Renal Single-Cell RNA Sequencing and Digital Cytometry in Dogs with X-Linked Hereditary Nephropathy
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. Single-Cell Suspension Preparation
2.3. Single-Cell RNA Sequencing
2.4. Sample Size Calculation
2.5. Data and Statistical Analysis
3. Results
3.1. Histopathological Evaluation of Kidney Biopsies
3.2. Unbiased Classification of Canine Renal Cells Using scRNA-Seq
3.3. Differential Gene Expression and Pathway Analysis
3.4. Digital Cytometry Using Bulk mRNA-Seq Data
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
20HETE | 20-hydroxyeicosatetraenoic acid |
CKD | Chronic kidney disease |
COL4A5 | α5 chain of the type IV collagen |
CYP4A11 | Cytochrome P450 family 4 subfamily A member 11 |
PANTHER | Protein Analysis THrough Evolutionary Relationships |
RNA-seq | RNA sequencing |
scRNA-seq | Single-cell RNA sequencing |
XLHN | X-linked Hereditary Nephropathy |
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Affected Male Dog | Heterozygous Female Dog | |
---|---|---|
Reads mapped to genome | 95.4% | 95.3% |
Number of cells examined | 12,778 | 13,190 |
Median genes per cell | 1575 | 1278 |
Total genes detected | 25,438 | 24,208 |
Cell Type | Marker Genes | Cell Number in Affected Male Dog | Cell Percentage in Affected Male Dog | Cell Number in Heterozygous Female Dog | Cell Percentage in Heterozygous Female Dog |
---|---|---|---|---|---|
B cell-1 | CD79B [31] | 364 | 2.85% | 394 | 2.99% |
B cell-2 | CD79B [31] CTSS [32] | 9 | 0.07% | 142 | 1.08% |
B cell-3 | (Determined by CellMarker [28]) | 908 | 7.11% | 853 | 6.47% |
Distal tubule cell-1 | UMOD, DEFB1, TMEM213 [31] | 650 | 5.09% | 573 | 4.34% |
Distal tubule cell-2 | DEFB1, ATP6V1G3 [31] | 205 | 1.60% | 918 | 6.96% |
Endothelial cell-1 | PECAM1, EMCN, FLT1, TEK [30] FAM167B, SOX17, MYCT1, TIE1, ADGRL4, SOX18, PTPRB [32] | 910 | 7.12% | 717 | 5.44% |
Endothelial cell-2 | PECAM1, EMCN, FLT1, TEK, ADGRL4, SOX18 [30] FAM167B, SOX17, MYCT1, TIE1, PTPRB [32] | 238 | 1.86% | 313 | 2.37% |
Endothelial cell-3 | PECAM1, EMCN [30] GPHBP1, MYCT1, TIE1, SOX18 [32] | 160 | 1.25% | 150 | 1.14% |
Endothelial cell-4 | PECAM1, EMCN [30] GPHBP1, MYCT1, TIE1, SOX18 [32] | 103 | 0.81% | 524 | 3.97% |
Intercalated cell | ATP6V1G3, ATP6V0D2, TMEM213 [31] | 843 | 6.60% | 223 | 1.69% |
Macrophage | LYZ, CD14 [31] C1QB, CTSS, CCL4, CCL3, AIF1, CX3CR1 [32] | 182 | 1.42% | 495 | 3.75% |
Medullary cell | FBLN5 [28] | 71 | 0.56% | 268 | 2.03% |
Mesangial cell | MYLL9, ITGA8 [30] | 909 | 7.11% | 37 | 0.28% |
Natural killer cell-1 | NKG7 [31] CD52, CCL4 [32] | 857 | 6.71% | 50 | 0.38% |
Natural killer cell-2 | NKG7 [31] CD52 [32] | 40 | 0.31% | 212 | 1.61% |
Podocyte | NPHS2, NPHS1, WT1, SYNPO [30] | 281 | 2.20% | 66 | 0.50% |
Proximal tubule cell-1 | SLC13A3, SLC34A1, GPX3 [31] RDH16 [32] | 1,031 | 8.07% | 347 | 2.63% |
Proximal tubule cell-2 | SLC13A3, SLC34A1, GPX3 [31] RDH16 [32] | 458 | 3.58% | 523 | 3.97% |
Proximal tubule cell-3 | GPX3 [31] RDH16 [32] | 1,431 | 11.20% | 1182 | 8.96% |
T cell-1 | IL7R [31] CD52 [32] | 1,586 | 12.41% | 2863 | 21.71% |
T cell-2 | IL7R [31] CD52 [32] | 781 | 6.11% | 620 | 4.70% |
T cell-3 | IL7R [31] NKG7 [31] CCL4 [32] | 95 | 0.74% | 66 | 0.50% |
T cell-4 | IL7R [31] CTSS, CX3CR1 [32] | 112 | 0.88% | 20 | 0.15% |
T cell-5 | CCL4, CCL3 [32] | 554 | 4.34% | 1634 | 12.39% |
Cell Types | PANTHER Pathways | Genes in the Pathway | Fold Enrichment | p Value |
---|---|---|---|---|
All cells | FAS signaling pathway | LMNA, ENSCAFG00845026419, JUN, GSN | 12.84 | 3.82 × 10−2 |
CCKR signaling map | CPE, CREM, CCK, JUN, MMP9, IER3, CCK, MEF2C | 4.66 | 2.24 × 10−2 | |
Integrin signaling pathway | COL1A1, COL1A2, ACAT2, COL6A3, COL1A2, FN1, COL3A1, COL1A1, FN1 | 4.23 | 4.62 × 10−2 | |
Podocytes | Integrin signaling pathway | COL11A1, COL4A1, ITGAV, VCL, COL1A2, ACTA2, ASAP1, COL6A3, NTN4, CAV1, COL1A2, COL5A2, FN1, COL8A2, ITGA2, LAMB1, COL4A2, FN1, COL4A4, ITGA6, COL5A3 | 4.52 | 1.47 × 10−6 |
Proximal tubule cell-2 | Inflammation mediated by chemokine and cytokine signaling pathway | CCL2, MYH11, ACTA2, ITGA2, CXCL10 | 8.45 | 1.14 × 10−2 |
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Chu, C.P.; Osorio, D.; Nabity, M.B. Renal Single-Cell RNA Sequencing and Digital Cytometry in Dogs with X-Linked Hereditary Nephropathy. Animals 2025, 15, 2061. https://doi.org/10.3390/ani15142061
Chu CP, Osorio D, Nabity MB. Renal Single-Cell RNA Sequencing and Digital Cytometry in Dogs with X-Linked Hereditary Nephropathy. Animals. 2025; 15(14):2061. https://doi.org/10.3390/ani15142061
Chicago/Turabian StyleChu, Candice P., Daniel Osorio, and Mary B. Nabity. 2025. "Renal Single-Cell RNA Sequencing and Digital Cytometry in Dogs with X-Linked Hereditary Nephropathy" Animals 15, no. 14: 2061. https://doi.org/10.3390/ani15142061
APA StyleChu, C. P., Osorio, D., & Nabity, M. B. (2025). Renal Single-Cell RNA Sequencing and Digital Cytometry in Dogs with X-Linked Hereditary Nephropathy. Animals, 15(14), 2061. https://doi.org/10.3390/ani15142061