C-type lectins are key players in immune regulation by driving distinct functions of antigen-presenting cells. The
C-type lectin CLEC16A gene is located at 16p13, a susceptibility locus for several
autoimmune diseases, including
multiple sclerosis. However, the function of this gene and its potential contribution to these diseases in humans are poorly understood. In this study, we found a strong upregulation of CLEC16A expression in the white matter of
multiple sclerosis patients (n = 14) compared to non-demented controls (n = 11), mainly in perivascular leukocyte infiltrates. Moreover, CLEC16A levels were significantly enhanced in peripheral blood mononuclear cells of
multiple sclerosis patients (n = 69) versus healthy controls (n = 46). In peripheral blood mononuclear cells, CLEC16A was most abundant in monocyte-derived dendritic cells, in which it strongly co-localized with
human leukocyte antigen class II. Treatment of these professional antigen-presenting cells with
vitamin D, a key protective environmental factor in
multiple sclerosis, downmodulated CLEC16A in parallel with
human leukocyte antigen class II. Knockdown of CLEC16A in distinct types of model and primary antigen-presenting cells resulted in severely impaired cytoplasmic distribution and formation of human leucocyte
antigen class II-positive late endosomes, as determined by immunofluorescence and electron microscopy. Mechanistically, CLEC16A participated in the molecular machinery of
human leukocyte antigen class II-positive late endosome formation and trafficking to perinuclear regions, involving the
dynein motor complex. By performing co-immunoprecipitations, we found that CLEC16A directly binds to two critical members of this complex, RILP and the HOPS complex. CLEC16A silencing in antigen-presenting cells disturbed RILP-mediated recruitment of
human leukocyte antigen class II-positive late endosomes to perinuclear regions. Together, we identify CLEC16A as a pivotal gene in
multiple sclerosis that serves as a direct regulator of the
human leukocyte antigen class II pathway in antigen-presenting cells. These findings are a first step in coupling
multiple sclerosis-associated genes to the regulation of the strongest genetic factor in
multiple sclerosis,
human leukocyte antigen class II.