Identifying mechanisms of kidney disease commonly involves comparing diseased samples with healthy reference tissues; however, the effects of variability in tissue procurement, storage, and donor characteristics remain underexplored. In this study, we systematically evaluated 3 reference tissue types — tumor nephrectomy (TN), pretransplant biopsies from living donors (LD), and percutaneous biopsies from healthy control volunteers (HC) — to determine their impact on differential gene expression across 3 diabetic kidney disease states. We observed distinct injury markers, cell state proportions, and gene signatures associated with procurement method, sex, and donor age. Adjustment for these confounding factors significantly influenced pathway analysis results. Specifically, correcting for age and sex eliminated significant enrichment of IFN-γ response when comparing the diabetes mellitus–resilient group and HC group. Processes related to biological aging were enriched in older reference tissues, potentially confounding disease-specific interpretations. Importantly, TNF signaling via NF-κB remained enriched in LD and TN samples relative to HC, even after accounting for confounders. These results underscore the critical importance of selecting appropriate control tissues and rigorously adjusting for confounding variables to reliably discern the molecular mechanisms underlying kidney diseases.

Reproducible biomarker identification and transplant rejection risk prediction remain fundamental yet unsolved challenges in transplantation medicine. Traditional approaches rely on hypothesis-driven analyses and domain expertise, limiting scalability and generalizability across diverse populations. We introduce Transplant-Agents, a data-driven multi-agent AI framework integrating large language models (LLMs) with machine learning algorithms for automated biomarker identification and rejection risk prediction. Agents interact through structured, iterative dialogue governed by predefined rules and criteria, converging on optimal biomarker sets reproducible across multiple iterations. We evaluated three multicenter clinical trial transplant datasets from ImmPort, comprising 683 patients across kidney, liver, and heart transplant cohorts. Transplant-Agents achieve AUROC scores of 0.93, 0.88, and 0.88. Feature importance analysis further confirms the stability, interpretability and potential generalizability of identified biomarkers. This work demonstrates that AI-agent frameworks can reliably reproduce established transplant biomarkers while enabling transparent, validated, and standardized risk prediction pipelines.

Understanding the unique susceptibility of the human kidney to pH dysfunction and injury in cystinosis is paramount to developing new therapies to preserve renal function. Renal proximal tubular epithelial cells (RPTECs) and fibroblasts isolated from patients with cystinosis were transcriptionally profiled. Lysosomal fractionation, immunoblotting, confocal microscopy, intracellular pH, TEM, and mitochondrial stress test were performed for validation. CRISPR, CTNS -/- RPTECs were generated. Alterations in cell stress, pH, autophagic turnover, and mitochondrial energetics highlighted key changes in the V-ATPases in patient-derived and CTNS -/- RPTECs. ATP6V0A1 was significantly downregulated in cystinosis and highly co-regulated with loss of CTNS . Correction of ATP6V0A1 rescued cell stress and mitochondrial function. Treatment of CTNS -/- RPTECs with antioxidants ATX induced ATP6V0A1 expression and improved autophagosome turnover and mitochondrial integrity. Our exploratory transcriptional and in vitro cellular and functional studies confirm that loss of Cystinosin in RPTECs, results in a reduction in ATP6V0A1 expression, with changes in intracellular pH, mitochondrial integrity, mitochondrial function, and autophagosome-lysosome clearance. The novel findings are ATP6V0A1’s role in cystinosis-associated renal pathology and among other antioxidants, ATX specifically upregulated ATP6V0A1, improved autophagosome turnover or reduced autophagy and mitochondrial integrity. This is a pilot study highlighting a novel mechanism of tubular injury in cystinosis.

IntroductionCytomegalovirus (CMV) viremia remains a major contributor to clinical complications in solid organ transplant (SOT) patients, including organ injury, morbidity and mortality. Given their critical role in antiviral defense, CD8+ T cells are essential for protective immunity against CMV.MethodsUsing single-cell RNA sequencing, we investigated the transcriptional signatures and developmental lineages of CD8+ T cells in eight immunosuppressed kidney transplant recipients (KTRs) who received organs from CMV-seropositive donors. Results were validated in a cohort of 62 KTRs using immunophenotyping.ResultsOur data revealed a significant influence of CMV serostatus on transcriptional variance of CD8+ memory T cells, associating with the first principal component from a global analysis of CD8+ T cells (p =0.0406), forming a continuum with five principal differentiation trajectories driven by CMV primary infection or reactivation. Following CMV primary infection, CD8+ T cells were hallmarked by restrained effector-memory differentiation. CD8+ T cells during CMV reactivation diverged non-linearly into senescent-like cells with signatures of arrested cell cycle, diminished translational activity and downregulated ZNF683 and longitudinally expanding effector cells with robust cytotoxic potential and upregulated ZNF683, acting as a reservoir for long-lived effector cells supporting long-term protection. Notably, CD28lo KLRG1hi IL-7R (CD127)lo HLA-DRhi CD8+ T cells present prior to the detection of viremia in CMV-seropositive patients emerged as a key feature distinguishing patients who did or did not undergo CMV reactivation after prophylaxis discontinuation (p =0.0163). Frequencies of these cells were also positively correlated with CMV-stimulated secretion of IFN-γ (p =0.0494), TNF-α (p =0.0358), MIP-1α (p =0.0262), MIP-1β (p =0.0043).DiscussionThese results provide insights into the transcriptional regulation that influences the generation of CD8+ T cell immunity to CMV and may inform strategics for monitoring host immune response to CMV to better identify and introduce therapeutic intervention to patients at risk of developing clinically significant CMV viremia.

Background. The current landscape of organ donation and transplantation (ODT) registries is not well established. This narrative review sought to identify and characterize the coverage, structure, and data capture of ODT registries globally. Methods. We conducted a literature search using Ovid Medline and web searches to identify ODT registries from 2000 to 2023. A list of ODT registries was compiled based on publications of registry design, studies, and reports. Extracted data elements included operational features of registries and the types of donor and recipient data captured. Results. We identified 129 registries encompassing patients from all continents except Antarctica. Most registries were active, received funding from government or professional societies, were national in scope, included both adult and pediatric patients, and reported patient-level data. Registries included kidney (n = 99), pancreas (n = 32), liver (n = 44), heart (n = 35), lung (n = 30), intestine (n = 15), and islet cell (n = 5) transplants. Most registries captured donor data (including living versus deceased) and recipient features (including demographics, cause of organ failure, and posttransplant outcomes) but there was underreporting of other domains (eg, donor comorbidities, deceased donor referral rates, waitlist statistics). Conclusions. This review highlights existing ODT registries globally and serves as a call for increased visibility and transparency in data management and reporting practices. We propose that standards for ODT registries, a common data model, and technical platforms for collaboration, will enable a high-functioning global ODT system responsive to the needs of transplant candidates, recipients, and donors.

Pancreas transplantation improves glycemic control and mortality in patients with diabetes but requires aggressive immunosuppression to control the alloimmune and autoimmune response. Recent developments in “omics” methods have provided gene transcript-based biomarkers for organ transplant rejection. The tissue Common Response Module (tCRM) score is developed to identify the severity of rejection in kidney, heart, liver, and lung transplants. Still, it has not yet been validated in pancreas transplants (PT). We evaluated the tCRM score’s relevance in PT and additional markers of acute cellular rejection (ACR) for PT. An analysis of 51 pancreas biopsies with ACR identified 37 genes and 56 genes significantly upregulated in the case of grade 3 and grade 2 ACR, respectively (P < .05). Significant differences were seen with higher grades of rejection among several transcripts. Of the 22 genes differentially expressed in grade 3 ACR, 18 were also differentially expressed in grade 2 ACR. The rejection signal was attributable to activated leukocytes’ infiltration. Significantly higher tCRM scores were found in grade 3 ACR (P = .007) and grade 2 ACR (P = .004), compared to normal samples. The tCRM score was able to distinguish treatment-resistant cases from those successfully treated for rejection.

Circulating factors resulting from immune dysfunction have been proposed as one of the causes for increased risk of graft loss associated with recurrence of focal segmental glomerulosclerosis (FSGS) after kidney transplant. However, the precise identity of the circulating factors and their sources remain incompletely characterized. In vivo studies in mouse models have implicated a role for immature bone marrow cells in the development of FSGS. Using single-cell RNA sequencing we have profiled >50,000 cells from bone marrow of FSGS patients with or without recurrence after kidney transplant and controls including healthy individuals and patients with end-stage renal disease due to non-FSGS causes. Bone marrow mononuclear cells from patients with recurrence of FSGS after transplant display an inflammatory phenotype with activation of cytokine and interferon signaling in neutrophils, T cells and B cells. We also observe a dramatically depleted B cell population in R-FSGS patients. Conditioned media from BMNCs of R-FSGS patients have higher levels of pro-inflammatory cytokine MIP-1α/CCL3, reduced anti-inflammatory chemokine CCL22 and cause injury in a human podocyte cell culture model. Our studies provide evidence for the role of bone marrow cells in FSGS associated inflammatory milieu and elucidate the transcriptional changes associated with the disease.### Competing Interest StatementThe authors have declared no competing interest.### Funding StatementFunding: The work presented in this manuscript was supported by funds from the NIDDK/NIH DK DK109720 to MS. AAS was supported by the Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior - Brasil (CAPES- Finance Code 001).### Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:BM aspirates from 8 FSGS patients and two control patients with end stage renal disease due to non FSGS related causes were collected with informed consent in compliance with UCSF Institutional Review Board (IRB #17-22287). BM-aspirates of age and gender matched 5 healthy donors were purchased from Lonza Inc and used as healthy control.I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.YesAll data produced in the present study are available upon reasonable request to the authors

The XVIth Banff Meeting for Allograft Pathology was held in Banff, Alberta, Canada, from September 19 to 23, 2022, as a joint meeting with the Canadian Society of Transplantation. In addition to a key focus on the impact of microvascular inflammation and biopsy-based transcript analysis on the Banff Classification, further sessions were devoted to other aspects of kidney transplant pathology, in particular T cell-mediated rejection, activity and chronicity indices, digital pathology, xenotransplantation, clinical trials, and surrogate endpoints. Although the output of these sessions has not led to any changes in the classification, the key role of Banff Working Groups in phrasing unanswered questions, and coordinating and disseminating results of investigations addressing these unanswered questions was emphasized. This paper summarizes the key Banff Meeting 2022 sessions not covered in the Banff Kidney Meeting 2022 Report paper and also provides an update on other Banff Working Group activities relevant to kidney allografts.

Introduction: The tissue Common Response Module (tCRM) score, which is based on the expression levels of 11 genes (BASP1, ISG20, PSMB9,RUNX3, TAP1, NKG7, LCK, INPP5D, CXCL9, CD6, CXCL10), was developed using genomics data from heart, liver, lung, and kidney tissue with acute cellular rejection (ACR). Using our institution’s repository of pancreas transplant specimens, we sought to validate the tCRM score in pancreas samples with ACR and to determine whether it correlates with treatment response. Methods: Fifty one formalin fixed paraffin embedded pancreas biopsy specimens: 14 normal, 14 Grade 1 (G1) ACR, 14 Grade 2 (G2) ACR, and 9 Grade 3 (G3) ACR were analysed using multiplex RNA sequencing. Differential gene expression and pathway analyses were performed using a panel of 804 unique genes, including the genes that make up the tCRM score. Whole transcriptome spatial RNA analysis is ongoing to further investigate patterns of gene expression in distinct regions and cell populations. Results: Significant differences in gene expression were seen in G2 and G3 ACR, but not G1 ACR, when compared with normal pancreas samples. Pathway analyses demonstrated that the genes enriched in G2 and G3 ACR were associated with inflammatory pathways like interferon signalling, antigen processing and presentation, and phagocytosis. A statistically significant difference was found in the tCRM scores for G2 ACR and G3 ACR, when compared to the tCRM score for normal pancreas tissue. Patients with rejection that was resistant to treatment (defined as recurrent rejection within 2 months of the initial rejection episode) had significantly higher tCRM scores (Figure 1). This difference remained significant for patients with G1 ACR, but was not significant for patients with G2 or G3 ACR (Figure 2).Conclusions: We found that the tCRM score not only correlates with commonly used histologic grading criteria, but also identifies patients with ACR who are at risk for treatment resistant rejection and thus may warrant more aggressive initial treatment with lymphodepleting agents. Further work using spatial transcriptomics, including whole transcriptome differential expression analysis and spatial deconvolution is underway to better elucidate the regions and cell populations involved in the development of acute pancreas rejection. Audrey Brown was supported by the UCSF National Institutes of Health (NIH) FAVOR T32 Training Grant, grant number 2T32AI125222-06A1.

Solid organ transplantation is a practical next treatment step to those suffering from end-organ injury and has been in practice since 1954 [1, 2]. According to 2018 SRTR (Scientific Registry of Transplant Recipients) annual report, there was a 24.6% increase in kidney transplants (tx) in the United States, due to higher availability of living and deceased donor allografts [3]. One- and 5-year graft survival rates among pediatric tx patients are 93–95% and 77–85%, respectively [4, 5]. A few known reasons for kidney damage that cause the patients to undergo kidney tx are renal dysplasia, obstructive uropathy, reflux nephropathy, focal segmental glomerulosclerosis, and lupus nephritis [5].