Hallmarks of allogeneic hematopoietic cell transplant success: A study on immune signatures and predictive features of graft versus host disease-free remission states from the SFGM-TC registry and cryostem biobank

Abstract Allogeneic hematopoietic cell transplantation (allo-HCT) remains the cornerstone of curative therapy for patients with myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). Despite significant advances in conditioning regimens, donor selection, and supportive care, allo-HCT is still associated with substantial morbidity/mortality. These adverse outcomes are primarily driven by disease relapse and graft-versus-host disease (GvHD), which continue to limit the full therapeutic potential of transplantation. Achieving a state of durable remission dominated by the beneficial graft-versus-leukemia (GvL) effect without immunologic toxicity remains a critical and yet elusive goal in transplant immunology. Here, by focusing on patients who achieved long-term survival without relapse or GvHD, we aimed to characterize the features associated with an optimal GvL effect, uncoupled from alloimmune toxicity. Leveraging a multicenter cohort of AML/MDS patients with comprehensive clinical data, immunogenetic and immune repertoire profiling, we undertook a multiscale analysis to decode the hallmarks of transplant success. We first analyzed national registry data to assess the frequency of truly event-free outcomes following allo-HCT for myeloid malignancies. Among 4,045 patients transplanted in France between 2010 and 2022, including 3,142 AML (77%) and 903 with MDS (23%), the 3-year (all grade) GvHD-free, relapse-free survival (GRFS) probability was only 14.2% (95% CI, 13.0–15.3), at a median follow-up of 32 months (IQR 14.2–59.7). On this cohort, multivariable Cox analysis confirmed the expected association between GRFS and several clinical variables, including disease status, GvHD prophylaxis, donor type, and T-cell depletion. Notably, when applying random survival forest models to account for complex, non-linear interactions integrating human leucocyte antigen (HLA) information, derived immunogenetic features outperformed standard clinical variables in predicting GRFS. Building on these findings, we next sought to explore the molecular correlates of successful transplantation by focusing on a well-characterized subset of patients with available biological specimens. To this end, we selected 55 recipients from the French national Cryostem cohort who had received peripheral blood stem cell transplants from HLA-matched donors following a reduced-intensity conditioning regimen. We performed T cell receptor (TCR) repertoire profiling on CD3⁺-enriched cell fractions to dissect the immunogenetic underpinnings of alloreactivity. Longitudinal sampling was conducted at approximately day 90 and 1 year post-transplant and patients were stratified into four groups based on their alloreactive outcomes over a 2-year follow-up period: Group I: no GvHD and no relapse; Group II : acute GvHD only; Group III : chronic GvHD only; and Group IV : relapse (either early, by day 90, or late, by 1 year). Quantitative analysis of TCR clonal expansion at day 90 revealed pronounced skewing in patients who developed acute GvHD, whereas those who relapsed early showed markedly reduced expansion. Patients free from both complications displayed intermediate expansion levels (p < 2 × 10⁻¹⁶). Diversity metrics also differed significantly between the acute GvHD and relapse groups, underscoring distinct immune dynamics. When focusing specifically on expanded clonotypes (defined as those exceeding the 95th percentile of expansion in a healthy control population) relapse samples exhibited a reduced number of distinct specificities compared to both acute GvHD and no-event groups. Qualitative physicochemical analyses further revealed that patients in sustained remission without acute GvHD had shorter CDR3 sequences (p= 0.007) enriched in aromatic residues (p=0.006). Consistent with early post-transplant findings, clonal expansion at 1 year post-transplant followed a similar pattern: it was highest in patients with chronic GvHD, lowest in those who relapsed, and intermediate in patients who remained event-free (p < 2 × 10⁻¹⁶), with the latter group exhibiting the highest TCR diversity scores. Taken together, these findings provide novel insights into the multimodal determinants of successful allogeneic transplantation, underscoring the potential utility of immunogenetic markers in further increasing the predictive value of traditional clinical variables and revealing distinct TCR repertoire architectures that may delineate patterns of alloreactivity.