MHC Class II Presentation

Gene co-expression module in CD8⁺ T cells

View this module in SCUBA

Why this annotation

This module is dominated by MHC class II genes: HLA-DPA1, HLA-DRA, HLA-DQB1, HLA-DRB1, HLA-DPB1, HLA-DQA1, HLA-DMA, HLA-DMB — all classical MHC-II alpha/beta chains or MHC-II peptide loading chaperones. CD74 (invariant chain/CLIP) is the canonical MHC-II chaperone. PSMB8 is an immunoproteasome subunit. JAKMIP1 (JAK interacting/microtubule protein) and COTL1 (actin-binding) are peripheral. Core coherence and all-core hub genes make this extremely high confidence. In CD8 T cells, MHC-II expression is unusual — it can occur in activated/exhausted CD8 T cells or may reflect minor contamination from antigen-presenting cells (dendritic cells, macrophages). However, CD8 T cells in tumor microenvironments and colon tissue can upregulate MHC-II. The uniform expression across subsets and the clean core coherence suggest this is a genuine MHC class II antigen presentation module, possibly marking a rare activated/bystander CD8 population or low-level APC contamination.

Genes

CD74, COTL1, HLA-DMA, HLA-DMB, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRA, HLA-DRB1, JAKMIP1, PSMB8

Most correlated modules

• ER-Golgi Trafficking · correlation 0.91
• IFN-gamma Stress Response · correlation 0.91
• Tumor mediated exhaustion · correlation 0.89
• TCR Proximal Signaling · correlation 0.86
• Cytotoxic Exhausted CD8 · correlation 0.82
• Stress-ISG Response · correlation 0.82
• BATF-driven Activation · correlation 0.81

Module annotations were drafted by a large language model from the module's genes, then reviewed and approved by a domain expert. See sources & licences.