Integrated transcriptomic and TCR profiling reveals local immune dysregulation of T cells in Gl aGvHD

Allogeneic hematopoietic cell transplantation (allo-HCT) is an effective therapy for hematological malignancies but is limited by acute graft-versus-host disease (aGvHD), particularly in the gastrointestinal (GI) tract. Diagnosis of gastrointestinal aGvHD (GI aGvHD) still relies on histopathology, and ~30% of patients develop steroid-refractory disease with poor prognosis and unclear mechanisms [1].

Donor T cells are key mediators of GvHD, and T cell receptor (TCR) repertoire profiling can reveal immune dysregulation through analysis of clonal expansion, diversity, and specificity [2, 3]. Studies in blood have reported variable TCR diversity depending on disease context, while tissue-based analyses suggest reduced diversity with private clonal expansions not reliably detected in circulation [2].

Identification of GvHD-specific TCR clonotypes remains a major challenge, as no shared clonotypes or clear antigen specificities have been established. Emerging computational approaches may enable inference of antigen specificity but have not yet been widely applied in GvHD [4]. This is particularly relevant for steroid-refractory disease, where persistent tissue-resident clonotypes may drive pathology [5].

While TCR sequencing provides insights into clonality, transcriptomic profiling reveals T cell function and regulation. However, integrated analyses combining both approaches in GvHD are limited.

In this study, we analyzed paired gastrointestinal biopsies and peripheral blood samples collected at the diagnosis of GI aGvHD. Using an integrated workflow of flow cytometry, gene expression profiling, and TCR sequencing, we investigated T cell characteristics in both tissue and blood.