Increased PD-L1 Expression in Acute Myeloid Leukemia with Fanconi Anemia/BRCA Mutations

Introduction:

Loss of DNA repair fidelity is a common feature of tumors and can drive genomic instability, tumor evolution, and therapy response. ¹ Fanconi anemia (FA) is a DNA damage response (DDR) pathway and biallelic germline mutations in the pathway lead to a bone marrow failure syndrome with a predisposition for cancer, especially acute myeloid leukemia (AML). Unfortunately, FA-AML is a secondary AML with very poor prognosis, with an increased risk for relapse even after initial cure with bone marrow transplantation. Therefore FA patients need further options for therapy.

DNA damage response (DDR) deficiency has emerged as a predictive biomarker of response to immune checkpoint inhibition. ² In some solid tumors, defective DDR leads to genomic instability, increased mutational burden, increased neo antigen expression and increased PD-L1 expression; and respond robustly to PD-1 checkpoint inhibitor therapy. The mutational burden and PD-L1 expression in FA-mutated tumors remain to be discovered. Therefore, we hypothesize that FA mutations in AML increase mutational burden and PD-L1 expression. This work can set the stage for future studies involving PD-1 blocking therapies for FA-mutated tumors.

Methods/Results:

To determine the mutational burden in FA-mutated tumors, we didwhole exome sequencing (WES)of three AML cell lines obtained from pediatric FA patients, all were FANCD1/BRCA2 mutated.^3,4 The three AML cell lines also represent a progression of AML disease- an early clone, a late clone and a relapsed AML after bone marrow transplantation. There was an average of 180,000 somatic mutations/case, pared down to 1,000 mutations after limiting calls with >10 reads and allele frequency >0.1%. Mutational burden of pediatric AML in non-FA patients has been reported to be ~10 mutations/case.⁵Therefore there is about a 100-fold increase in mutations in AML from FA patients compared to AML from non-FA patients.Then we determined PD-L1 mRNA and protein expression of the three FANCD1/BRCA2 mutated AML cells with quantitative PCR and flow cytometry respectively. We found increasing PD-L1 mRNA expression from early to late to relapsed clones (2^^-ΔCt values 1.21x10^-5, 1.54x10^-5, and 7.02x10^-5 respectively; p-value<0.05). Interestingly, interferon-gamma (IFN-g), a known inducer and regulator of PD-L1 expression, is detected at high levels in the bone marrow of FA patients.⁵ We find that PD-L1 expression significantly increases in FANCD1/BRCA2 mutated AML cells after treatment with physiologic doses of IFN-g (fold change in 2^^-ΔΔCt before and after treatment with 5ng IFN-g for early clone (x16.55 fold change) late clone (x38.46 fold change) and relapsed clone (x17.57 fold change), p-value<0.05. We also found stable PD-L1 protein expression on the cell surface (% PD-L1-positive cells for early clone (15.2%), late clone (17.7%), and relapsed AML (18.9%).

Conclusions: Our data show there is a high mutational load in FA-AML cell lines, which also express PD-L1. Both of these tumor characteristics are predictors of response to PD-1 checkpoint inhibitor immunotherapy. This will lead to future work on PD-1 blockade as a potential therapeutic option for FA-AML.