DO (HLA-DO, in human; murine H2-O) is a highly conserved nonclassical major histocompatibility complex class II (MHC II) accessory molecule mainly expressed in the thymic medulla and B cells. Previous reports have suggested possible links between DO and autoimmunity, Hepatitis C (HCV) infection, and cancer, but the mechanism of how DO contributes to these diseases remains unclear. Here, using a combination of various in vivo approaches, including peptide elution, mixed lymphocyte reaction, T-cell receptor (TCR) deep sequencing, tetramer-guided naïve CD4 T-cell precursor enumeration, and wholebody imaging, we report that DO affects the repertoire of presented self-peptides by B cells and thymic epithelium. DO induces differential effects on epitope presentation and thymic selection, thereby altering CD4 T-cell precursor frequencies. Our findings were validated in two autoimmune disease models by demonstrating that lack of DO increases autoreactivity and susceptibility to autoimmune disease development. Lack of the MHC Class II chaperone H-2O causes susceptibility to autoimmune diseases PLOS Biology | https://doi.org/10.1371/journal.pbio.3000590 February 18, 2020 3 / 29Fig 2. Naïve DO-KO mice have an expanded CD4 T-cell compartment as well as increased expression of Tregs. (A) Breakdown of T-cell compartment in the spleens of naïve DO-WT (white) and DO-KO (red) mice. N = 8 mice per group. Data are represented as mean ± SEM. (B). Subdivision of the CD4 T-cell compartment showed that DO-KO mice have increased percentage of CD4 + CD25 + -expressing cells. N = 8 mice per group. Data are represented as mean ± SEM. (C). Naïve expression of the Foxp3 transcription factor in naïve CD4 + T cells from DO-WT (white) and DO-KO (red) mice. N = 21 mice per group. Experimental results depicted in this figure can be found in S2 Data. Data are represented as mean ± SEM. DO, HLA-DO; Foxp3, forkhead box P3; KO, knockout; Treg, regulatory T cell; WT, wild-type. https://doi.org/10.1371/journal.pbio.3000590.g002 Lack of the MHC Class II chaperone H-2O causes susceptibility to autoimmune diseases PLOS Biology | https://doi.org/10.1371/journal.pbio.3000590 February 18, 2020 5 / 29 mice. (A) Representative curves showing the time course of disease development in DO-KO (red) and DO-WT mice (white). N = 5 mice per group, representative of >15 repeat experiments. Score system: 0 = no symptoms, 1 = limp tail, 2 = limp tail + partial hind limb paralysis, 3 = limp tail + total Lack of the MHC Class II chaperone H-2O causes susceptibility to autoimmune diseases PLOS Biology | https://doi.EAE was induced as previously described in both DO-WT and DO-KO mice. Mice were humanely killed on Day 17 of disease, brains and spinal columns were pooled, and infiltrating Lack of the MHC Class II chaperone H-2O causes susceptibility to autoimmune diseases PLOS Biology | https://doi.