Determine the effects of Wdr4 on global translation efficiency via ribosome profiling (Ribo-seq)

Tumor-associated macrophages (TAMs) play a pivotal role in shaping the tumor microenvironment in hepatocellular carcinoma (HCC), significantly influencing disease progression and patient outcomes. WDR4, a tRNA-binding scaffold essential for N7-methylguanosine (m7G) methylation, has an undefined role in HCC-associated TAMs. Here, we found that WDR4 expression is markedly upregulated in HCC-infiltrating TAMs and correlates with poor prognosis in patients. Using HCC mouse models, we demonstrated that WDR4 depletion reprograms TAMs toward an anti-tumor phenotype and suppresses HCC progression. To investigate the impact of WDR4 on translational efficiency, we performed ribosome profiling (Ribo-seq) on Wdr4-deficient TAMs. To ensure reproducibility and minimize potential off-target effects, we included TAMs sorted from orthotopic HCC-bearing Wdr4 conditional knockout mice, as well as immortalized bone marrow-derived macrophages (iBMDMs) with Wdr4 knocked out using two independent sgRNAs.