Immunogenetic Drivers in Post-Transplant Acute Myeloid Leukemia Recurrence: Genomic Dysfunction of Human Leukocyte Antigen Diversity

Structural and functional variability of human leukocyte antigen (HLA) is the foundation for competent anti-tumor and infectious adaptive immune responses. HLA genomic heterogeneity enables the presentation of a broad immune-peptidome, sustaining an efficient diversification of T cell receptor repertoires (TCR). ^1,2,3 Any perturbation impacting this diversity may be at the basis of pathological processes, hampering antigen presentation capabilities and T-cell reactivity. In allogeneic hematopoietic cell transplantation (allo-HCT) setting, the graft versus leukemia (GvL) effect should ensure disease control allowing the recognition of recipient neoantigen burden by donor T-cell effectors. However, the molecular dissection of graft versus host responses (GvH) remains elusive. Herein, by means of a broad immunogenetic study of a cohort of patients with myeloid malignancies who received a donor matched allo-HCT, we investigated how dysfunction of HLA variability could have an impact on alloreactive responses, ultimately hindering disease control. To that end, we combined NGS-based HLA genotyping and TCR-beta sequencing to molecularly characterize the HLA region in terms of locus-specific divergence and somatic mutational profile, and dissect features and clonotypic spectra of TCR repertoires.

We first hypothesized that more diverse HLA genotypes could better present leukemic neoantigen burden than less diverse complexes, enhancing the GvL effect. Hence, we performed a matched-pair analysis between allo-HCT recipients relapsing after 3mo (median 6.2 mo. [IQR=4.6-12]), N=75) compared to patients without recurrence (N=193, matched for ethnicity, age, disease, graft source and conditioning regimens) and characterized the patterns of HLA evolutionary divergence (HED), ¹ a metric recently conceived to quantitate the pair-wise distance (based on physiochemical composition) between the amino acids located within the peptide-binding groove of two homologous HLA alleles. Overall, the relapsed group was characterized by a lower global (class I/II) mean HED (p=.0029) compared to non-relapsed patients, with major differences seen for C (p=.0041), DQB1 (p=.0291), and DPB1 (p=.0396) loci. When studying the landscape of post-transplant TCR reconstitution (+3 months) in a subset of 25 patients, we observed an inverse correlation between TCR clonal expansion and global HED (AdjR ²=0.04, p=<2e-16), contributing to decrease the diversity of TCR repertoires in patients with lower HED. Although not different in number, the expansion of clonotypes with known anti-cancer specificity was higher in non-relapsing group (p=6.3e-08), possibly underlying a better tumor-surveillance. Next, we sought to investigate the patterns of somatic HLA dysfunction in relapsing patients (intended as allelic loss or mutations). Indeed, through a recently implemented HLA mutational calling algorithm, we observed somatic events encompassing both class I and II alleles in 23% (N=8/34 profiled patients). Interestingly, when analyzing patients with relapse who received a donor lymphocyte infusion-based treatment (DLI), none of the cases harboring mutational events (N=4/4) responded to this salvage strategy. It is noteworthy that in this last group, one patient relapsed with an extramedullary localization along with the acquisition of HLA mutations. HLA mutated group had a higher (although not significant) leukemia mutational burden compared to non-mutated group (mean number of leukemia-associated mutations: 3.6 vs 1.9/patient), underscoring the need for further driver mutational events compensating the possible lower immunogenic potential of HLA mutant clones. Despite a mild increase in mutational burden, driver hits (such as IDH1/2, FLT3, TP53, NPM1) were never present in patients carrying HLA aberrations, who instead harbored in a few cases mainly lesions in epigenetic regulators and chromatin modifiers (TET2, EP300, DNMT3A, EZH2).

Altogether these findings pinpoint the role of the dysfunction of the structural variability of HLA complexes within both germline (HED) and somatic (HLA loss/mutations) scenarios as mechanisms hampering a successful neoantigen presentation and TCR recovery processes, possibly conveying a higher risk of disease relapse or treatment-resistance.