Molecular signatures discriminating different types of rejection in human liver transplants

The role of antibody-mediated rejection (AMR) after liver transplantation (LT) remains controversial. Chronic AMR (cAMR) is often subclinical and may be missed without surveillance biopsies (svLbx). Transcriptome analyses have previously characterized molecular changes in T cell-mediated rejection (TCMR) after solid organ transplantation. We aimed to identify molecular signatures of cAMR after LT.

Indication and surveillance biopsies from two prospective institutional biorepositories were screened. We performed bulk RNA sequencing on liver biopsies (discovery cohort: n = 71; Hannover validation cohort: n = 58; Barcelona validation cohort: n = 29). Downstream analyses explored the molecular features of cAMR, clinical TCMR, and subclinical TCMR, compared to no histological rejection.

Nineteen percent of LT recipients with donor-specific antibodies had cAMR in the training cohort. Of these patients, 57% had normal/near normal liver enzymes, with cAMR detected only by svLbx. cAMR was associated with subsequent cirrhosis in 40-50% of cases and exhibited differentially expressed genes (DEGs) uniquely enriched in pathways related to fibrogenesis, complement activation, and TNFα signaling. In contrast, clinical TCMR was not associated with recurrent cirrhosis and showed DEGs enriched in antigen presentation, interferon signaling, and T cell receptor signaling. Subclinical TCMR was molecularly almost indistinguishable from no histological rejection. DEG profiles showed a high degree of concordance between the discovery and validation cohorts.

We report a distinct transcriptomic profile of cAMR after LT, characterized by inflammatory and fibrogenic pathways, consistent with findings in other solid organ transplant settings. This molecular identity is associated with a high risk of liver graft failure.

Chronic antibody-mediated rejection (AMR) is a recognized relevant cause of graft injury and unfavorable patient outcomes after kidney, heart and lung transplantation, but the role of chronic AMR after liver transplantation (LT) is controversial. Therefore, we aimed to characterize rejection phenotypes after LT on a molecular basis, as done in other solid organ transplant settings, to identify unique features of chronic AMR. Our findings identify chronic AMR as a molecularly distinct clinical phenotype of rejection after LT, often presenting with normal liver enzymes (validated in three independent cohorts) and associated with a recurrent cirrhosis rate of 40-50%. Our work supports the use of surveillance graft biopsies for the detection of a fibrosis-associated phenotype of chronic AMR. The molecular signature may be used in the future by researchers and clinicians to discriminate chronic AMR from graft injury of other causes.