Computational inference of eIF4F complex function and structure in human cancers

The canonical eukaryotic initiation factor 4F (eIF4F) complex, composed of eIF4G1, eIF4A1, and the cap-binding protein eIF4E, plays a crucial role in cap-dependent translation initiation in eukaryotic cells (1). However, cap-independent initiation can occur through internal ribosomal entry sites (IRESs), involving only eIF4G1 and eIF4A1 present, which is considered to be a complementary process to cap-dependent initiation in tumors under stress conditions (2). The selection and molecular mechanism of specific translation initiation in human cancers remains poorly understood. Thus, we analyzed gene copy number variations (CNVs) in TCGA tumor samples and found frequent amplification of genes involved in translation initiation. Copy number gains in EIF4G1 and EIF3E frequently co-occur across human cancers. Additionally, EIF4G1 expression strongly correlates with genes from cancer cell survival pathways including cell cycle and lipogenesis, in tumors with EIF4G1 amplification or duplication. Furthermore, we revealed that eIF4G1 and eIF4A1 protein levels strongly co-regulate with ribosomal subunits, eIF2, and eIF3 complexes, while eIF4E co-regulates with 4E-BP1, ubiquitination, and ESCRT proteins. Using Alphafold predictions, we modeled the eIF4F structure with and without eIF4G1-eIF4E binding. The modeling for cap-dependent initiation suggests that eIF4G1 interacts with eIF4E through its N-terminal eIF4E-binding domain, bringing eIF4E near the eIF4A1 mRNA binding cavity and closing the cavity with both eIF4G1 HEAT-2 domain and eIF4E. In the cap-independent mechanism, -helix5 of eIF4G1 HEAT-2 domain instead directly interacts with the eIF4A1 N-terminal domain to close the mRNA binding cavity without eIF4E involvement, resulting in a stronger interaction between eIF4G1 and eIF4A1. Significance StatementTranslation initiation is primarily governed by eIF4F, employing a "cap-dependent" mechanism, but eIF4F dysregulation may lead to a "cap-independent" mechanism in stressed cancer cells. We found frequent amplification of translation initiation genes, and co-occurring copy number gains of EIF4G1 and EIF3E genes in human cancers. EIF4G1 amplification or duplication may be positively selected for its beneficial impact on the overexpression of cancer survival genes. The co-regulation of eIF4G1 and eIF4A1, distinctly from eIF4E, reveals eIF4F dysregulation favoring cap-independent initiation. Alphafold predicts changes in the eIF4F complex assembly to accommodate both initiation mechanisms. These findings have significant implications for evaluating cancer cell vulnerability to eIF4F inhibition and developing treatments that target cancer cells with dependency on the translation initiation mechanism.