In kidney transplantation, ongoing alloimmune processes-commonly triggered by HLA incompatibilities-can trigger chronic transplant rejection, affecting the microcirculation and the tubulointerstitium. Continuous inflammation may lead to progressive, irreversible graft injury, culminating in graft dysfunction and accelerated transplant failure. Numerous experimental and translational studies have delineated a complex interplay of different immune mechanisms driving rejection, with antibody-mediated rejection (AMR) being an extensively studied rejection variant. In microvascular inflammation, a hallmark lesion of AMR, natural killer (NK) cells have emerged as pivotal effector cells. Their essential role is supported by immunohistologic evidence, bulk and spatial transcriptomics, and functional genetics. Despite significant research efforts, a substantial unmet need for approved rejection therapies persists, with many trials yielding negative outcomes. However, several promising therapies are currently under investigation, including felzartamab, a monoclonal antibody targeting the surface molecule CD38, which is highly expressed in NK cells and antibody-producing plasma cells. In an exploratory phase 2 trial in late AMR, this compound has demonstrated potential in resolving molecular and morphologic rejection activity and injury, predominantly by targeting NK cell effector function. These findings inspire hope for effective treatments and emphasize the necessity of further pivotal trials focusing on chronic transplant rejection.

Antibody-mediated rejection (ABMR) is a major cause of graft loss in kidney transplantation, often associated with de novo donor-specific antibodies (dnDSA). The detection of clinically relevant dnDSA relies on evaluating reactivity in single antigen bead (SAB) assays. Immunogenetic mismatches between donor and recipient, particularly involving human leukocyte antigens (HLA), underpin dnDSA development. Understanding this relationship could improve pre-transplant risk assessment and organ allocation.

We analyzed 1296 kidney transplant patients to study dnDSA development, its relation to age, gender, and the role of HLA-derived peptide mismatches using the Predicted Indirectly Recognizable HLA Epitopes II (PIRCHE II) score. We categorized dnDSA based on bead reactivity patterns and HLA typing into true, possible, and false dnDSA.

During follow-up, 25% of recipients developed dnDSA, 9.3% true, 7.7% possible, and 7.9% false. True dnDSA primarily targeted HLA-DQ (38%), while HLA-C and HLA-DP were uncommon (5% and 3%). Higher PIRCHE II scores were significantly associated with true and possible dnDSA against HLA Class II compared to false dnDSA, supporting our dnDSA classification. For true and possible dnDSA, the single locus PIRCHE II score strongly correlated with locus-specific dnDSA, while the total PIRCHE II score did not appear to influence locus-specific dnDSA development. Younger recipients exhibited a higher risk of dnDSA development, while gender had no impact.

Locus-specific PIRCHE II scores are useful in predicting dnDSA risk post-transplantation, particularly in younger recipients. Promoting transplants with low PIRCHE II scores against key HLA loci like HLA-DQ in younger recipients could improve outcomes.

The role of antibodies in kidney transplant (KT) has evolved significantly over the past few decades. This role of antibodies in KT is multifaceted, encompassing both the challenges they pose in terms of antibody-mediated rejection (AMR) and the opportunities for improving transplant outcomes through better detection, prevention, and treatment strategies. As our understanding of the immunological mechanisms continues to evolve, so too will the approaches to managing and harnessing the power of antibodies in KT, ultimately leading to improved patient and graft survival. This narrative review explores the multifaceted roles of antibodies in KT, including their involvement in rejection mechanisms, advancements in desensitization protocols, AMR treatments, and their potential role in monitoring and improving graft survival.

HLA matching is critical for successful kidney transplantation. This study aimed to investigate the impact of eplet mismatches and Predicted Indirectly Recognizable HLA Epitopes (PIRCHE-II) scores on the development of de novo donor-specific antibodies (dnDSA) and graft survival in a Tunisian cohort, characterized by a high prevalence of living donors and significant genetic diversity in HLA profiles.

This retrospective study included 112 adult kidney transplant recipients who underwent transplantation between 2012 and 2018. Donor and recipient HLA typing was performed using One Lambda Labtype PCR-SSO and PCR-SSP kits, with high-resolution typing inferred using validated tools and reference datasets. Luminex DSA screening (One Lambda) was conducted at transplantation, during follow-up for graft dysfunction or proteinuria, and at the study's conclusion. Eplet mismatches and PIRCHE-II scores were calculated using EpVix and PIRCHE-II software.

Nineteen patients (17 %) developed dnDSA, predominantly targeting HLA-DQ, with a median detection timeframe of 50 months (range: 11-106 months) post-transplantation. Male donor sex was negatively associated with dnDSA development, while prolonged cold ischemia time was a significant risk factor. Molecular HLA-DQ mismatches and high PIRCHE-II scores were significantly associated with dnDSA. Factors independently associated with reduced death-censored graft survival included history of transfusion after transplantation, allelic DRB1 mismatch, dnDSA development, and elevated PIRCHE-II score.

Our findings highlight the critical role of HLA-DQ compatibility in kidney transplantation and suggest that molecular HLA-DQ matching should be considered in kidney allocation strategies to minimise alloimmune responses and improve long-term graft outcomes.

Given the lack of specificity of current blood and urine testing and the resistance/inability to perform pancreas allograft biopsies, additional noninvasive investigational tools to assess the risk for rejection are needed. This study examines the clinical impact of molecular HLA matching in a large single-center simultaneous pancreas-kidney (SPK) transplant program.

The study cohort comprised 238 SPK recipients between 2012 and 2021. The number of HLA mismatches, eplet, Snow (that counts the number of protein-specific surface-accessible donor HLA amino acid mismatches), and predicted indirectly recognizable T-cell epitope (PIRCHE, version 4.2; 100%) loads were calculated on the basis of 2-field HLA-A, -B, -C, -DRB1, and -DQB1 typing of recipients and donors. Univariable and multivariable Cox proportional hazard, as well as Kaplan-Meier analyses, were performed considering either first rejection events of a graft or a composite endpoint of de novo donor-specific antibodies, first rejection, and uncensored graft failure of either organ.

Kaplan-Meier analyses considered class II PIRCHE groups separated by a threshold of 7. From the considered histocompatibility metrics, multivariable regression analysis revealed only PIRCHE-II derived from donor HLA class II as statistically significantly correlated with clinical events and rejection after SPK, mostly driven by pancreas rejections. Furthermore, longer dialysis time and the induction agent had significant negative impacts on the defined composite endpoint.

Our data support the clinical benefit of incorporating PIRCHE scores for the interpretation of class II HLA mismatches among patients undergoing SPK transplantation.

The development of de novo donor-specific antibodies (dnDSA) and antibody-mediated rejection (AMR) remains a barrier to long-term graft and patient survival. Most dnDSA are directed against mismatched donor HLA-DQ antigens. Here, we describe a novel algorithm, which we have termed categorical amino acid mismatched epitope, to evaluate HLA-DQ mismatches.

In this algorithm, amino acid residues of HLA-DQ protein were categorized into 4 groups based on their chemical characteristics. The likelihood of categorically mismatched peptides presented by the recipient's HLA-DRB1 was expressed as a normalized value, %Rank score. Categorical HLA-DQ mismatches were analyzed in 386 heart transplant recipients who were mismatched with their donors at the HLA-DQB1 locus.

We found that the presence of DQB1 mismatches with %Rank score ≤1 was associated with the development of dnDSA ( P  = 0.002). Furthermore, dnDSA increased the risk of AMR only in recipients who had DQ mismatches with %Rank score ≤1 (hazard ratio = 5.8), but the freedom from AMR was comparable between recipients with dnDSA and those without dnDSA if %Rank scores of DQ mismatching were >1.

These results suggest that HLA-DQ mismatches evaluated by the categorical amino acid mismatched epitope algorithm can stratify the risk of development of dnDSA and AMR in heart transplant recipients.

Renal transplant recipients with donor-specific anti-HLA antibodies are at an increased risk of antibody-mediated rejection (ABMR). Early protocolized renal biopsies may serve as a strategy to improve diagnosis in this patient population.

We evaluated 155 highly sensitized renal transplant recipients with cPRA class I + II >90% pre-transplant from 2015 to 2022. Patients with protocol biopsies within the first 2 weeks post-transplant were included.

A total of 122 patients were included in the study. Of these, 13 (10.6%) were diagnosed with very early antibody-mediated rejection (veABMR) within the first 2 weeks post-transplant. This corresponds to 52% (13/25 patients) of all ABMR cases reported during the follow-up of this population. The graft survival rates at 1 and 3 years were significantly lower in patients with veABMR (P < .001) compared with patients without rejection in the early protocol biopsy. In terms of severity, the veABMR cohort exhibited a hazard ratio (HR) of 10.33 (95% confidence interval 3.23-33.06, P < .001) for graft failure. The presence of donor-specific antibodies class II on the day of transplantation and a higher percentage of eplet mismatch (EpMM), particularly EpMM DQA1, correlated with the development of veABMR.

Early protocol biopsies play a pivotal role in the early detection of veABMR in high-risk immunological patients. Patients with veABMR face significant risks of graft loss, despite early treatment of rejection.

The presence of de novo donor-specific antibody (dnDSA) has detrimental effect on allograft outcomes in kidney transplantation. As humoral responses in transplantation are elicited targeting non-self-epitopes on donor HLA proteins, assessing HLA mismatches at the molecular level provides a refined means for immunological risk stratification.

In the present study, we utilized three HLA molecular mismatch assessment algorithms, Snow, HLAMatchmaker, and PIRCHE-II, to evaluate the independent and synergistic association of B cell and T cell epitope mismatches with dnDSA development in a cohort of 843 kidney transplant recipients.

Our results demonstrated that B cell and T cell epitope mismatches at HLA Class I and DRB1/DQB1 loci are remarkably increased in dnDSA-positive recipients, even after normalization by allele mismatch numbers in individual study subjects. Furthermore, elevated Snow, verified eplet mismatches, and PIRCHE-II scores are significantly associated with dnDSA occurrence individually and in combination.

Our findings highlight the value of utilizing B cell and T cell epitope mismatch evaluation in living donor selection and immunological risk stratification to improve transplant outcomes.

In the last two decades, many studies based on omics technologies have contributed to defining the clinical, immunological, and histological fingerprints of chronic antibody-mediated rejection (CAMR), the leading cause of long-term kidney allograft failure. However, the full biological machinery underlying CAMR has only been partially defined, likely due to the fact thatsingle-omics technologies capture only specific aspects of the biological system and fail to provide a comprehensive understanding of this clinical complication.

This study integrated mass spectrometry-based proteomic profiling of serum samples from 19 patients with clinical and histological evidence of CAMR and 26 kidney transplant recipients with normal graft function and histology (CTR) with transcriptomic analysis of peripheral blood mononuclear cells (PBMCs) from an independent cohort of 10 CAMR and 8 CTR patients. Data analysis was conducted using unsupervised hierarchical clustering (multidimensional scaling with k-means) and Spearman's correlation test. Partial least squares discriminant analysis (PLS-DA) with the importance in projection (VIP) score identified key proteins differentiating CAMR from CTR. ELISA was used to validate the omics results.

Proteomic analysis identified 18 proteins that significantly differentiated CAMR from CTR (p < 0.01): five were more abundant (CHI3L1, LYZ, PRSS2, CPQ, IGLV3-32), while 13 were less abundant (SERPINA5, SERPING1, KNG1, CAMP, VNN1, BTD, WDR1, PON3, AHNAK2, MELTF, CA1, CD44, CUL1). Transcriptomic profiling revealed 6 downregulated and 33 upregulated genes in CAMR versus CTR (p < 0.01). Notably, only 2 biological elements were significantly deregulated in both omics analyses: chitinase-3-like protein 1 (CHI3L1) and plasma protease inhibitor C1 (SERPING1). CHI3L1, previously associated with the severity of tissue damage in kidney diseases, was up-regulated in CAMR in both transcriptomics and proteomics, while SERPING1, a serine esterase inhibitor that blocks the classical and lectin pathway of complement, was up-regulated in CAMR in transcriptomics but down-regulated in proteomics. ELISA validated the omics results, and the ROC curve showed that CHI3L1 has good discrimination power between CAMR and CTR (AUC of ROC curve of 0.81).

Our multi-omics data, although performed in a relatively small cohort of patients, revealed new systemic biological elements involved in the pathogenesis of CAMR and identified CHI3L1 as a new potential biomarker and/or therapeutic target for this important clinical complication. Future validation of these findings in larger patient cohorts should be conducted to better evaluate their clinical utility.

De novo donor-specific antibody (dnDSA) generation is the most important marker of antibody-mediated rejection (AMR). However, not all dnDSAs induce AMR. The effects of mismatched eplets on dnDSA production and the occurrence AMR remain controversial. We analyzed 64 cases of dnDSA positive kidney transplantation that occurred between 2017 and 2021 at our center to reveal the relationships between mismatched eplet and dnDSA generation and the characteristics of antibody-specific and AMR associated mismatched eplets. Among the 64 dnDSA positive cases, 114 dnDSA were produced. Both the average production time and medium fluorescence index (MFI) value of human leukocyte antigen (HLA) II dnDSA were higher than those of HLA I (time, p = 0.024; MFI, p = 0.032). More HLA II dnDSAs were generated in the AMR group (p < 0.001). The frequency of HLA II dnDSAs was higher in cases of longer antibody generation time, higher MFI, and AMR( p < 0.05). The differences in the numbers of mismatched HLA I and II eplets were statistically significant between the rejection and no rejection groups (p = 0.030). dnDSA-specific and AMR associated mismatched eplets were strongly correlated (p < 0.0001). The dominant mismatched eplets included 41 T, 163R, 25Q, 78 V, 47QL and 55PP. dnDSA-specific eplets accounted for majority of the total mismatched eplets of donors and recipients. The amino acids with increased proportions of dnDSA-specific eplets were mainly non-polarity amino acids (p < 0.0001). AMR-associated mismatched eplets accounted for majority of the dnDSA-specific mismatched eplets. Arginine, histidine, glutamine, glutamate, lysine and asparagine levels increased significantly in the rejection group compared with the no rejection group (p < 0.001). The amino acids with increased proportions of AMR-associated mismatched eplets were all polar (p < 0.0001) and mainly positively charged (p < 0.0001). The polarity and charge of amino acids in mismatched eplets may be the key factors affecting the occurrence of AMR after kidney transplantation.

The immune-mediated rejection of transplanted organs is a complex interplay between T cells and B cells, where the recognition of HLA-derived epitopes plays a crucial role. Several algorithms of molecular compatibility have been suggested, each focusing on a specific aspect of epitope immunogenicity.

Considering reported death-censored graft survival in the SRTR dataset, we evaluated four models of molecular compatibility: antibody-verified Eplets, Snow, PIRCHE-II and amino acid matching. We have statistically evaluated their co-dependency and synergistic effects between models systematically on 400,935 kidney transplantations using Cox proportional hazards and XGBoost models.

Multivariable models of histocompatibility generally outperformed univariable predictors, with a combined model of HLA-A, -B, -DR matching, Snow and PIRCHE-II yielding highest AUC in XGBoost and lowest BIC in Cox models. Augmentation of a clinical prediction model of pre-transplant parameters by molecular compatibility metrics improved model performance particularly considering long-term outcomes.

Our study demonstrates that the use of multiple specialized molecular HLA matching predictors improves prediction performance, thereby improving risk classification and supporting informed decision-making in kidney transplantation.

Lung transplantation is a life-saving therapeutic option for many chronic end-stage pulmonary diseases, but long-term survival may be limited by rejection of the transplanted organ. Since HLA disparity between donor and recipient plays a major role in rejection, we performed a single center, retrospective observational cohort analysis in our lung transplant cohort (n = 128) in which we calculated HLA compatibility scores for B-cell epitopes (HLAMatchmaker, HLA-EMMA), T-cell epitopes (PIRCHE-II) and missing self-induced NK cell activation (KIR Ligand Calculator). Adjusted Cox proportional hazards model was used to investigate the association between mismatched scores and time to development of donor-specific antibodies (DSA) post-transplant, time to first biopsy-proven acute rejection episode, freedom from CLAD, graft survival and overall survival. For time to first DSA, HLA-EMMA DQB1 scores and PIRCHE-II DQB1 scores were significantly associated with more rapidly developing anti-HLA-DQ antibodies. HLA-EMMA DQB1 score was significantly associated with worse survival. KIR ligand Host-versus-Graft (HvG) mismatches was significantly associated with worse graft survival (CLAD or death) and shorter time to first biopsy-proven rejection when 2 mismatches were present. We demonstrated that HLA-DQB1 compatibility scores and KIR ligand HvG 2 mismatches may allow for identification of recipients at risk of poor long-term outcomes after lung transplantation.

Most kidney transplant patients who undergo biopsies are classified as having no rejection based on consensus thresholds. However, we hypothesized that because these patients have normal adaptive immune systems, T cell-mediated rejection (TCMR) and antibody-mediated rejection (ABMR) may exist as subthreshold activity in some transplants currently classified as no rejection. To examine this question, we studied genome-wide microarray results from 5086 kidney transplant biopsies (from 4170 patients). An updated molecular archetypal analysis designated 56% of biopsies as no rejection. Subthreshold molecular TCMR and/or ABMR activity molecular activity was detectable as elevated classifier scores in many biopsies classified as no rejection, with ABMR activity in many TCMR biopsies and TCMR activity in many ABMR biopsies. In biopsies classified as no rejection histologically and molecularly, molecular TCMR classifier scores correlated with increases in histologic TCMR features and molecular injury, lower estimated glomerular filtration rate, and higher risk of graft loss, and molecular ABMR activity correlated with increased glomerulitis and donor-specific antibody. No rejection biopsies with high subthreshold TCMR or ABMR activity had a higher probability of having TCMR or ABMR, respectively, diagnosed in a future biopsy. We conclude that many kidney transplant recipients have unrecognized subthreshold TCMR or ABMR activity, with significant implications for future problems.

Human leukocyte antigen (HLA) is a group of glycoproteins encoded by the major histocompatibility complex (MHC) that plays a pivotal role in the host's immune defense. Given that the MHC represents the most polymorphic region in the human genome, HLA typing is crucial in organ transplantation. It significantly influences graft rejection, graft-versus-host disease, and the overall patient outcome by mediating the discrimination between self and nonself. HLA typing technology began with serological methods and has evolved rapidly alongside advances in molecular technologies, progressing from DNA-based typing to next- or third-generation sequencing. These advancements have increased the accuracy of HLA typing and reduced ambiguities, leading to marked improvements in transplantation outcomes. Additionally, numerous novel HLA alleles have been identified. In this review, we explore the developmental history and future prospects of HLA typing technology, which promises to further benefit the field of transplantation.

The human leukocyte antigen (HLA) system is the main cause of organ transplant loss through the recognition of HLAs present on the graft by donor-specific antibodies raised by the recipient. It is therefore of key importance to identify all potentially immunogenic B-cell epitopes on HLAs in order to refine organ allocation. Such HLAs epitopes are currently characterized by the presence of polymorphic residues called "eplets". However, many polymorphic positions in HLAs sequences are not yet experimentally confirmed as eplets associated with a HLA epitope. Moreover, structural studies of these epitopes only consider 3D static structures.

We present here a machine-learning approach for predicting HLA epitopes, based on 3D-surface patches and molecular dynamics simulations. A collection of 3D-surface patches labeled as Epitope (2117) or Nonepitope (4769) according to Human Leukocyte Antigen Eplet Registry information was derived from 207 HLAs (61 solved and 146 predicted structures). Descriptors derived from static and dynamic patch properties were computed and three tree-based models were trained on a reduced non-redundant dataset. HLA-Epicheck is the prediction system formed by the three models. It leverages dynamic descriptors of 3D-surface patches for more than half of its prediction performance. Epitope predictions on unconfirmed eplets (absent from the initial dataset) are compared with experimental results and notable consistency is found.

Structural data and MD trajectories are deposited as open data under doi: 10.57745/GXZHH8. In-house scripts and machine-learning models for HLA-EpiCheck are available from https://gitlab.inria.fr/capsid.public_codes/hla-epicheck.

De novo donor-specific antibodies (dnDSAs) affect long-term outcomes of kidney transplantation (KT). A higher Predicted Indirectly ReCognizable Human Leukocyte Antigen (HLA) Epitopes (PIRCHE-II) score correlates with various clinical outcomes, including dnDSA formation. However, a detailed analysis of the relationship between the PIRCHE-II score and anti-donor T-cell response is lacking. Therefore, this study investigated the relationship between PIRCHE-II scores associated with dnDSA formation and mixed lymphocyte reaction results of anti-donor T-cell response.

Data of 105 adult living-donor KT recipients were retrospectively assessed.

Of the 105 patients, 13.3 % developed dnDSAs during the observation period. The PIRCHE-II score at the HLA-DQ locus (PIRCHE-DQ) was significantly higher in patients with dnDSA formation than in those without. The incidence of dnDSA formation was significantly higher in the PIRCHE-DQ ≥ 77 group than in the PIRCHE-DQ < 77 group. The proportion of patients with increased anti-donor T-cell response was significantly higher in the PIRCHE-DQ ≥ 77 group than in the PIRCHE-DQ < 77 group before KT and at 4 and 5 years after KT.

PIRCHE-DQ may predict dnDSA formation and anti-donor T-cell response. Reducing the immunosuppressive drug dose in cases of high PIRCHE-DQ might not be prudent.

Rejection remains a major obstacle to successful kidney transplantation. The complex pathophysiology of rejection depends on a fine-tuned interplay between the innate and adaptive immune systems.

This review provides a comprehensive analysis of the pathophysiology of rejection of kidney grafts, performed through careful selection of most relevant papers available on the topic in the PubMed database. The two types of rejection usually observed at the kidney biopsy, i.e. cellular and humoral rejection, are described with an accurate outline of the biological processes that lead to their development.

The incidence of T-cell-mediated rejection is decreasing, and most cases promptly respond to appropriate immunosuppression. However, late diagnosis or incomplete response to treatment may have deleterious consequences in the long term. The main issue is represented by antibody-mediated rejection, which unsatisfactorily responds to aggressive immunosuppression, especially when diagnosed late. Prevention of acute ABMR rests on HLA-specific antibody detection prior to transplantation, adequate immunosuppression, and optimal patients' compliance. Late diagnosis and poor response to treatment inevitably lead to chronic ABMR, for which no therapies are currently available.

Kidney retransplantations are associated with an increased risk of rejection and reduced graft survival compared to first transplantations, notably due to HLA sensitization. The impact of repeated eplet mismatches on retransplantation outcome has not been investigated. We retrospectively assessed the risk of antibody-mediated rejection (ABMR) and graft loss associated with preformed DSA targeting Repeated Eplet MisMatches (DREMM) in sensitized patients undergoing kidney retransplantation. We included 45 retransplanted patients with preformed DSA against the second donor. We determined HLA incompatibilities at the eplet levels, and the eplet target of the DSA using HLAMatchmaker®. Repeated mismatches were more frequent at the eplet (87%) than at the antigenic level (22%), but were not associated with the risk of ABMR. The eplet specificity of the DSA revealed that 60% of patients (n = 27) had DREMM. The presence of DREMM was associated with a higher frequency of ABMR (70% versus 28%, P = 0.005) and with a lower death-censored graft survival (log-rank test, P = 0.01). However, in multivariate Cox model, we could not show that DREMM were associated with the risk of ABMR. In conclusion, this study suggests that identifying DREMM may be an interesting clinical tool, however further larger studies are necessary to precise their exact predictive value.

Alloimmunization remains a major obstacle to successful kidney transplantation, mainly due to the formation of anti-HLA antibodies. In recent years, non-HLA antibodies have emerged as additional immunologic factors that can potentially contribute to graft rejection. The aim of this study was to investigate the prevalence and specificity of both anti-HLA and non-HLA antibodies in patients with end-stage renal disease on a waiting list for kidney transplantation. Serum samples from 74 patients were analyzed using complement-dependent cytotoxicity and solid-phase assays. IgG anti-HLA antibodies were identified in 43.2% of participants, while IgG non-HLA antibodies were detected in 91.9%. The most frequent non-HLA antibodies included anti-ENO1 (28.4%), anti-FIBR1 (23.0%) and anti-PRKCZ (23.0%). A significant difference was found between the number of distinct IgG anti-HLA and IgG non-HLA antibody specificities. However, no significant correlation was found between the number of IgG non-HLA antibody specificities and previous alloimmunization events or dialysis treatments. These results suggest that non-HLA antibodies, although often overlooked, can sometimes play a critical role in transplant outcomes. Routine testing for non-HLA antibodies, in addition to mandatory anti-HLA antibody screening and identification, could improve immunologic risk assessment in transplant patients and post-transplant care.

Several molecular mismatch assessment approaches exist, but data on their combined use are limited. In this study, we aimed to define distinct risk groups for rejection based on the combination of three molecular mismatch assessment approaches (i.e., eplet mismatch count, the number of highly immunogenic eplets and PIRCHE-II score) in 439 consecutive immunological standard risk transplantations. For each molecular mismatch assessment approach, ROC analyses were used to define cut-offs for prediction of (sub) clinical rejection according to Banff 2019 classification within the first year post-transplant as a reference. If all three scores were below the cut-off, the patient was assigned to the low-risk group (19% of patients); if all three scores were above the cut-off, the patient was assigned to the high-risk group (21% of patients). The one-year incidence of (sub) clinical rejection was 12% in the low-risk group and 33% in the high-risk group (p = 0.003). Internal validation of the assigned risk groups for prediction of other outcomes revealed a high consistency: clinical rejection (6% vs. 24%; p = 0.004), ATG-treated rejection (1% vs. 16%; p < 0.001) and development of de novo HLA-DSA at 5 years post-transplant (6% vs. 25%; p = 0.003). The molecular mismatch risk group was an independent predictor for (sub) clinical rejection (high-risk vs. low-risk: hazard ratio 3.11 [95%-CI 1.50-6.45]; p = 0.002). We conclude that combining molecular mismatch approaches allows us to distinguish low- and high-risk groups among standard renal allograft recipients. Independent validation in other patient populations and different ethnicities is required.

Optimizing immunologic compatibility in organ transplantation extends beyond the conventional approach of Human Leukocyte Antigen (HLA) antigen matching, which exhibits significant limitations. A broader comprehension of the roles of classical and non-classical HLA genes in transplantation is imperative for enhancing long-term graft survival. High-resolution molecular HLA genotyping, despite its inherent challenges, has emerged as the cornerstone for precise patient-donor compatibility assessment. Leveraging understanding of eplet biology and indirect immune activation, eplet mismatch calculators and the PIRCHE-II algorithm surpass traditional methods in predicting allograft rejection. Understanding minor histocompatibility antigens may also present an opportunity to personalize the compatibility process. While the application of molecular matching in deceased donor organ allocation presents multiple technical, logistical, and conceptual barriers, rendering it premature for mainstream use, several other areas of donor-recipient matching and post-transplant management are ready to incorporate molecular matching. Provision of molecular mismatch scores to physicians during potential organ offer evaluations could potentially amplify long-term outcomes. The implementation of molecular matching in living organ donation and kidney paired exchange programs is similarly viable. This article will explore the current understanding of immunologic matching in transplantation and the potential applications of epitope and non-epitope molecular biology and genetics in clinical transplantation.

Cytomegalovirus (CMV) infection is related to acute rejection and graft loss after kidney transplantation, though the underlying mechanism remains largely unknown. Some CMV strains produce a peptide that is identical to a peptide sequence found in the leader peptide of specific HLA-A and -C alleles. In this retrospective study of 351 kidney transplantations, we explored whether CMV-seropositive recipients without the VMAPRTLIL, VMAPRTLLL or VMAPRTLVL HLA class I leader peptide receiving a transplant from a donor with this peptide, faced an increased risk of T-cell-mediated rejection (TCMR) in the first 90 days after transplantation. An independent case-control cohort was used for validation (n = 122). The combination of recipient CMV seropositivity with the VMAPRTLIL peptide mismatch was associated with TCMR with a hazard ratio (HR) of 3.06 (p = 0.001) in a multivariable analysis. Similarly, the VMAPRTLLL peptide mismatch was associated with TCMR revealing a HR of 2.61 (p = 0.008). Transplantations featuring either a VMAPRTLIL or a VMAPRTLLL peptide mismatch had a significantly higher cumulative TCMR incidence (p < 0.0001), with the primary impact observed in the first 2 weeks post-transplantation. The findings could be validated in an independent cohort. Together, our data strongly suggest that CMV-positive recipients without an HLA peptide identical to a CMV peptide yet transplanted with a donor who does possess this peptide, have a significantly increased risk of early TCMR. Considering the prevention of such an leader peptide mismatch in these patients or adjusting immunosuppression protocols accordingly may hold promise in reducing the incidence of early TCMR.

Following transplantation, human CD4+T cells can respond to alloantigen using three distinct pathways. Direct and semi-direct responses are considered potent, but brief, so contribute mostly to acute rejection. Indirect responses are persistent and prolonged, involve B cells as critical antigen presenting cells, and are an absolute requirement for development of donor specific antibody, so more often mediate chronic rejection. Novel in vitro techniques have furthered our understanding by mimicking in vivo germinal centre processes, including B cell antigen presentation to CD4+ T cells and effector cytokine responses following challenge with donor specific peptides. In this review we outline recent data detailing the contribution of CD4+ T follicular helper cells and antigen presenting B cells to donor specific antibody formation and antibody mediated rejection. Furthermore, multi-parametric flow cytometry analyses have revealed specific endogenous regulatory T and B subsets each capable of suppressing distinct aspects of the indirect response, including CD4+ T cell cytokine production, B cell maturation into plasmablasts and antibody production, and germinal centre maturation. These data underpin novel opportunities to control these aberrant processes either by targeting molecules critical to indirect alloresponses or potentiating suppression via exogenous regulatory cell therapy.

Optimizing graft survival and diminishing human leukocyte antigen (HLA) sensitization are essential for pediatric kidney transplant recipients. More precise HLA matching predicting epitope mismatches could reduce alloreactivity. We investigated the association of predicted HLA B- and T-cell molecular mismatches with the formation of de novo donor-specific antibodies, HLA antibodies, rejection, and graft survival.

Forty-nine pediatric kidney transplant recipients transplanted from 2009 to 2020 were retrospectively studied. Donors and recipients were high-resolution HLA typed, and recipients were screened for HLA antibodies posttransplant. HLA-EMMA (HLA Epitope MisMatch Algorithm) and PIRCHE-II (Predicted Indirectly ReCognizable HLA Epitopes) predicted the molecular mismatches. The association of molecular mismatches and the end-points was explored with logistic regression.

Five recipients (11%) developed de novo donor-specific antibodies. All five had de novo donor-specific antibodies against HLA class II, with four having HLA-DQ antibodies. We found no associations between PIRCHE-II or HLA-EMMA with de novo donor-specific antibodies, HLA sensitization, graft loss, or rejection. However, we did see a tendency towards an increased odds ratio in PIRCHE-II predicting de novo donor-specific antibodies formation, with an odds ratio of 1.12 (95% CI: 0.99; 1.28) on HLA class II.

While the study revealed no significant associations between the number of molecular mismatches and outcomes, a notable trend was observed - indicating a reduced risk of dnDSA formation with improved molecular match. It is important to acknowledge, however, that the modest population size and limited observed outcomes preclude us from making definitive conclusions.

The development of de novo donor-specific HLA antibodies (dnDSAs) following solid organ transplantation is considered a major risk factor for poor long-term allograft outcomes. The prediction of dnDSA development is a boon to transplant recipients, yet the assessment of allo-HLA immunogenicity remains imprecise. Despite the recent technological advances, a comprehensive evaluation of allo-HLA immunogenicity, which includes both B and T cell allorecognition, is still warranted. Recent studies have proposed using mismatched HLA epitopes (antibody and T cell) as a prognostic biomarker for humoral alloimmunity. However, the identification of immunogenic HLA mismatches has not progressed despite significant improvements in the identification of permissible mismatches. Certainly, the prediction of dnDSA development may benefit permissible HLA mismatched organ transplantations, personalized immunosuppression, and clinical trial design. However, characteristics that go beyond the listing of mismatched HLA antibody epitopes and T cell epitopes, such as the generation of HLA T cell epitope repertoires, recipient's HLA class II phenotype, and immunosuppressive regiments, are required for the precise assessment of allo-HLA immunogenicity.

The peptide presentation by donor and recipient major histocompatibility complex (MHC) molecules is the major driver of T-cell responses in transplantation. In this review, we address an emerging area of interest, the application of immunopeptidome in transplantation, and describe the potential opportunities that exist to use peptides for targeting alloreactive T cells. The immunopeptidome, the set of peptides presented on an individual's MHC, plays a key role in immune surveillance. In transplantation, the immunopeptidome is heavily influenced by MHC-derived peptides, delineating a key subset of the diverse peptide repertoire implicated in alloreactivity. A better understanding of the immunopeptidome in transplantation has the potential to open up new approaches to identify, characterize, longitudinally quantify, and therapeutically target donor-specific T cells and ultimately support more personalized immunotherapies to prevent rejection and promote allograft tolerance.

Defining HLA mismatch at the molecular compared with the antigen level has been shown to be superior in predicting alloimmune responses, although data from across different patient populations are lacking. Using HLA-Matchmaker, HLA-EMMA and PIRCHE-II, this study reports on the association between molecular mismatch (MolMM) and de novo donor-specific antibody (dnDSA) in an ethnically diverse kidney transplant population receiving a steroid-sparing immunosuppression protocol. Of the 419 patients, 51 (12.2%) patients had dnDSA. De novo DSA were seen more frequently with males, primary transplants, patients receiving tacrolimus monotherapy, and unfavorably HLA-matched transplants. There was a strong correlation between MolMM load and antigen mismatch, although significant variation of MolMM load existed at each antigen mismatch. MolMM loads differed significantly by recipient ethnicity, although ethnicity alone was not associated with dnDSA. On multivariate analysis, increasing MolMM loads associated with dnDSA, whereas antigen mismatch did not. De novo DSA against 8 specific epitopes occurred at high frequency; of the 51 patients, 47 (92.1%) patients with dnDSA underwent a pretreatment biopsy, with 21 (44.7%) having evidence of alloimmune injury. MolMM has higher specificity than antigen mismatching at identifying recipients who are at low risk of dnDSA while receiving minimalist immunosuppression. Immunogenicity consideration is important, with more work needed on identification, especially across different ethnic groups.

Eurotransplant established the acceptable mismatch (AM) program to facilitate timely kidney transplantations of highly sensitized patients, but long-term granular clinical and immunological outcomes regarding overall graft survival and de novo DSA (dnDSA) formation are still intensively researched. The right choice of induction therapy in patients with differing immunological risk is not conclusively determined, as well as the impact of human leukocyte antigen (HLA) epitope matching on dnDSA formation.

This monocentric, retrospective study analyzed 94 patients transplanted within the AM program between 2000 and 2019 compared to case-control matched cohorts of non- (PRA 0-5%; PRA-0) and intermediately sensitized (PRA 6-84%; PRA-6/84) patients transplanted through Eurotransplant Kidney Allocation System.

Estimated 10-year overall graft survival between the PRA-0 and AM cohorts was similar, whereas PRA-6/84 was significantly disadvantageous compared to PRA-0. Estimated 10-year incidence of antibody-mediated rejection rates was significantly lower in the PRA-0 group compared to AM and PRA-6/84 groups. Compared to the AM group, estimated incidence of de novo donor-specific antibody (dnDSA) was significantly lower in PRA-0 patients, with no differences between the AM and PRA-6/84 cohorts. The PRA-6/84 cohort was the only subgroup in which interleukin-2 receptor antagonist (IL2RA) induction was associated with longer overall graft survival, patient survival, and graft survival compared to depleting induction (ATG or OKT3). Broad HLA-A, -B, -DR mismatches (mmABDR) and HLA epitope mismatches determined by Eplets and PIRCHE-II were predictive for dnDSA formation in the total cohort, and the AM subgroup.

The high efforts expended on AM patients are justified to allow timely organ transplantation with acceptable risk profile and non-inferior outcomes. IL2RA induction in intermediately sensitized patients is associated with superior overall graft survival, patient survival, and graft survival compared to ATG/OKT3 induction, without negative effects on rejection episodes or dnDSA formation. In silico epitope matching might further help reduce dnDSA formation, particularly in high-risk AM patients.

PIRCHE scores in organ and stem cell transplantation have been shown to correlate with increased risk of donor-specific HLA antibodies and graft-versus-host disease, respectively. With advancements of the PIRCHE application server, it is critical to compare the predicted scores with previous versions. This manuscript compares the newly introduced PIRCHE version 4.2 with its predecessor version 3.3, which was widely used in retrospective studies, using a virtual cohort of 10,000 transplant pairs. In the stem cell transplantation module, both versions yield identical results in 100% of the test population. In the solid organ module, 97% of the test population has identical PIRCHE scores. The deviating cases (3%) were attributed to refinements in the PIRCHE algorithm's specification. Furthermore, the magnitude of the difference is likely to be below the detection limit for clinical effects, confirming the equivalence in PIRCHE scores between versions 3.3 and 4.2.

HLA matching in solid organ transplant is performed with the aim of assessing immunologic compatibility in order to avoid hyperacute rejection and assess the risk of future rejection events. Molecular mismatch algorithms are intended to improve granularity in histocompatibility assessment and risk stratification. PIRCHE-II uses HLA genotyping to predict indirectly presented mismatched donor HLA peptides, though most clinical validation studies rely on imputing high resolution (HR) genotypes from low resolution (LR) typing data. We hypothesized that use of bona fide HR typing could overcome limitations in imputation, improving accuracy and predictive ability for donor-specific antibody development and acute rejection. We performed a retrospective analysis of adult and pediatric kidney transplant donor/recipient pairs (N = 419) with HR typing and compared the use of imputed LR genotyping verses HR genotyping for PIRCHE-II analysis and outcomes. Imputation success was highly dependent on the reference population used, as using historic Caucasian reference populations resulted in 10 % of pairs with unsuccessful imputation while multiethnic reference populations improved successful imputation with only 1 % unable to be imputed. Comparing PIRCHE-II analysis with HR and LR genotyping produced notably different results, with 20 % of patients discrepantly classified to immunologic risk groups. These data emphasize the importance of using multiethnic reference panels when performing imputation and indicate HR HLA genotyping has clinically meaningful benefit for PIRCHE-II analysis compared to imputed LR typing.

To optimize outcomes in solid organ transplantation, the HLA genes are regularly compared and matched between the donor and recipient. However, in many cases a transplant cannot be fully matched, due to widespread variation across populations and the hyperpolymorphism of HLA alleles. Mismatches of the HLA molecules in transplanted tissue can be recognized by immune cells of the recipient, leading to immune response and possibly organ rejection. These adverse outcomes are reduced by analysis using epitope-focused models that consider the immune relevance of the mismatched HLA.PIRCHE, an acronym for Predicted Indirectly ReCognizable HLA Epitopes, aims to categorize and quantify HLA mismatches in a patient-donor pair by predicting HLA-derived T cell epitopes. Specifically, the algorithm predicts and counts the HLA-derived peptides that can be presented by the host HLA, known as indirectly-presented T cell epitopes. Looking at the immune-relevant epitopes within HLA allows a more biologically relevant understanding of immune response, and provides an expanded donor pool for a more refined matching strategy compared with allele-level matching. This PIRCHE algorithm is available for analysis of single transplantations, as well as bulk analysis for population studies and statistical analysis for comparison of probability of organ availability and risk profiles.

Recent advances in hardware and software enabled the use of artificial intelligence (AI) algorithms for analysis of complex data in a wide range of daily-life use cases. We aim to explore the benefits of applying AI to a specific use case in transplant nephrology: risk prediction for severe posttransplant events. For the first time, we combine multinational real-world transplant data, which require specific legal and technical protection measures.

The German-Canadian NephroCAGE consortium aims to develop and evaluate specific processes, software tools, and methods to (1) combine transplant data of more than 8000 cases over the past decades from leading transplant centers in Germany and Canada, (2) implement specific measures to protect sensitive transplant data, and (3) use multinational data as a foundation for developing high-quality prognostic AI models.

To protect sensitive transplant data addressing the first and second objectives, we aim to implement a decentralized NephroCAGE federated learning infrastructure upon a private blockchain. Our NephroCAGE federated learning infrastructure enables a switch of paradigms: instead of pooling sensitive data into a central database for analysis, it enables the transfer of clinical prediction models (CPMs) to clinical sites for local data analyses. Thus, sensitive transplant data reside protected in their original sites while the comparable small algorithms are exchanged instead. For our third objective, we will compare the performance of selected AI algorithms, for example, random forest and extreme gradient boosting, as foundation for CPMs to predict severe short- and long-term posttransplant risks, for example, graft failure or mortality. The CPMs will be trained on donor and recipient data from retrospective cohorts of kidney transplant patients.

We have received initial funding for NephroCAGE in February 2021. All clinical partners have applied for and received ethics approval as of 2022. The process of exploration of clinical transplant database for variable extraction has started at all the centers in 2022. In total, 8120 patient records have been retrieved as of August 2023. The development and validation of CPMs is ongoing as of 2023.

For the first time, we will (1) combine kidney transplant data from nephrology centers in Germany and Canada, (2) implement federated learning as a foundation to use such real-world transplant data as a basis for the training of CPMs in a privacy-preserving way, and (3) develop a learning software system to investigate population specifics, for example, to understand population heterogeneity, treatment specificities, and individual impact on selected posttransplant outcomes.

DERR1-10.2196/48892.

De novo donor-specific antibody (dnDSA) generation and acute rejection (AR) are the main factors affecting long-term graft survival. This study aims to investigate human leukocyte antigen (HLA) eplet mismatching (MM), delayed graft function (DGF), and tacrolimus (TAC) trough levels on the occurrence of dnDSA and AR in the early stages after kidney transplantation (KT).

This retrospective study included 526 cases of deceased donation KT. The effects of DGF, HLA eplet MM, and TAC trough levels on dnDSA and AR occurrence were analyzed with logistic regression analysis.

Multivariate logistic regression analysis showed the independent risk factor of dnDSA generation was HLA B eplet MM (OR: 1.201, 95% CI: 1.007-1.431, P = 0.041). The independent risk factors of AR occurrence include DGF (OR: 4.045, 95% CI: 1.047-15.626, P = 0.043), HLA B eplet MM (OR: 1.090, 95% CI: 1.000-1.187, P = 0.050), and TAC trough levels at 12 months (OR: 0.750, 95% CI: 565-0.997, P = 0.048). HLA B eplet MM combined with DGF and TAC trough levels at 12 months increased the predictive value of dnDSA (AUC 0.735) and AR (AUC 0.730) occurrence. HLA B eplet MM > 9 and TAC trough levels below 5.95 ng/mL at 12 months could increase the risk of early AR occurrence.

HLA B eplet MM, DGF, and TAC trough levels at 12 months after KT could affect the occurrence of dnDSA and AR in the early stage of KT.

(1) Background: Renal transplantation (KT) is the most efficient treatment for chronic kidney disease among pediatric patients. Antigenic matching and epitopic load should be the main criteria for choosing a renal graft in pediatric transplantation. Our study aims to compare the integration of new histocompatibility predictive algorithms with classical human leukocyte antigen (HLA) matching regarding different types of pediatric renal transplants. (2) Methods: We categorized our cohort of pediatric patients depending on their risk level, type of donor and type of transplantation, delving into discussions surrounding their mismatching values in relation to both the human leukocyte antigen Matchmaker software (versions 4.0. and 3.1.) and the most recent version of the predicted indirectly identifiable HLA epitopes (PIRCHE) II score. (3) Results: We determined that the higher the antigen mismatch, the higher the epitopic load for both algorithms. The HLAMatchmaker algorithm reveals a noticeable difference in eplet load between living and deceased donors, whereas PIRCHE II does not show the same distinction. Dialysis recipients have a higher count of eplet mismatches, which demonstrates a significant difference according to the transplantation type. Our results are similar to those of four similar studies available in the current literature. (4) Conclusions: We suggest that an integrated data approach employing PIRCHE II and HLAMatchmaker algorithms better predicts histocompatibility in KT than classical HLA matching.