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. After euthanizing the LLC1 xenograft mouse model, single cells were obtained from the mouse cancer tissues. From this population, CD45-positive immune cells were separated using Aria Fusion (Becton Dickinson) flow cytometry. A library for single-cell RNA sequencing was constructed using the 10x Genomics 5' single cell RNA-seq kit. This library was then sequenced using next-generation sequencing (NGS) on the Illumina HiSeq 2500 platform. Raw reads were mapped to the Mus musculus mm10 reference genome utilizing the CellRanger pipeline (20) v6.1.0 from 10X genomics.