PD-L1/PD-L2/JAK2 (PDJ amplicon) expression is a marker of response to immunotherapy (IO) in triple negative breast cancer (TNBC).

Background
The PDJ amplicon contains three functionally linked, druggable genes (PD-L1, PD-L2, and JAK2), but the impact of its expression on IO response in TNBC has not been well-characterized.

Methods
The Tempus Lens Platform was used to identify patients (pts) diagnosed with metastatic TNBC (mTNBC) who underwent clinical sequencing using the Tempus xT (DNA) and xR (RNA) assays. Pts had tumor purity ≥40%, stage IV disease at sampling, and tissue collected within 365 days before first-line (1L) therapy. RNA-seq data were normalized as log2(TPM+1). The 80th percentile of gene expression was used to define high/low expressors of JAK2, PD-L1, and PD-L2. PD-L1 combined positive score (CPS) was determined by Tempus immunohistochemistry. Pts were classified by Tempus Immune Profile Score (IPS, low/high) and immune cell infiltration was estimated using quanTIseq. Clinicopathologic data and immune biomarkers were compared using Chi-squared/Fisher’s exact/Wilcoxon rank sum tests. Real-world overall survival (rwOS) was defined as time from 1L IO treatment to death or last known follow up. Median OS was estimated using Kaplan-Meier curves and compared using log rank tests.

Results
JAK2-high pts (142/708) were enriched for PD-L1 CPS ≥ 10 (55% vs 17%, P<0.001) and high IPS (67% vs 22%, P<0.001). JAK2-high pts also had higher B cell, macrophage, CD8 T cell, and regulatory T cell infiltration compared to JAK2-low. In the IO-treated cohort, JAK2-high pts (56/218) had longer median rwOS compared to JAK2-low (NR vs 17.1 months; P=0.011). High expression of PD-L1 and PD-L2 was also associated with high PD-L1 CPS and IPS and increased tumor immune infiltration. High PD-L1 (22.7 vs 17.1 months; P=0.041) and PD-L2 (25.1 vs 16.4 months, P=0.007) were also associated with improved rwOS on IO.

Conclusions
High JAK2, PD-L1, and PD-L2 expression in mTNBC are associated with immune infiltration, high PD-L1 CPS score and high IPS, likely contributing to the OS benefit observed in IO-treated pts with high expression of these genes. These results support further investigation of PDJ amplicon expression, especially JAK2, as a predictive biomarker for IO response in TNBC.