Investigating the role of signal peptide peptidase in tumor immune evasion via Qa-1-mediated peptide presentation

Canonical leader peptides, derived from the signal sequences of classical MHC class I molecules, are presented by HLA-E in humans and Qa1 in mice. These peptides serve as ligands for the NKG2A/CD94 receptor complex on NK cells and CD8 + T cells, promoting immune homeostasis. Disruptions of this inhibitory axis-such as during viral infection-can lead to the display of novel peptides that override this inhibition and activate immune responses. However, the mechanisms controlling canonical peptide presentation remain unclear. To better understand how Qa1-restricted inhibitory peptide presentation is regulated, we targeted Signal Peptide Peptidase (SPP), an ER-resident protease that cleaves signal peptides. SPP was knocked out in two tumor models: YUMMER melanoma and KPC pancreatic adenocarcinoma. Changes in Qa1-bound peptides were evaluated using mass spectrometry, and tumor growth was assessed in vivo. Loss of SPP markedly reduced canonical peptide loading in both tumor models. SPP-deficient melanoma tumors were strongly rejected in vivo, while pancreatic tumors lacking SPP showed no such reduction, despite similar decreases in canonical inhibitory peptide levels. Interestingly, the dominant Qa1-bound peptide in both models remained the canonical peptide, indicating that alternative, SPP-independent mechanisms can liberate and generate this peptide for presentation. In the KPC model, novel peptides with potential inhibitory properties were identified. Ongoing studies aim to determine whether these peptides can sustain immune suppression in the absence of the canonical peptide. Our findings demonstrated that even in the absence of SPP, alternative mechanisms maintain inhibitory peptide presentation in tumor cells. Ongoing studies targeting other SPP family members and newly identified candidate inhibitory peptides aim to elucidate these compensatory pathways. A clearer definition of the Qa1/HLA-E inhibitory pathway will help determine whether this axis can be more effectively disrupted to improve anti-tumor immune responses.