Chapuis, Aude G.Lahman, Miranda Claire2023-01-212023-01-212022Lahman_washington_0250E_25001.pdfhttp://hdl.handle.net/1773/49739Thesis (Ph.D.)--University of Washington, 2022Acute myeloid leukemia (AML) is the most common acute leukemia in adults. AML often responds to initial chemotherapy, but a majority of patients will relapse with resistant disease leaving a critical need for more effective therapies. Hematopoietic stem cell transplantation can prevent relapse long term through donor T cell-mediated elimination of leukemic cells. However, this anti-leukemic effect is unpredictable, and transplant can have detrimental side effects, including graft versus host disease (GVHD). New therapies focus the anti-leukemic effect and bypass potential GVHD by using engineered T cells with a defined T cell receptor (TCRs) that recognize proteasome-generated peptide fragments from tumor-associated proteins. Such ‘TCR-T’ cells rely on the targeted peptide to be processed and then presented by the restricting human leukocyte antigen (HLA). Cells can express standard- and immuno-proteasome isoforms, which can generate ‘distinct’ (isoform-dependent) or ‘mutual’ (isoform-independent) peptides. We investigated a clinical scenario in which the targeted AML modulated proteasome composition to eliminate processing of the targeted ‘distinct’ peptide, leading to loss of recognition by the adoptively transferred TCR-T cells and AML progression. Instead, an alternative TCR recognizing a ‘mutual’ peptide could respond to the progressive AML. Our data point to a mechanism whereby AML can evade immune recognition through modulation of proteasome isoform expression. This further implies that TCR-T cell therapy could be enhanced if tailored to target ‘mutual’ peptides. To determine the relative proportions of HLA-restricted ‘distinct’ and ‘mutual’ peptides and to identify promising TCR-T cell targetable peptides less likely to evade recognition, we utilized an emerging peptide discovery platform, Artemis, that employs soluble HLAs to bypasses immunoprecipitation of endogenous HLAs. Artemis-identified peptides revealed that the proportions of ‘mutual’ and ‘distinct’ peptides were specific to each HLA allele, with HLA-A*02:01 presenting the fewest ‘mutual’ peptides and HLA-A*11:01 presenting the most. We recovered 37 peptides from three AML-associated proteins of interest, 19 (51%) were ‘mutual’ peptides and some peptides (11%) were previously identified. Our findings demonstrate that defining isoform-specific proteasomal processing is critical to optimal peptide selection for TCR-T cell therapy and Artemis is an effective platform to identify ‘mutual’ peptides.application/pdfen-USCC BYCancerHLA presentationImmunopeptidomeImmunoproteasomeImmunotherapyProteasomeCellular biologyImmunologyPathologyThesis