DDX54 downregulation enhances anti-PD1 therapy in immune-desert lung tumors with high tumor mutational burden

High tumor mutational burden (TMB) is a predictive biomarker for the responsiveness of cancer to immune checkpoint inhibitor therapy that indicates whether immune cells can sufficiently recognize cancer cells as non-self. However, about 30% of all cancers from The Cancer Genome Atlas are classified as immune-desert tumors lacking T cell infiltration despite high TMB. Since the underlying mechanism of these immune-desert tumors has yet to be unraveled, there is a pressing need to transform such immune-desert tumors into immune-inflamed tumors and thereby enhance their responsiveness to anti-PD1 therapy. Here, we present a systems framework for identifying immuno-oncotargets, based on analysis of gene regulatory networks, and validating the effect of these targets in transforming immune-desert into immune-inflamed tumors. In particular, we identify DEAD-box helicases 54 (DDX54) as a master regulator of immune escape in immune-desert lung cancer with high TMB, and show that knockdown of DDX54 can increase immune cell infiltration and lead to improved sensitivity to anti-PD1 therapy. This study employs a syngeneic mouse model of lung cancer to investigate the role of Ddx54 in tumor biology and its interaction with anti-PD1 immunotherapy. Four formalin-fixed paraffin-embedded (FFPE) tissue blocks were obtained from mice bearing Lewis Lung Carcinoma 1 (LLC1) tumors under distinct experimental conditions:1. Sample #1: Mice injected with wild-type (WT) LLC1 cells and treated with an isotype control antibody. 2. Sample #2: Mice injected with Ddx54 knockdown (KD) LLC1 cells and treated with an isotype control antibody. 3. Sample #3: Mice injected with WT LLC1 cells and treated with an anti-PD1 antibody. 4. Sample #4: Mice injected with Ddx54 KD LLC1 cells and treated with an anti-PD1 antibody.Each treatment group consists of replicates to ensure statistical robustness. Utilizing the Xenium Mouse 5K spatial transcriptomics workflow, spatial gene expression profiles were generated for each FFPE tissue block. This approach allows for the spatial mapping of transcriptomic changes within the tumor microenvironment, facilitating the comparison between WT and Ddx54 KD tumors under both control and immunotherapy conditions. The design enables the assessment of how Ddx54 modulation affects tumor response to anti-PD1 therapy, immune cell infiltration, and overall tumor gene expression landscapes.