Proteomic profiling of unannotated microproteins in human placenta reveals XRCC6P1 as a negative regulator of translation

Ribosome profiling and mass spectrometry have revealed thousands of previously unannotated small and alternative open reading frames (sm/alt-ORFs) that are translated into micro-/alt-proteins in mammalian cells. However, their prevalence across human tissues and biological roles remain largely unexplored. The placenta is an ideal model for identifying unannotated microproteins and alt-proteins due to its considerable protein diversity that is required to sustain fetal development during pregnancy. Here, we profiled unannotated microproteins and alt-proteins in human placenta tissues from preeclampsia patients or healthy individuals by mass spectrometry, identified 66 unannotated microproteins or alt-proteins, and validated the expression of five microproteins biochemically. We further demonstrated that one microprotein, XRCC6P1, associates with translation initiation complex eIF3, and negatively regulates translation. Thus, we revealed a hidden sm/alt-ORF-encoded proteome in the human placenta, which may advance the mechanism studies for placenta development, as well as placental disorders such as preeclampsia.