Cell–cell communication analysis for F6: inflammatory myofibroblasts and skin immune cells (Methods).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

TCM, T central memory.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

e, Proportion of F6: inflammatory myofibroblasts in IBD by intestinal tissue inflammation status and linear regression of proportion with inflammation scores with 95% CI.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

f, Schematic summary of cell–cell interactions for F3: FRC-like fibroblasts and F6: inflammatory myofibroblasts.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Schematic in f were created using BioRender.com.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

a, Proportion of disease-associated F3: FRC-like fibroblasts, F6: inflammatory myofibroblasts and F7: myofibroblasts in non-skin tissues by disease (left) and disease category (right).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

b, Dotplot of F3: FRC-like expression across diseases (skin and non-skin) (left).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Dotplot of F6: inflammatory myofibroblasts gene expression across diseases (skin and non-skin) (right).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Diseases with a minimum of 50 cells.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

c, H&E slide of lesional atopic dermatitis skin with annotation of perivascular infiltrate regions (top left).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Niche identification and proportion of cells in the perivascular superficial niche (bottom left).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Composition of the perivascular superficial niche in 10x Genomics Xenium.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Insert: zoomed in version of perivascular niche cluster.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

d, Cell–cell communication analysis for F6: inflammatory myofibroblasts and skin immune cells (Methods).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

TCM, T central memory.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

e, Proportion of F6: inflammatory myofibroblasts in IBD by intestinal tissue inflammation status and linear regression of proportion with inflammation scores with 95% CI.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

f, Schematic summary of cell–cell interactions for F3: FRC-like fibroblasts and F6: inflammatory myofibroblasts.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Schematic in f were created using BioRender.com.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

F6: inflammatory myofibroblasts were abundant in cancer and inflammation but relatively uncommon in established fibrosis (Fig. 7a,b), consistent with skin data (Fig. 4b).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Inflammatory myofibroblasts are well described in IBD, and we confirmed equivalence of these cells to skin F6: inflammatory myofibroblasts (Supplementary Note 3 and Extended Data Fig. 8g).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

To further assess the clinical relevance of F6 in IBD, we used an scRNA-seq dataset with clinical metadata.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

F6: inflammatory myofibroblasts were significantly elevated in inflamed tissue, compared to non-inflamed tissue, and their prevalence correlated with clinical inflammation severity scores (Fig. 7e).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Receptor–ligand analysis suggested that F6: inflammatory myofibroblasts recruit and maintain neutrophils (CXCL5/6/8-CXCR2 and CSF3-CSF3R), macrophages/monocytes (CCL5/26-CCR1 and CSF3-CSF3R) and B cells (CXCL13/CXCR5) in the skin (Fig. 7c and Methods).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

These genes were highly expressed in the skin during wound healing, acne and hidradenitis suppurativa, as well as in IBD and lung cancer (Fig. 7b), suggesting a similar mechanism for recruitment of immune cells across tissues.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Overall, our results suggest that F3: FRC-like (CCL19CD74TNFRSF13B and IL33/IL15) and F6: inflammatory myofibroblasts (IL11MMP1CXCL5IL7R) mediate distinct immune niches driving pathology in the skin and other tissues (Fig. 7f).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Given the similar transcriptomic profiles of adult skin F3: FRC-like and intestinal T reticular cells, we hypothesized that these fibroblasts had similar origins in their respective tissues.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Intestinal FRCs are found in the Peyer’s patch and are thought to arise from prenatal lymphoid tissue organizer (LTo) cells; however, the skin does not harbor the equivalent of Peyer’s patch and the origin of F3: FRC-like cells remains unknown.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

To explore F3 ontogeny from a developmental perspective, we first integrated adult and prenatal skin fibroblasts and identified the corresponding fibroblast populations (Supplementary Note 4).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

This identified that adult F3: FRC-like fibroblasts correlated with prenatal skin CCL19 fibroblasts (Fig. 8a,b).Fig.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

8Adult skin F3: FRC-like fibroblasts potentially arise from prenatal skin LTo cells.a, UMAP visualization for prenatal human skin and adult skin colored by cell type and (insert) age group.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

b, Heatmap of adult skin gene module scores applied to prenatal skin fibroblasts.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

c, UMAP visualization for prenatal human skin and intestine.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Insert: cluster of LTo-like cells.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

(m)LTo: (mesenchymal) lymphoid tissue organizer.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Dotplot of marker gene expression for LTo-like cells by tissue.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

d, Dotplot of expression of F3: FRC-like fibroblasts and LTo-associated marker genes in healthy adult skin F3: FRC-like fibroblasts, prenatal skin CCL19 fibroblasts and intestinal mLTo cells.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

e, Dotplot of expression of marker genes for adult skin F3: FRC-like fibroblasts and LTo-associated marker genes in diseased adult skin, by disease, for diseases with a minimum of 100 F3: FRC-like fibroblasts.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

DRESS, drug reaction with eosinophilia and systemic symptoms.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

f, Dotplot of expression of F3: FRC-like fibroblast marker genes in mouse steady-state cross-tissue atlas (Buechler et al.).

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

g, Proportion of Ccl19 fibroblasts (labels from original study) in mouse in different healthy tissues (including mouse flank skin) and of F3: FRC-like fibroblasts in healthy human skin.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Illustrations in f and g were partly created using BioRender.com.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

a, UMAP visualization for prenatal human skin and adult skin colored by cell type and (insert) age group.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

b, Heatmap of adult skin gene module scores applied to prenatal skin fibroblasts.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

c, UMAP visualization for prenatal human skin and intestine.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Insert: cluster of LTo-like cells.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

(m)LTo: (mesenchymal) lymphoid tissue organizer.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

Dotplot of marker gene expression for LTo-like cells by tissue.

PMC12479362

A single-cell and spatial genomics atlas of human skin fibroblasts reveals shared disease-related fibroblast subtypes across tissues.

d, Dotplot of expression of F3: FRC-like fibroblasts and LTo-associated marker genes in healthy adult skin F3: FRC-like fibroblasts, prenatal skin CCL19 fibroblasts and intestinal mLTo cells.