Biopsy-based transcriptomics in kidney transplantation: Where do we stand in 2025?

Despite advances in the physiopathological understanding of kidney transplantation immunology, kidney transplant rejection remains the leading cause of allograft loss. The current gold standard for diagnosing rejection is histological assessment of kidney transplant biopsies. Biopsy-based transcriptomics have been the subject of numerous studies, enabling the analysis of hundreds of transcripts expressed in biopsy samples. These tools allow for the identification of new pathophysiological pathways, providing a better understanding of rejection and potentially revealing therapeutic targets. Biopsy-based transcriptomics may also improve the diagnosis of rejection, in particular antibody-mediated rejection. However, the use of these tools in routine practice is limited due to restricted availability, the challenge of interpreting data from hundreds of transcripts without clear guidelines, and their cost. In addition, due to the limited accessibility of molecular tools, their exact impact on patient management has not yet been determined. This update provides an overview of biopsy-based transcriptomics in 2025, focusing on the limitations of current diagnostic methods for rejection, the molecular biology tools available, and their use in clinical practice.