Alexis Varin, PhD

INTRODUCTION: Understanding the complexity of pathways involved in allograft injuries after solid organ transplantation is essential for precise definitions of rejection subtypes and improved overall outcomes. High throughput technologies and the recently available computational methods make it now possible to address such complex biological questions. Here, we performed a unique compilation of six omics datasets (170,000 variables) from a multi-center study encompassing 131 kidney transplant recipients. METHODS: Using multi-omics factor analysis (MOFA), we investigated sources of variability in patient blood, urine and their allograft at the epigenetic and transcriptomic levels. RESULTS: Integrating the different omics layers, MOFA delimited eight hidden factors in an unsupervised manner. We identified specific factors that reflect allograft rejection and their multicellular complex immune profiles, complement activation, monocyte crosstalk, or immune modifications associated with induction treatment. CONCLUSIONS: These cross-compartment large datasets translated into an understandable biological picture provide a new framework to solve complex biological questions, not unique to transplant medicine.

In solid organ transplantation, monocytes and macrophages play a cross-cutting role in the rejection process, irrespective of the transplanted tissue and the type of rejection. Here, we integrated multiple single-cell assays (>150,000 cells) with a broad spectrum of blood-derived and renal allograft-derived cells. We observed 6 myeloid cell trajectories enriched in the allograft during rejection, ranging from circulating CD14+ monocytes to differentiated macrophages in the kidney, with one trajectory culminating in a pro-inflammatory macrophage expressing CXCL9 and CXCL10. By analyzing over 850 biopsies using deconvolution, we report that they are absent in pre-transplant allografts, while these CXCL10+ macrophages are the immune cells most associated with inflammation during acute rejection. Furthermore, a survival study of over 500 biopsies indicates that they increase the risk of graft loss independently of other immune cells. CXCL10+ macrophages differentiate from recipient monocytes, and we have identified 6 major genes associated with their differentiation, including LILRB2. In vitro, mimicking allogenic activation of blood monocytes via the CD47/SIRP-a axis induced overexpression of LILRB2, suggesting that CXCL10+ macrophages are activated by this pathway. Finally, we show that macrophages overexpressing LILRB2 induce the proliferation of autologous T lymphocytes. Altogether, the present study provides further insight into the pro-inflammatory axes of recipient-derived monocytes/macrophages, and suggests LILRB2 as a therapeutic target.