Kidney transplant (KT) short-term outcomes have steadily improved over the last several decades, however, similar progress in long-term allograft survival has not yet been reached largely due to chronic allograft injury (CAI). In our previous funding cycle, we identified a gene expression signature in deceased donor kidney biopsies at pre-KT that was predictive of graft function, measured by eGFR, at 24-months post-KT. Further, our single- cell/nucleus transcriptome profiles yielded several important findings including that KT recipients with acute kidney injury have increased fibroblasts and macrophages (both donor- and recipient-origin) with a macrophage subset characterized by fibroblast-like markers; donor-derived macrophages were present in functioning kidney grafts with interstitial fibrosis and tubular atrophy (IFTA) more than 24-mo post-KT; and paired single-cell peripheral blood mononuclear cells (PBMCs) showed immune cell type specific profiles reflecting graft injury. Thus, our results revealed the unappreciated role of donor kidney cells (immune and non-immune) on tissue repair and local immunomodulation, which plays a critical role in response to injury and determines graft function. Moreover, post-KT graft survival is determined by a complex interplay between donor and recipient factors. Thus, our findings guided the establishment of our new hypothesis that early measurable donor and donor-recipient cellular interactions and molecular profiles are strong indicators of chronic inflammatory responses and maladaptive repair circuits, shaping long-term graft outcomes. Therefore, in this funding cycle, we will elucidate the effects of donor cell type-specific drivers of injury that exacerbate the initial donor/recipient immune- and non-immune cell interactions in response to injury and determine how these events are reflected in the peripheral samples, allowing non-invasive graft monitoring by using cell type-specific markers of injury. This will be accomplished by leveraging our large unique available resource that includes donor biopsies (pre-KT) with paired longitudinal recipient biopsies and PBMCs (post-KT) along with KT recipient clinical outcomes to pursue the following specific aims: Aim 1. Assess donor and recipient cells' origin, function, and interactions that play a role in graft injury. Aim 2. Uncover cell type-specific molecular signatures from peripheral immune cells derived from KT recipients at pre-implantation and longitudinally post-KT, reflecting immune risk status and kidney graft function. Aim 3. Establish a novel statistical method for developing a composite score using high-dimensional donor/recipient molecular and clinical/demographic variables to predict graft function. This study will provide (i) cell type-specific gene signatures and regulatory regions that control the transition between healthy and diseased kidney graft states, eventually guiding efforts to reprogram cells to promote repair after injury, (ii) cell type specific gene profiles within recipient PBMCs that can longitudinally inform ongoing graft injury/repair and assist with better matching of patients and organs for improved long-term outcomes, and (iii) combined scores for pre-KT immune risk and post-KT graft function prediction using timely and cost-effective cell type-specific markers.

Despite the improved short-term outcomes in kidney transplantation (KT), comparable progress in long-term allograft survival has not been achieved with chronic allograft injury (CAI) accounting for most of the cases of graft loss. Results of our planned studies will identify early molecular pathways predating eventual graft repair or deterioration which will allow for the exploration of new therapeutic targets that have the potential to prevent irreversible kidney damage. Novel prognostic biomarkers will enable the early identification of patients at higher risk for progression to CAI, allowing for the development of new therapeutic modalities that have the potential to avoid irreversible graft injury and improve long-term outcomes.