Noninvasive methods to assess the risk of kidney transplant rejection

Molecular immune monitoring in kidney transplant rejection: a state-of-the-art review

Although current regimens of immunosuppressive drugs are effective in renal transplant recipients, long-term renal allograft outcomes remain suboptimal. For many years, the diagnosis of renal allograft rejection and of several causes of renal allograft dysfunction, such as chronic subclinical inflammation and infection, was mostly based on renal allograft biopsy, which is not only invasive but also possibly performed too late for proper management. In addition, certain allograft dysfunctions are difficult to differentiate from renal histology due to their similar pathogenesis and immune responses. As such, non-invasive assays and biomarkers may be more beneficial than conventional renal biopsy for enhancing graft survival and optimizing immunosuppressive drug regimens during long-term care. This paper discusses recent biomarker candidates, including donor-derived cell-free DNA, transcriptomics, microRNAs, exosomes (or other extracellular vesicles), urine chemokines, and nucleosomes, that show high potential for clinical use in determining the prognosis of long-term outcomes of kidney transplantation, along with their limitations.

Relevant biomarkers of kidney allograft rejection

This review focuses on the new relevant biomarkers proposed for the diagnosis of different types of allograft rejections. The immune response against the transplanted tissues can lead to rejection. Kidney allograft rejection occurs when the recipient component's immune system reacts against the donor's cells. MicroRNAs, dd-cf DNA, CD103 markers, CXCR3 chemokine receptor, IP-10, KIR genes, HLA antibodies, the perforin and granzyme B molecules - the constant assessment of all these parameters could prevent acute rejection episodes and kidney injuries. In this way, both immune response and tissue destruction biomarkers are essential for the long-term survival of kidney-transplanted patients. They also contribute to personalizing treatments, precisely personalized immunosuppressive regiments.

Validation of a gene expression signature to measure immune quiescence in kidney transplant recipients in the CLIA setting

Aim: Allograft rejection remains a major cause of graft failure in kidney transplantation. Here the authors report the validation of a non-invasive molecular diagnostic assay, AlloMap Kidney, using peripheral blood. Methods: The AlloMap Kidney test is a gene expression profile utilizing the RNA-seq platform to measure immune quiescence in kidney transplant patients. Results/Conclusions: Analytical validation showed robust performance characteristics with an accuracy correlation coefficient of 0.997 and a precision coefficient of variation of 0.049 across testing. Clinical validation from the prospective, multi-center studies of 235 samples (66 rejection and 169 quiescence specimens) demonstrated the sensitivity of 70% and specificity of 66% for allograft rejection, while the negative predictive value was 95% to discriminate rejection from quiescence at 10% prevalence of rejection.

Thrombospondin-1, Platelet Factor 4, and Galectin-1 are Associated with Engraftment in Patients with Sickle Cell Disease Who Underwent Haploidentical HSCT

Sickle cell disease (SCD) is an inherited red blood cell disorder that leads to significant morbidity and early mortality. The most widely available curative approach remains allogeneic hematopoietic stem cell transplantation (HSCT). HLA-haploidentical (haplo) HSCT expands the donor pool considerably and is a practical alternative for these patients, but traditionally with an increased risk of allograft rejection. Biomarkers in patient plasma could potentially help predict HSCT outcome and allow treatment at an early stage to reverse or prevent graft rejection. Reliable, noninvasive methods to predict engraftment or rejection early after HSCT are needed. We sought to detect variations in the plasma proteomes of patients who engrafted compared with those who rejected their grafts. We used a mass spectrometry-based proteomics approach to identify candidate biomarkers associated with engraftment and rejection by comparing plasma samples obtained from 9 engrafted patients and 10 patients who experienced graft rejection. A total of 1378 proteins were identified, 45 of which were differentially expressed in the engrafted group compared with the rejected group. Based on bioinformatics analysis results, information from the literature, and immunoassay availability, 7 proteins-thrombospondin-1 (Tsp-1), platelet factor 4 (Pf-4), talin-1, moesin, cell division control protein 42 homolog (CDC42), galectin-1 (Gal-1), and CD9-were selected for further analysis. We compared these protein concentrations among 35 plasma samples (engrafted, n = 9; rejected, n = 10; healthy volunteers, n = 8; nontransplanted SCD, n = 8). ELISA analysis confirmed the significant up-regulation of Tsp-1, Pf-4, and Gal-1 in plasma samples from engrafted patients compared with rejected patients, healthy African American volunteers, and the nontransplanted SCD group (P < .01). By receiver operating characteristic analysis, these 3 proteins distinguished engrafted patients from the other groups (area under the curve, >0.8; P < .05). We then evaluated the concentration of these 3 proteins in samples collected pre-HSCT and at days +30, +60, +100, and +180 post-HSCT. The results demonstrate that Tsp-1 and Pf-4 stratified engrafted patients as early as day 60 post-HSCT (P < .01), and that Gal-1 was significantly higher in engrafted patients as early as day 30 post-HSCT (P < .01). We also divided the rejected group into those who experienced primary (n = 5) and secondary graft rejection (n = 5) and found that engrafted patients had significantly higher Tsp-1 levels compared with patients who developed primary graft rejection at days +60 and +100 (P < .05), as well as higher Pf-4 levels compared with patients who developed primary graft rejection at post-transplantation (PT) day 100. Furthermore, Tsp-1 levels were significantly higher at PT days 60 and 100 and Pf-4 levels were higher at PT day 100 in engrafted patients compared with those who experienced secondary graft rejection. Increased concentrations of plasma Gal-1, Tsp-1, and Pf-4 could reflect increased T regulatory cells, IL-10, and TGF-β, which are essential players in the initiation of immunologic tolerance. These biomarkers may provide opportunities for preemptive intervention to minimize the incidence of graft rejection.

Clinical Validation of an Immune Quiescence Gene Expression Signature in Kidney Transplantation

Background

Despite advances in immune suppression, kidney allograft rejection and other injuries remain a significant clinical concern, particularly with regards to long-term allograft survival. Evaluation of immune activity can provide information about rejection status and help guide interventions to extend allograft life. Here, we describe the validation of a blood gene expression classifier developed to differentiate immune quiescence from both T cell-mediated rejection (TCMR) and antibody-mediated rejection (ABMR).

Methods

A five-gene classifier (DCAF12, MARCH8, FLT3, IL1R2, and PDCD1) was developed on 56 peripheral blood samples and validated on two sample sets independent of the training cohort. The primary validation set comprised 98 quiescence samples and 18 rejection samples: seven TCMR, ten ABMR, and one mixed rejection. The second validation set included eight quiescence and 11 rejection samples: seven TCMR, two ABMR, and two mixed rejection. AlloSure donor-derived cell-free DNA (dd-cfDNA) was also evaluated.

Results

AlloMap Kidney classifier scores in the primary validation set differed significantly between quiescence (median, 9.49; IQR, 7.68-11.53) and rejection (median, 13.09; IQR, 11.25-15.28), with P<0.001. In the second validation set, the cohorts were statistically different (P=0.03) and the medians were similar to the primary validation set. The AUC for discriminating rejection from quiescence was 0.786 for the primary validation and 0.800 for the second validation. AlloMap Kidney results were not significantly correlated with AlloSure, although both were elevated in rejection. The ability to discriminate rejection from quiescence was improved when AlloSure and AlloMap Kidney were used together (AUC, 0.894).

Conclusion

Validation of AlloMap Kidney demonstrated the ability to differentiate between rejection and immune quiescence using a range of scores. The diagnostic performance suggests that assessment of the mechanisms of immunologic activity is complementary to allograft injury information derived from AlloSure dd-cfDNA. Together, these biomarkers offer a more comprehensive assessment of allograft health and immune quiescence.

A Three-Gene Peripheral Blood Potential Diagnosis Signature for Acute Rejection in Renal Transplantation

Background: Acute rejection (AR) remains a major issue that negatively impacts long-term allograft survival in renal transplantation. The current study aims to apply machine learning methods to develop a non-invasive diagnostic test for AR based on gene signature in peripheral blood. Methods: We collected blood gene expression profiles of 251 renal transplant patients with biopsy-proven renal status from three independent cohorts in the Gene Expression Omnibus database. After differential expression analysis and machine learning algorithms, selected biomarkers were applied to the least absolute shrinkage and selection operator (LASSO) logistic regression to construct a diagnostic model in the training cohort. The diagnostic ability of the model was further tested in validation cohorts. Gene set enrichment analysis and immune cell assessment were also conducted for further investigation. Results: A novel diagnostic model based on three genes (TSEN15, CAPRIN1 and PRR34-AS1) was constructed in the training cohort (AUC = 0.968) and successfully verified in the validation cohort (AUC = 0.925) with high accuracy. Moreover, the diagnostic model also showed a promising value in discriminating T cell-mediated rejection (TCMR) (AUC = 0.786). Functional enrichment analysis and immune cell evaluation demonstrated that the AR model was significantly correlated with adaptive immunity, especially T cell subsets and dendritic cells. Conclusion: We identified and validated a novel three-gene diagnostic model with high accuracy for AR in renal transplant patients, and the model also performed well in distinguishing TCMR. The current study provided a promising tool to be used as a precise and cost-effective non-invasive test in clinical practice.

CYC1, SDHA, UQCRC1, UQCRQ, and SDHB might be important biomarkers in kidney transplant rejection

BACKGROUND

Kidney transplant rejection is considered as a vital factor of kidney transplant failure. Therefore, it's necessary to search for effective biomarkers for kidney transplant surveillance.

METHODS

In this study, we conducted time-series gene expression profiles analysis of samples from kidney transplant patients with different post-transplant days through weighted gene co-expression network analysis (WGCNA). Associations between gene co-expression modules and days post-transplant were determined through spearman rank correlation analysis. Potential kidney transplant rejection-related modules were subjected to gene functional enrichment analysis through clusterProfiler and protein-protein interaction analysis via STRING database.

RESULTS

A total of 11 gene co-expression modules were identified, and the pink module which was mainly involved in "energy derivation by oxidation of organic compounds" and "Huntington disease" showed significant correlation with the phenotypic trait "days post-transplant". CYC1, SDHA, UQCRC1, UQCRQ, and SDHB in the pink module exhibited high scores in the protein-protein interaction network analysis.

CONCLUSIONS

We reported several potential genes may be associated with the kidney transplant rejection, which should provide novel biomarkers for kidney transplant surveillance.

Multiplexed real-time polymerase chain reaction cell-free DNA assay as a potential method to monitor stage IV colorectal cancer

BACKGROUND

Liquid biopsy is a new area in cancer diagnostics that measures cell-free DNA in plasma from tumor that may serve as a monitoring tool in colorectal cancer patients.

METHODS

Multiplexed real-time polymerase chain reaction based on multicopy retro-transposable elements (targeting 80 base pair and 265 base pair sequences and an internal-positive-control) was used to evaluate the ability of cell-free DNA concentration and DNA Integrity Index to discriminate cancer from healthy patients. A cohort of 40 healthy controls and 39 stage IV colorectal patient's plasma were interrogated. The potency of each biomarker was measured by using receiver operating characteristic curves and derived area under the curve measures.

RESULTS

Significant differences in cell-free DNA concentration and DNA integrity index were observed between controls and stage IV patients with a limit of detection <0.1 pg/μL. Investigation of the ability of both biomarker candidates to differentiate cancer from healthy patients showed an area under the curve of 0.9891 and 0.9859 for 80 base pair and 265 amplicons respectively and 0.8603 for DNA integrity index-265/80.

CONCLUSIONS

After establishing differences in cell-free DNA levels between healthy and treated and untreated stage IV patients, the multiplexed real-time polymerase chain reaction measurements of retro-transposable elements in cancer patient plasma potentially possess the ability to monitor therapy responsiveness in near real time.

Intravoxel incoherent motion analysis of renal allograft diffusion with clinical and histopathological correlation in pediatric kidney transplant patients: A preliminary cross-sectional observational study

The purpose of this study was to compare IVIM values in pediatric renal transplants with histopathology and clinical management change. Fifteen pediatric renal transplant recipients (mean 15.7±2.9 years) were prospectively scanned on a 3T MR scanner with multi-b DTI, prior to same-day transplant biopsy. IVIM maps from 14 subjects were analyzed (one excluded due to motion). Mean values were computed from cortical ROIs and medullary ROIs corresponding to the biopsy site. Subjects were also grouped according to whether or not the biopsy resulted in a change in clinical management. Cortico-medullary IVIM estimates and histopathologic Banff scores were correlated with KT. Cortico-medullary IVIM differences between the "change" and "no change" groups was compared with Mann-Whitney U test. Cortical D_p showed significant moderate negative correlation with Banff t and ci scores (KT=-0.497, P=.035 and KT=-0.46, P=.046) and moderate positive correlation with Banff i score (KT=0.527, P=.028). Cortical P_f showed significant moderate correlation with ci and ct scores (KT=0.489, P=.035 and KT=0.457, P=.043). Tissue diffusivity, D_t , estimated with IVIM was significantly different between the "change" and "no change" groups in medullary ROIs (U=6, P=.021). IVIM analysis has potential as a noninvasive biomarker in assessment of pediatric renal allograft pathology.

Reduced PARP1 as a Serum Biomarker for Graft Rejection in Kidney Transplantation

A serum proteomics platform enabling expression Profiling in transplantation-associated clinical subsets gives an opportunity to identify non-invasive biomarkers that can accurately predict transplant outcome. In this study, we attempted to identify candidate serum biomarkers that could predict kidney allograft rejection/injury, regardless of its etiological and therapeutic heterogeneity. Using serum samples collected from kidney transplantation patients and healthy controls, we first employed Clontech-500 Ab microarrays to Profile acute rejection (AR) and chronic graft injury (CGI) versus stable graft function (SF) and normal kidneys (NK). Using GenePattern analysis of duplicate arrays on pooled samples, we identified gender-independent biomarkers PARP1, MAPK1, SRP54, DP1, and p57 (FDR ≈ 25%), the concordant downregulation of which represented a detrimental Profile common for both rejection/ injury types (AR-CGI). The reverse phase arrays qualified a 2-fold upregulation of PARP1 with an ROC of 0.87 in individual samples from patients with SF vs. AR-CGI rendering serum PARP1 as a biomarker for early prognosis. Ingenuity Pathways Analysis (IPA) connected PARP1 to some other markers (MAPK1), elucidating their possible interactions and connections to the immune response and graft-versus-host disease signaling. The downregulation of serum PARP1 in the damaged graft tissues, represents a perspective non-invasive marker, predicting the failing kidney graft, regardless of rejection/injury causes or gender. Thus, the successful identification of PARP1 as a bio-marker in limited patient cohorts demonstrates that serum proteomics platform empowered by the GenePattern- and IPA-based Bioinformatics algorithm can guarantee a successful development of the clinically applicable prognostic biomarker panel.

Non-invasive imaging of allogeneic transplanted skin graft by 131I-anti-TLR5 mAb

Although ¹⁸F-fluorodeoxyglucose (¹⁸F-FDG) uptake can be used for the non-invasive detection and monitoring of allograft rejection by activated leucocytes, this non-specific accumulation is easily impaired by immunosuppressants. Our aim was to evaluate a ¹³¹I-radiolabelled anti-Toll-like receptor 5 (TLR5) mAb for non-invasive in vivo graft visualization and quantification in allogeneic transplantation mice model, compared with the non-specific radiotracer ¹⁸F-FDG under using of immunosuppressant. Labelling, binding, and stability studies were performed. BALB/c mice transplanted with C57BL/6 skin grafts, with or without rapamycin treatment (named as allo-treated group or allo-rejection group), were injected with ¹³¹I-anti-TLR5 mAb, ¹⁸F-FDG, or mouse isotype ¹³¹I-IgG, respectively. Whole-body phosphor-autoradiography and ex vivo biodistribution studies were obtained. Whole-body phosphor-autoradiography showed ¹³¹I-anti-TLR5 mAb uptake into organs that were well perfused with blood at 1 hr and showed clear graft images from 12 hrs onwards. The ¹³¹I-anti-TLR5 mAb had significantly higher graft uptake and target-to-non-target ratio in the allo-treated group, as determined by semi-quantification of phosphor-autoradiography images; these results were consistent with ex vivo biodistribution studies. However, high ¹⁸F-FDG uptake was not observed in the allo-treated group. The highest allograft-skin-to-native-skin ratio (A:N) of ¹³¹I-anti-TLR5 mAb uptake was significantly higher than the ratio for ¹⁸F-FDG (7.68 versus 1.16, respectively). ¹³¹I-anti-TLR5 mAb uptake in the grafts significantly correlated with TLR5 expression in the allograft area. The accumulation of ¹³¹I-IgG was comparable in both groups. We conclude that radiolabelled anti-TLR5 mAb is capable of detecting allograft with high target specificity after treatment with the immunosuppressive drug rapamycin.

Immune cell function assay does not identify biopsy-proven pediatric renal allograft rejection or infection

Management of pediatric renal transplant patients involves multifactorial monitoring modalities to ensure allograft survival and prevent opportunistic infection secondary to immunosuppression. An ICFA, which utilizes CD4 T-cell production of ATP to assess immune system status, has been used to monitor transplant recipients and predict susceptibility of patients to rejection or infection. However, the validity of this assay to reflect immune status remains unanswered. In a two-yr retrospective study that included 31 pediatric renal transplant recipients, 42 patient blood samples were analyzed for immune cell function levels, creatinine, WBC (white blood cell) count, immunosuppressive drug levels, and viremia, concurrent with renal biopsy. T-cell ATP production as assessed by ICFA levels did not correlate with allograft rejection or with the presence or absence of viremia. ICFA levels did not correlate with serum creatinine or immunosuppressive drug levels, but did correlate with WBC count. The ICFA is unreliable in its ability to reflect immune system status in pediatric renal transplantation. Further investigation is necessary to develop methods that will accurately predict susceptibility of pediatric renal transplant recipients to allograft rejection and infection.

Changes of progesterone-induced blocking factor in patients after kidney transplantation

The prediction of graft rejection can play an important part in graft survival. Analysis of immune reactions has shown that graft rejection shares mechanisms with recurrent abortions during pregnancy. Progesterone-induced blocking factor (PIBF), a mediator of progesterone that blocks natural killer cell activity in peripheral blood, produces antiabortive effects. The aim of this study was to examine the PIBF concentration in the urine of transplanted recipients. The study included 116 white adults (70 men and 46 women) of median age 49.3 years, who had undergone kidney transplantations. The median duration after transplantation was 3.46 years. The average period between renal disease and our measurement was 12.3 years, and the median interval between graft rejection and our study was 1.75 years. Urine samples were used to measure PIBF concentrations by an enzyme-linked immunsorbent assay. PIBF urinary concentrations decreased significantly in patients who experienced ≥1 rejection episode (31.8±2.2 ng/mL) compared with those without any episode (22.7±1.2 ng/ml; P<.01). Moreover, the urinary PIBF level was significantly lower among patients who had increased creatinine and urea nitrogen levels in blood samples (P<.05 and P<.01, respectively). Decreased PIBF values in kidney transplant patients followed previous rejection episodes. A close negative correlation was observed between urinary PIBF concentrations and blood levels of creatinine and urea nitrogen. These findings suggested that PIBF detection may predict graft rejection in transplant recipients.

Lymphocyte ATP immune cell function assay in pediatric renal transplants: is it useful?

The ultimate goal for an allograft is a balanced immunosuppression to provide the longest graft survival with minimal side effects. In this retrospective study, we correlate the immunosuppresion level as determined using the Cylex assay (Immu know, Columbia, MD) with clinical events. Demographic data such as age at the time of transplant, gender, ethnicity, time posttransplantation, tacrolimus level, and induction therapy were correlated with Cylex levels. Cylex from children with an infection or acute rejection were compared to those from stable patients. All children received induction with basiliximab or thymoglobulin followed by a standard regimen with tacrolimus, steroids, and mycophenolate mofetil. Fifty-nine Cylex results were obtained in 44 pediatric renal transplant recipients. Cylex values ranged from 20 ng/mL to 728 ng/mL. We did not find significant correlation between any of the demographic characteristics studied (tacrolimus level, induction therapy, acute rejection, and Cylex levels). Fifteen patients had severe infections requiring hospitalization: 11 of 15 (73%) had Cylex<130 ng/mL; these levels differed significantly from those obtained in patients without infections. We concluded that clinical utility of Cylex is limited in children with kidney transplants because it did noes correlate with the prescribed dosage of medications or with rejection. However, low Cylex levels were highly correlated with serious infections.

Immune monitoring and biomarkers to predict chronic allograft dysfunction

Late failure of a kidney transplant continues to be a major problem after transplantation, in spite of more potent immunosuppressive strategies and the focus of clinical management shifting toward prolonging long-term graft survival. It is now recognized that graft failure occurs because of two major complications: death with a functioning graft and intrinsic allograft failure. Recent studies of late kidney graft loss have indicated a complexity of findings, including etiologies that are both immune and non-immune. These studies suggest that late graft failure is not an inevitable fact and that further investigation into the etiology of transplant graft failure may lead to a new understanding of the biology that will provide novel therapeutic strategies and biomarkers. In this review, we will focus on late allograft failure due to intrinsic injury to the transplant. The role of immune monitoring will be discussed in the context of monitoring for ongoing injury or for identifying late injury. A variety of methodologies have been used, including genomics, proteomics, and metabolomics, not only for monitoring allograft injury but also for identifying markers of graft failure that are more sensitive than serum creatinine. The available studies, as they relate to late or chronic graft injury, will also be reviewed.

Novel diagnostics in renal transplantation

Renal transplantation is the treatment of choice for many patients with end stage renal disease. While significant progress has been achieved in short-term outcomes, long-term graft survival has only marginally improved. More than 50% of transplanted kidneys from deceased donors fail within ten years; and from living donors, within 12 years. A lack of clinical tools to accurately monitor the allograft is a major causative factor in this lack of progress. This paper discusses newly available methods used to assess allograft status with emphasis on the role of circulating chimerism in renal transplantation as a diagnostic indicator for rejection and injury.