GSE130973 Human Skin Aging
Single-cell transcriptomes of sun-protected human skin (Solé-Boldo et al.,
Communications Biology 2020). Analysis here covers QC, clustering, UMAP,
cell-type annotation and an old versus young comparison on the GEO filtered matrix
(GSE130973; 2 young + 3 old donors). Numbers below are from this rerun,
not copied from the paper abstract.
UMAP overview
Leiden clusters · parent cell type · age group · donor (y1/y2 young; o1–o3 old).
Donors and cell types
GEO overall design: y1=25y, y2=27y, o1=53y, o2=70y, o3=69y. Barcode suffixes
-1…-5 follow that sample order. Fibroblast clusters are further
labelled with the four paper subtypes (secretory papillary / reticular, mesenchymal, proinflammatory)
then collapsed to a parent Fibroblast class for composition.
| Donor | Age | Years | Cells |
|---|---|---|---|
| y1 | Young | 25 | 3130 |
| y2 | Young | 27 | 2564 |
| o1 | Old | 53 | 3332 |
| o2 | Old | 70 | 2222 |
| o3 | Old | 69 | 4549 |
| Cell type | Cells | Old % | Young % |
|---|---|---|---|
| Endothelial | 1202 | 7 | 8.7 |
| Fibroblast | 6123 | 42 | 33 |
| Keratinocyte | 4294 | 37 | 9.7 |
| Macrophage_DC | 1723 | 9.8 | 12.9 |
| Melanocyte | 81 | 0.4 | 0.7 |
| Smooth_muscle | 1194 | 2.9 | 15.9 |
| T_cell | 1180 | 0.9 | 19.1 |
| Cluster | Parent | Fine label |
|---|---|---|
| 0 | Fibroblast | Fibroblast_proinflammatory |
| 1 | Macrophage_DC | Macrophage_DC |
| 2 | Fibroblast | Fibroblast_secretory_reticular |
| 3 | Fibroblast | Fibroblast_proinflammatory |
| 4 | T_cell | T_cell |
| 5 | Keratinocyte | Keratinocyte |
| 6 | Keratinocyte | Keratinocyte |
| 7 | Smooth_muscle | Smooth_muscle |
| 8 | Endothelial | Endothelial |
| 9 | Keratinocyte | Keratinocyte |
| 10 | Keratinocyte | Keratinocyte |
| 11 | Keratinocyte | Keratinocyte |
| 12 | Fibroblast | Fibroblast_mesenchymal |
| 13 | Endothelial | Endothelial |
| 14 | Smooth_muscle | Smooth_muscle |
| 15 | Keratinocyte | Keratinocyte |
| 16 | Melanocyte | Melanocyte |
Old vs Young composition
Composition shift across the five donors. Interpret percentages against the measured cell counts — this matrix is whole-skin, not a purified fibroblast sort.
Differential expression — Old vs Young
Wilcoxon rank-sums on all QC cells; top 12 up/down by adjusted p-value. Fibroblast-restricted DE is shown underneath when available.
Up in Old (aged ↑)
| Gene | log2FC | padj |
|---|---|---|
| KRT1 | 2.84 | 0.0e+0 |
| CXCL14 | 1.96 | 0.0e+0 |
| SFN | 2.45 | 0.0e+0 |
| S100A2 | 2.36 | 0.0e+0 |
| KRT14 | 1.85 | 0.0e+0 |
| DMKN | 3 | 0.0e+0 |
| LY6D | 2.58 | 4.3e-233 |
| IL8 | 1.73 | 1.8e-217 |
| SOD2 | 1.25 | 3.9e-217 |
| KRT10 | 1.64 | 9.9e-217 |
| SAT1 | 1.08 | 2.3e-214 |
| FTL | 0.54 | 1.1e-178 |
Down in Old (aged ↓)
| Gene | log2FC | padj |
|---|---|---|
| MALAT1 | -0.57 | 0.0e+0 |
| HBB | -3.05 | 1.9e-263 |
| ZFP36 | -0.92 | 4.0e-157 |
| S100A4 | -0.76 | 6.6e-136 |
| MT-CO1 | -0.53 | 2.6e-111 |
| ARHGDIB | -1.6 | 5.0e-104 |
| TMEM66 | -1.13 | 4.9e-100 |
| FLNA | -1.18 | 7.4e-85 |
| HBA2 | -2.9 | 4.5e-69 |
| MYL9 | -1.35 | 5.5e-63 |
| TPM2 | -1.63 | 5.6e-62 |
| CD52 | -1.68 | 3.1e-58 |
Fibroblast-only Old vs Young
Same test restricted to cells annotated as Fibroblast.
| Gene ↑ Old | log2FC | padj |
|---|---|---|
| FTH1 | 0.74 | 4.4e-236 |
| FTL | 0.67 | 3.7e-203 |
| NEAT1 | 1.27 | 1.1e-196 |
| TMSB4X | 0.64 | 1.8e-166 |
| RPL10 | 0.38 | 1.1e-117 |
| CXCL14 | 1.28 | 8.8e-117 |
| PTMA | 0.53 | 8.6e-112 |
| CD81 | 1.53 | 7.5e-109 |
| Gene ↓ Old | log2FC | padj |
|---|---|---|
| MT-ND1 | -1.66 | 3.5e-291 |
| MT-ND2 | -1.47 | 1.0e-237 |
| UQCRB | -2.31 | 5.1e-235 |
| MT-CYB | -1.25 | 1.9e-219 |
| MT-ATP6 | -1.22 | 8.3e-208 |
| MT-CO3 | -1.03 | 4.3e-193 |
| MT-ND3 | -1.44 | 2.7e-187 |
| MT-ND4 | -1.02 | 2.7e-179 |
ECM / priming vs inflammatory markers
Paper thesis: ageing reduces fibroblast functional priming and shifts communication. Bars are mean log-normalised expression in Fibroblast / Keratinocyte / Endothelial. Page text follows the measured table, not a canned “ELN always down” claim.
| Age | Cell type | COL1A1 | COL1A2 | ELN | DCN | LUM | MFAP5 | APCDD1 | WIF1 | CCL19 | APOE | CXCL2 | CXCL12 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Old | Endothelial | 0.346 | 0.392 | 0.125 | 0.956 | 0.303 | 0.074 | 0.084 | 0.026 | 0.112 | 0.376 | 1.562 | 0.194 |
| Old | Fibroblast | 2.362 | 2.803 | 0.501 | 4.13 | 2.403 | 0.841 | 0.522 | 0.478 | 0.437 | 1.541 | 2.121 | 1.564 |
| Old | Keratinocyte | 0.646 | 0.758 | 0.071 | 1.433 | 0.471 | 0.112 | 0.183 | 0.068 | 0.301 | 1.593 | 1.128 | 0.361 |
| Young | Endothelial | 0.325 | 0.372 | 0.146 | 0.695 | 0.108 | 0.039 | 0.09 | 0.004 | 0.1 | 0.199 | 1.06 | 0.299 |
| Young | Fibroblast | 2.925 | 3.165 | 0.519 | 4.097 | 1.836 | 0.859 | 0.679 | 0.363 | 0.459 | 1.549 | 1.505 | 1.809 |
| Young | Keratinocyte | 0.568 | 0.601 | 0.059 | 1.122 | 0.185 | 0.056 | 0.284 | 0.052 | 0.135 | 1.347 | 0.791 | 0.237 |
Cluster marker genes (top)
Wilcoxon marker genes per Leiden cluster.
| Cluster | Fine label | Top markers |
|---|---|---|
| 0 | Fibroblast_proinflammatory | CXCL14 · DCN · APOD · CFD · GSN · PTGDS · SOD2 · TNFAIP6 · CFH · ZFP36 |
| 1 | Macrophage_DC | CD74 · HLA-DRB1 · HLA-DRA · HLA-DPB1 · HLA-DPA1 · HLA-DQA1 · HLA-DQB1 · TMSB4X · TYROBP · LYZ |
| 2 | Fibroblast_secretory_reticular | DCN · CFD · FBLN1 · GSN · SLPI · COL1A2 · IGFBP5 · IGFBP6 · WISP2 · LUM |
| 3 | Fibroblast_proinflammatory | S100A6 · SFRP2 · DCN · COL3A1 · COL1A2 · GSN · KRT14 · APOE · S100A2 · COL1A1 |
| 4 | T_cell | CD52 · IL32 · ARHGDIB · TMSB4X · CD3D · PTPRCAP · TMEM66 · CD69 · MALAT1 · CXCR4 |
| 5 | Keratinocyte | DMKN · KRT10 · KRT1 · LGALS7B · LY6D · SFN · DSP · KRTDAP · LYPD3 · RPLP1 |
| 6 | Keratinocyte | KRT14 · KRT5 · S100A2 · MIR205HG · SFN · SERPINB2 · RPLP1 · SERPINB5 · COL17A1 · LGALS7B |
| 7 | Smooth_muscle | TAGLN · MYL9 · ACTA2 · TPM2 · ADIRF · CPE · C11orf96 · MYH11 · TINAGL1 · MALAT1 |
| 8 | Endothelial | TM4SF1 · IFI27 · SPARCL1 · DARC · TSC22D1 · AC011526.1 · SPRY1 · SELE · GNG11 · CD74 |
| 9 | Keratinocyte | KRT14 · S100A2 · SFN · RPLP1 · LGALS7B · MIR205HG · KRT5 · SERPINB5 · DSP · DMKN |
| 10 | Keratinocyte | TM4SF1 · IFI27 · SPARCL1 · TSC22D1 · SPRY1 · DARC · RCAN1 · ELTD1 · MCTP1 · PLVAP |
| 11 | Keratinocyte | HLA-DRB5 · HLA-DRA · HLA-DPA1 · HLA-DQB1 · HLA-DPB1 · CD74 · HLA-DQA1 · HLA-DRB1 · LYZ · IL8 |
| 12 | Fibroblast_mesenchymal | COL1A1 · COL1A2 · COL3A1 · COL5A2 · LUM · ASPN · HTRA1 · POSTN · MEG3 · FN1 |
| 13 | Endothelial | TFF3 · CCL21 · TFPI · CLDN5 · MMRN1 · GNG11 · ECSCR · PROX1 · SNCG · RAMP2 |
| 14 | Smooth_muscle | TAGLN · ACTA2 · TPM2 · MYL9 · ADIRF · C11orf96 · CRISPLD2 · ADRA2A · ID4 · MYH11 |
| 15 | Keratinocyte | CXCR4 · CD52 · HBB · CYTIP · PTPRC · IGLL5 · CD3D · ARHGDIB · SAMSN1 · LTB |
| 16 | Melanocyte | DCT · MLANA · TYRP1 · PMEL · MITF · PLP1 · CAPN3 · APOE · GPM6B · APOD |