OBJECTIVE: To investigate the mechanistic underpinnings and treatment response of lupus nephritis (LN) in activated PI3K-delta syndrome type 1 (APDS1) using pathway-specific therapy and advanced spatial proteomics. METHOD: We conducted mechanistic investigation of refractory class V LN in an 18-year-old female with genetically confirmed APDS1 (PIK3CD c.3061G>
A, p.E1021K mutation). Response to leniolisib, a selective PI3Kδ inhibitor, was evaluated through clinical parameters and flow cytometry of peripheral blood lymphocytes. Kidney tissue immune architecture was characterized using Multiplexed Ion Beam Imaging Time-of-Flight Spectrometry (MIBI-TOF), comparing the APDS1-LN tissue signature with 12 childhood-onset LN patients (cLN) and 5 healthy controls (HC). RESULTS: Leniolisib treatment normalized hyperactive PI3Kδ signaling, resulting in significant improvements in proteinuria, complement levels, and peripheral edema after failing three years of conventional immunosuppressives. MIBI-TOF spatial proteomics revealed a distinct tissue-specific immunopathology with significantly increased proportions of CD8+ T cells (21.6% in APDS1 vs. 12.0% in typical LN, p=0.0410) and M1 macrophages (42.0% in APDS1 vs. 9.0% in typical LN, p=0.1445) clustering around glomeruli with immune complex deposition. This immune signature aligns with the constitutively active PI3Kδ pathway's effect on lymphocyte exhaustion and inflammatory phenotype. CONCLUSION: This investigation advances rheumatology by demonstrating that APDS1-associated LN displays a specific tissue immune signature and responds to targeted inhibition of the causative molecular pathway. Our findings provide mechanistic insights into genetic drivers of autoimmunity and support pathway-specific therapeutic approaches for refractory autoimmune manifestations in primary immunodeficiencies.