Table 1 Pathway-based deconvolution of interstitial genes and expression changes in disease.

REF, reference samples; DN, diabetic nephropathy; FIB, fibroblast; END, endothelial cell; VSMC, vascular smooth muscle cell or pericyte; IMM, immune cell.

A: Pathway-based deconvolution of unique DEGs uncovered in regional transcriptomics of the interstitium
GeneExp*PCell typeRelated cluster(s)Predicted cell
origin§
Reference
COL1A11.270.0000018FIBC28Fibroblast(40)
COL6A21.790.0000002FIBC28Fibroblast(41)
CELA3A1.290.0010768FIBC28Fibroblast(4244)
TAS2R381.520.0000242END, VSMC, and FIBC23, C24, C27, and C28Fibroblast and
endothelial
(45, 46)
KISS11.260.0000796END, VSMC, and FIBC23, C24, C27, and C28Fibroblast and
endothelial
(47)
F21.110.0021807ENDC23 and C24Endothelial(48)
LBP1.090.0026784END and VSMCC23 and C24Endothelial(49)
LPA1.440.0008546ENDC23 and C24Endothelial(50, 51)
NCF21.180.0024971IMMC30Neutrophil(52)
SIGLEC11.120.0075341IMMC30Macrophage(53)
CD3D1.070.0033362IMMC30T lymphocyte(54)
GZMB1.400.0011656IMMC30CD8+ lymphocyte(55)
KLRC4-KLRK11.120.0012396IMMC30NK cell(56)
TPSB21.530.0000181IMMC30Mast cell(20, 57)
CADM31.080.0050414END, VSMC, FIB, and
IMM
C23–24, C27–28,
and C30
Epithelial(58)
B: Interstitial gene expression changes in diabetic nephropathy
GeneExp*PBroad cell type
groupǁ
Related cluster(s)Log2 exp ratio: DN/
REF
P Ref v DN
MYH110.790.024689VSMCC27−9.191.08 ×10−6
RPGR0.460.046132ENDC24 and C25−2.933.65 × 10−2
FAR20.680.019020ENDC23−3.849.49 × 10−4
LUM0.690.023555FIBC28−3.813.03 × 10−3
ZFPM2-AS10.850.010638VSMC and FIBC27 and C28−4.023.16 × 10−3
CPE0.680.021649VSMCC27−2.688.63 × 10−2
CCDC30.770.020488ENDC24−2.445.37 × 10−3
PTRF0.710.008293END and VSMCC24 and C27−2.368.48 × 10−2
JAM20.890.007941ENDC24−2.952.03 × 10−2
ZFPM20.880.004205VSMC and FIBC27 and C28−2.682.40 × 10−2

*Exp indicates expression ratio of the interstitial compartment compared with the mean of all other compartments after log2 conversion.

P: P value for the comparison of expression between the interstitium and other compartments.

‡The gene was a member of KEGG pathways enriched in the cell type(s) listed. Pathway enrichment is based on DEGs in the snDrop RNAseq dataset.

§Predicted cell origin is based on the membership of the gene to enriched pathways of cell types and cross-referenced in the literature.

ǁBroad cell type group refers to the dimensionally reduced cell types within the snDrop RNAseq dataset.

P: P value for the comparison of expression between the interstitium of the reference and diabetic nephropathy samples.