Invariant chain controls HLA-DQ folding and shapes the HLA class II proxiome

The invariant chain (Ii) trimerizes in the endoplasmic reticulum and swiftly associates with nascent alpha and beta chains of major histocompatibility complex class II (MHCII) molecules. Ii was ascribed many roles pertaining to the antigen presentation capacity of MHCII molecules. The lack of Ii in knockout mice revealed its isotype- and cell type-dependent impact over the folding and trafficking of MHCII molecules. In humans, the role of Ii was mainly assessed in transfected cells. Here, using the CRISPR-Cas9 system, we addressed the impact of inactivating the Ii genes on the expression and functions of MHCII molecules in human B cell lines. Our results revealed that the absence of Ii had very little impact, at least quantitatively, on the surface display of multiple HLA-DR and HLA-DP allotypes. However, Ii had a strong influence on the folding of the many HLA-DQ allotypes expressed in Raji and LG2 cells. Both the p33 and p35 isoforms of Ii could independently restore HLA-DQ expression at the plasma membrane. The loss of Ii did not prevent the presentation of the HA307-318 peptide from the inactivated influenza X31 virus, in line with the fact that this epitope is loaded onto recycling HLA-DR molecules. We also found that Ii reduces the expression of LFA-1, a function that is most likely related to the ability of its cytoplasmic domain to act as a transcriptional regulator. Finally, using a biotin ligation assay in vivo, we identified Ii-dependent proximity partners of the HLA-DRβ cytoplasmic tail. Altogether, these results highlighted the pleiotropic functions of Ii in humans and uncovered new actors involved in the antigen presentation function of MHCII molecules.