Table 2.

Pathway-level analysis shows downregulated expression of genes involved in immune/inflammatory processes after sparsentan treatment

Up Pathways		Down Pathways
Control vs. EIC		EIC vs. EIC+S120		EIC vs. EIC+S60
Pathway	P Value	Pathway	P Value	Pathway	P Value
Cytokine-mediated signaling pathway	2.53E-08	Cytokine-mediated signaling pathway	2.97E-09	Cellular response to type I interferon	1.49E-08
Cellular response to type I interferon	2.53E-08	Cellular response to type I interferon	3.87E-09	Type I interferon signaling pathway	1.49E-08
Type I interferon signaling pathway	2.53E-08	Type I interferon signaling pathway	3.87E-09	Cytokine-mediated signaling pathway	2.90E-07
Neutrophil activation involved in immune response	3.52E-05	Neutrophil activation involved in immune response	1.24E-05	Neutrophil activation involved in immune response	0.001
Neutrophil degranulation	6.37E-05	Neutrophil degranulation	2.40E-05	Neutrophil degranulation	0.002
Neutrophil-mediated immunity	8.22E-05	Neutrophil-mediated immunity (GO:0002446)	3.08E-05	Antigen processing and presentation of exogenous peptide antigen via MHC class I	0.002
Cellular response to cytokine stimulus	7.33E-04	Cellular response to cytokine stimulus	0.001	Neutrophil-mediated immunity	0.002
Antigen processing and presentation of exogenous peptide antigen via MHC class I	0.003	Antigen processing and presentation of exogenous peptide antigen via MHC class I	0.001	Response to interferon-gamma	0.003
Response to interferon-gamma	0.004	Response to interferon-gamma	0.001	Response to interferon-beta	0.005
Response to cytokine	0.004	Antigen processing and presentation of exogenous peptide antigen via MHC class I, tap-dependent	0.003	Antigen processing and presentation of exogenous peptide antigen via MHC class I, tap-dependent)	0.005

WGCNA analysis between grouped pairs (Control vs. EIC, EIC vs. EIC + S120, EIC vs. EIC + S60) was performed to find module eigengenes that correlate with glomerular phenotypes (nuclei per glomerulus and Ki-67 positivity). Genes from the modules significantly associated with the cellular phenotypes were then grouped and subjected to GSEA GO biological process pathway analysis. Top 10 pathways for each pairwise analysis are shown. LFC of genes within each pathway were identified using DESeq2 data and found to be decreased compared with the LFC of the upregulated genes in control vs. EIC. DESeq2, differential expression analysis for sequence 2; EIC, engineered immune complexes; GO, gene ontology; GSEA, gene set enrichment analysis; INF, interferon; LFC, log₂ fold change; MHC1, major histocompatibility complex class I; S60, sparsentan 60 mg/kg; S120, sparsentan 120 mg/kg; WGCNA, weighted gene correlation network analysis.