Effects of DNA Methylation on Progression to Interstitial Fibrosis and Tubular Atrophy in Renal Allograft Biopsies: A Multi-Omics Approach.

Progressive fibrosis of the interstitium is the dominant final pathway in renal destruction in native and transplanted kidneys. Over time, the continuum of molecular events following immunological and nonimmunological insults lead to interstitial fibrosis and tubular atrophy and culminate in kidney failure. We hypothesize that these insults trigger changes in DNA methylation (DNAm) patterns, which in turn could exacerbate injury and slow down the regeneration processes, leading to fibrosis development and graft dysfunction. Herein, we analyzed biopsy samples from kidney allografts collected 24 months posttransplantation and used an integrative multi-omics approach to understand the underlying molecular mechanisms. The role of DNAm and microRNAs on the graft gene expression was evaluated. Enrichment analyses of differentially methylated CpG sites were performed using GenomeRunner. CpGs were strongly enriched in regions that were variably methylated among tissues, implying high tissue specificity in their regulatory impact. Corresponding to this methylation pattern, gene expression data were related to immune response (activated state) and nephrogenesis (inhibited state). Preimplantation biopsies showed similar DNAm patterns to normal allograft biopsies at 2 years posttransplantation. Our findings demonstrate for the first time a relationship among epigenetic modifications and development of interstitial fibrosis, graft function, and inter-individual variation on long-term outcomes.

BK Polyomavirus-Specific 9mer CD8 T Cell Responses Correlate With Clearance of BK Viremia in Kidney Transplant Recipients: First Report From the Swiss Transplant Cohort Study.

BK polyomavirus (BKPyV) causes premature kidney transplant (KT) failure in 1-15% of patients. Because antivirals are lacking, most programs screen for BKPyV-viremia and, if positive, reduce immunosuppression. To evaluate the relationship of viremia and BKPyV-specific immunity, we examined prospectively cryopreserved plasma and peripheral blood mononuclear cells at the time of transplantation (T0) and at 6 mo (T6) and 12 mo (T12) after transplant from 28 viremic KT patients and 68 nonviremic controls matched for the transplantation period. BKPyV IgG seroprevalence was comparable between cases (89.3%) and controls (91.2%; p = 0.8635), but cases had lower antibody levels (p = 0.022) at T0. Antibody levels increased at T6 and T12 but were not correlated with viremia clearance. BKPyV-specific T cell responses to pools of overlapping 15mers (15mer peptide pool [15mP]) or immunodominant CD8 9mers (9mer peptide pool [9mP]) from the early viral gene region were not different between cases and controls at T0; however, clearance of viremia was associated with stronger 9mP responses at T6 (p = 0.042) and T12 (p = 0.048), whereas 15mP responses were not informative (T6 p = 0.359; T12 p = 0.856). BKPyV-specific T cells could be expanded in vitro from all patients after transplant, permitting identification of 78 immunodominant 9mer epitopes including 50 new ones across different HLA class I. Thus, 9mP-responses may be a novel marker of reconstituting CD8 T cell function that warrants further study as a complement of plasma BKPyV loads for guiding immunosuppression reduction.

Systems Biology in Kidney Transplantation: The Application of Multi-Omics to a Complex Model.

In spite of reduction of rejection rates and improvement in short-term survival post-kidney transplantation, modest progress has occurred in long-term graft attrition over the years. Timely identification of molecular events that precede clinical and histopathological changes might help in early intervention and thereby increase the graft half-life. Evolution of "omics" tools has enabled systemic investigation of the influence of the whole genome, epigenome, transcriptome, proteome and microbiome on transplant function and survival. In this omics era, systemic approaches, in-depth clinical phenotyping and use of strict validation methods are the key for further understanding the complex mechanisms associated with graft function. Systems biology is an interdisciplinary holistic approach that focuses on complex and dynamic interactions within biological systems. The complexity of the human kidney transplant is unlikely to be captured by a reductionist approach. It appears essential to integrate multi-omics data that can elucidate the multidimensional and multilayered regulation of the underlying heterogeneous and complex kidney transplant model. Herein, we discuss studies that focus on genetic biomarkers, emerging technologies and systems biology approaches, which should increase the ability to discover biomarkers, understand mechanisms and stratify patients and responses post-kidney transplantation.

Intestinal infection at onset of mycophenolic acid-associated chronic diarrhea in kidney transplant recipients.

BACKGROUND: Chronic diarrhea after kidney transplantation is often attributed to mycophenolic acid (MPA) toxicity. We hypothesize that intestinal infections contribute to the pathogenesis of chronic MPA-associated diarrhea. METHODS: In this retrospective study, all patients (n = 726) receiving a kidney transplant between 2000 and 2010 at the University Hospital Zurich were followed until July 2014 for occurrence of chronic diarrhea (≥4 weeks). Infectious triggers at diarrhea onset were assessed by reviewing medical history, stool microbiology, and histology of colon biopsies. RESULTS: In 46 patients (6.3% of the cohort), a total of 51 episodes of chronic diarrhea during MPA treatment were documented. The diarrhea episodes were often severe, as confirmed by significant weight loss. The cumulative incidence of chronic diarrhea was uniformly distributed throughout the post-transplant period, with 2.0%, 5.1%, and 9.6% at 1, 5, and 10 years, respectively. Evidence was found for intestinal infection at diarrhea onset in 38 episodes (74.5%). Occurrence of diarrhea onset showed a seasonal distribution with peaks in April and October/November. Specific antimicrobial treatment alone was associated with a 19% resolution rate only, whereas combination with dose reduction of MPA or switch from mycophenolate mofetil to enteric-coated mycophenolate sodium resulted in a 22.7% and 76.5% resolution rate, respectively. Change to an MPA-free regimen was associated with a 100% resolution rate. CONCLUSION: These results provide first evidence for a contribution of intestinal infections in chronic post-transplant diarrhea associated with MPA treatment.

Effect of Twice-Yearly Denosumab on Prevention of Bone Mineral Density Loss in De Novo Kidney Transplant Recipients: A Randomized Controlled Trial.

We conducted an open-label, prospective, randomized trial to assess the efficacy and safety of RANKL inhibition with denosumab to prevent the loss of bone mineral density (BMD) in the first year after kidney transplantation. Ninety kidney transplant recipients were randomized 1:1 2 weeks after surgery to receive denosumab (60 mg at baseline and 6 months) or no treatment. After 12 months, total lumbar spine areal BMD (aBMD) increased by 4.6% (95% confidence interval [CI] 3.3-5.9%) in 46 patients in the denosumab group and decreased by -0.5% (95% CI -1.8% to 0.9%) in 44 patients in the control group (between-group difference 5.1% [95% CI 3.1-7.0%], p < 0.0001). Denosumab also increased aBMD at the total hip by 1.9% (95% CI, 0.1-3.7%; p = 0.035) over that in the control group at 12 months. High-resolution peripheral quantitative computed tomography in a subgroup of 24 patients showed that denosumab increased volumetric BMD at the distal tibia and radius (all p < 0.05). Biomarkers of bone turnover (C-terminal telopeptide of type I collagen, procollagen type I N-terminal propeptide) markedly decreased with denosumab (all p < 0.0001). Episodes of cystitis and asymptomatic hypocalcemia occurred more often with denosumab, whereas graft function, rate of rejections, and incidence of opportunistic infections were similar. In conclusion, denosumab increased BMD in the first year after kidney transplantation but was associated with more frequent episodes of urinary tract infection.

What's hot, what's new at WTC--clinical science.

More than 3000 abstracts of innovative and exciting findings, covering the whole field of organ transplantation, were presented at the World Transplant Congress 2014. Key areas of presentations across all organs and tissues included HLA antibodies, antibody-mediated rejection, living donation, immunosuppression, organ perfusion and surgical procedures. In addition, cutting edge science and future perspectives were presented in state-of-the-art lectures. This review will present highlights of this meeting and demonstrate strength and success of clinical sciences in transplantation.

Increased resting energy expenditure in children with attention-deficit-hyperactivity disorder.

BACKGROUND: Attention Deficit Hyperactivity Disorder (ADHD) is one of the most frequently reported neuropsychiatric disorders in childhood. However, there is limited data on the biological basis for this disorder. Disturbances in neurotransmitters have been suggested to play a pathophysiologic role. Phenotypically an increased prevalence of obesity has been reported. OBJECTIVE: To investigate resting energy expenditure (REE) and diet-induced thermogenesis in stimulant medication-naïve children with ADHD. DESIGN: Case control study of 12 pre-pubertal boys with ADHD of the hyperactive-impulsive type and 12 control boys without ADHD. Anthropometric testing and indirect calorimetry were performed before and after a standardized meal. REE and thermogenesis were measured in each subject at 2 time points. In an independent group of 60 boys with ADHD, BMI standard deviation scores (BMI-SDS) were compared to age-adapted reference values. RESULTS: REE was on average 6.5 kcal/kg fat free mass/day higher in the ADHD compared to the control group (p<0.01). In contrast, the thermogenic effect of food was not different between the two groups (average increase by 16%, p=n.s.). The repeat measurements, an average of 5±1 months apart, were highly reproducible in all subjects. Age and restlessness did not explain the differences in REE. Boys with ADHD had similar BMI-SDS values (mean BMI-SDS -0.10±0.98) as reference groups. CONCLUSIONS: REE, in contrast to diet-induced thermogenesis, is higher in medication-naïve boys with ADHD. The normal BMI levels suggest increased energy intake in these children.

FOXP3 expression in human kidney transplant biopsies is associated with rejection and time post transplant but not with favorable outcomes.

Expression of the transcription factor forkhead box P3 (FOXP3) in transplant biopsies is of interest due to its role in a population of regulatory T cells. We analyzed FOXP3 mRNA expression using RT-PCR in 83 renal transplant biopsies for cause in relationship to histopathology, clinical findings and expression of pathogenesis-based transcript sets assessed by microarrays. FOXP3 mRNA was higher in rejection (T-cell and antibody-mediated) than nonrejection. Surprisingly, some native kidney controls also expressed FOXP3 mRNA. Immunostaining for FOXP3 was consistent with RT-PCR, showing interstitial FOXP3+ lymphocytes, even in some native kidney controls. FOXP3 expression correlated with interstitial inflammation, tubulitis, interstitial fibrosis, tubular atrophy, C4d positivity, longer time posttransplant, younger donors, class II panel reactive antibody >20% and transcript sets reflecting inflammation and injury, but unlike these features was time dependent. In multivariate analysis, higher FOXP3 mRNA was independently associated with rejection, T-cell-associated transcripts, younger donor age and longer time posttransplant. FOXP3 expression did not correlate with favorable graft outcomes, even when the analysis was restricted to biopsies with rejection. Thus FOXP3 mRNA expression is a time-dependent feature of inflammatory infiltrates in renal tissue. We hypothesize that time-dependent entry of FOXP3-positive cells represents a mechanism for stabilizing inflammatory sites.

Expression of B cell and immunoglobulin transcripts is a feature of inflammation in late allografts.

To assess the significance of B-cell and plasma cell infiltrates in renal allografts, we compared expression of B-cell-associated transcripts (BATs) and immunoglobulin transcripts (IGTs) to histopathology and function in 177 renal allograft biopsies for clinical indications. BAT and IGT expression correlated with immunostaining for B cells and plasma cells and with expression of B-cell and plasma cell transcription factors. BATs and IGTs were increased in both T-cell-mediated and antibody-mediated rejection. BAT and IGT scores were strongly related to time posttransplant: biopsies <5 months expressed less BATs and did not express increased IGTs. In contrast, T-cell-associated transcripts were independent of time posttransplant. In biopsies > or =5 months, BAT and IGT scores correlated with interstitial inflammation, tubular atrophy and interstitial fibrosis. By regression tree analysis, the only variables independently correlated with BATs and IGTs were time and inflammation. Expression of BATs and IGTs correlated with renal function, but this relationship was due to differences in early versus late biopsies: BATs and IGTs were not related to function or future function after correcting for time.

The transcriptome of human cytotoxic T cells: measuring the burden of CTL-associated transcripts in human kidney transplants.

Having defined CTL-associated transcripts (CATs) in CTL in vitro, we used microarrays to quantify the burden of CAT sets compared with individual transcripts in human renal transplant biopsies with T-cell mediated rejection (TCMR). CAT sets in TCMR resembled diluted CTL RNA, maintaining overall hierarchy of expression relative to CTL in vitro. NK selective sets were not detected in TCMR, indicating the CATs mainly reflect T cells. We selected 25 highly expressed CATs that diluted quantitatively in kidney RNA (QCATs) and remained detectable after 32-fold dilution. QCAT burden in 14 kidneys with TCMR was 3 to 15% of CTL RNA, correlating with infiltration. One biopsy diagnosed as TCMR only by endothelialitis had little interstitial infiltrate and lowest CAT burden. CAT sets were more consistent than individual CATs such as perforin or granzyme B, which showed heterogeneity. In luster and principal component analysis, QCATs grouped biopsies with TCMR together, in close relationship to in vitro CTL. Thus QCAT sets robustly measure the burden of CTL and effector memory T cells in biopsies as %CTL RNA, in a manner not achieved by measurement of individual transcripts.

The transcriptome of the implant biopsy identifies donor kidneys at increased risk of delayed graft function.

Improved assessment of donor organ quality at time of transplantation would help in management of potentially usable organs. The transcriptome might correlate with risk of delayed graft function (DGF) better than conventional risk factors. Microarray results of 87 consecutive implantation biopsies taken postreperfusion in 42 deceased (DD) and 45 living (LD) donor kidneys were compared to clinical and histopathology-based scores. Unsupervised analysis separated the 87 kidneys into three groups: LD, DD1 and DD2. Kidneys in DD2 had a greater incidence of DGF (38.1 vs. 9.5%, p < 0.05) than those in DD1. Clinical and histopathological risk scores did not discriminate DD1 from DD2. A total of 1051 transcripts were differentially expressed between DD1 and DD2, but no transcripts separated DGF from immediate graft function (adjusted p < 0.01). Principal components analysis revealed a continuum from LD to DD1 to DD2, i.e. from best to poorest functioning kidneys. Within DD kidneys, the odds ratio for DGF was significantly increased with a transcriptome-based score and recipient age (p < 0.03) but not with clinical or histopathologic scores. The transcriptome reflects kidney quality and susceptibility to DGF better than available clinical and histopathological scoring systems.

Microarray analysis of rejection in human kidney transplants using pathogenesis-based transcript sets.

Microarrays offer potential for objective diagnosis and insights into pathogenesis of allograft rejection. We used mouse transplants to annotate pathogenesis-based transcript sets (PBTs) that reflect major biologic events in allograft rejection-cytotoxic T-cell infiltration, interferon-gamma effects and parenchymal deterioration. We examined the relationship between PBT expression, histopathologic lesions and clinical diagnoses in 143 consecutive human kidney transplant biopsies for cause. PBTs correlated strongly with one another, indicating that transcriptome disturbances in renal transplants have a stereotyped internal structure. This disturbance was continuous, not dichotomous, across rejection and nonrejection. PBTs correlated with histopathologic lesions and were the highest in biopsies with clinically apparent rejection episodes. Surprisingly, antibody-mediated rejection had changes similar to T-cell mediated rejection. Biopsies lacking PBT disturbances did not have rejection. PBTs suggested that some current Banff histopathology criteria are unreliable, particularly at the cut-off between borderline and rejection. Results were validated in 51 additional biopsies. Thus many transcriptome changes previously described in rejection are features of a large-scale disturbance characteristic of rejection but occurring at lower levels in many forms of injury. PBTs represent a quantitative measure of the inflammatory disturbances in organ transplants, and a new window on the mechanisms of these changes.

Modulation of gene expression by alloimmune networks following murine heart transplantation.

The objective of our study was to analyze gene expression profiles in a complex in vivo model of solid organ transplantation, and to investigate the effects of single-gene deletions on alloimmunity. Using algorithms to generate dendrograms and self-organizing maps, we differentiated the alloimmune profiles of 16 transgenic knockout mouse strains, and identified subsets of genes that correlate with the duration of graft survival and provide candidates for prognostic and diagnostic indicators following transplantation in our model system.

Effect of mycophenolate mofetil on kidney graft function and body weight in patients with chronic allograft nephropathy.

BACKGROUND: Chronic allograft nephropathy (CAN) is the most common cause of late graft loss. A beneficial effect of mycophenolate mofetil (MMF) on CAN was observed, although, due to the loss of body weight (BW) under MMF, serum creatinine (sCr) and reciprocal sCr may be unsuitable markers of graft function. METHODS: In 17 kidney transplant patients with CAN, azathioprine (Aza) was replaced by MMF. The remaining therapy was not changed; specifically, the cyclosporine (CsA) dose was not decreased. The mean values and regression coefficients of reciprocal sCr, CCr, urinary creatinine excretion (uCr x V), proteinuria, BW, blood pressure (BP), serum cholesterol (sChol), and serum triglycerides (sTG) versus time were analyzed 12 months before and after institution of MMF by a paired-comparison t test. RESULTS: The mean regression coefficient of reciprocal sCr differed significantly before and after conversion to MMF (mean -0.01 +/- 0.01 vs +0.012 +/- 0.029 mg/dL per month), suggesting improved graft function. However, the mean values of BW (74 +/- 15 vs 71 +/- 15 kg, P <.001) and uCr x V (1152 +/- 321 vs 1065 +/- 266 mg per 24 hours, P=.0897) decreased, making the increase in CCr less significant (mean -1.16 +/- 2.69 vs 0.40 +/- 1.79 mL/min per month, P <.05). BP, sChol, sTG, and proteinuria before and after conversion did not differ significantly. Among patients with long-term stable graft function at 36.5 +/- 16.9 months after conversion to MMF there was an almost significant improvement in renal protein excretion. CONCLUSIONS: MMF improved graft function, although this effect was overestimated using reciprocal sCr. Other risk factors, such as BP, sChol, and sTG, showed no significant differences, suggesting that MMF accounted for the improvement in CAN. The course of proteinuria under MMF seems to be of prognostic significance.

Immune monitoring in organ transplantation using neopterin.

Transplantation has become an established and successful therapy. Rejections and infections are the principal immune-related complications in the post-transplant course. A reliable and early diagnosis is necessary to prevent graft failure and patient morbidity. Despite the immunologic nature of these complications the diagnostic procedures still rely on functional tests and organ biopsies. Non-invasive monitoring remains to be one of the major goals in transplant medicine. Neopterin is a sensitive marker of the cellular immune response. It reflects the activation of macrophages and can be easily measured in serum, plasma, urine or other body fluids. This review summarises studies on the diagnostic value of neopterin in transplant medicine. Based on these results key factors for immune monitoring in regard to neopterin are evaluated. In particular the unspecificity of diagnostic immune markers, the kinetics of the immune response, the importance of adjustment of neopterin to kidney function, and quantitative differences in immune pathways against viruses and allografts are discussed. Reflecting these points a concept to use neopterin for non-invasive immune monitoring in the clinical routine is presented. This approach calculates probabilities for specific post-transplant complications based on daily measurements of neopterin, a combination with the acute phase reactant amyloid A, and a modification of the likelihood ratio concept.

Assessment of cytomegalovirus infections using neopterin and a new immunoblot.

Human cytomegalovirus (HCMV) infections are a major cause of morbidity and mortality in immunocompromised patients despite advances in diagnostic tests and antiviral therapies. The underlying study investigates the diagnostic value of the immune marker neopterin and a recently developed HCMV-specific western blot to detect HCMV infections and to differentiate them into either syndromes or diseases. The mean period of observation was 1428 days. Thirteen HCMV diseases and nine syndromes were diagnosed retrospectively. The first appearance of clinical signs or symptoms was always associated with a marked increase of serum and urine neopterin. The HCMV-specific IgM response followed in the mean 9 days later. Median values and the course of the neopterin levels were significantly higher during the HCMV diseases. In addition, the strength of the humoral immune response was related to the severity of the HCMV infection. Patients with HCMV diseases developed antibodies against a higher number of epitopes. The anti-HCMV IgM response persisted in more than 80% of the patients for longer than 3 years. In conclusion, combining the HCMV-specific western blot and neopterin permit detection of the immune response against HCMV, reflect the severity of the infection and might guide the anti-viral therapy.

Aggregation pheromone for the pepper weevil,Anthonomus eugenii cano (Coleoptera: Curculionidae): Identification and field activity.

This study describes the identification of an aggregation pheromone for the pepper weevil,Anthonomus eugenii and field trials of a synthetic pheromone blend. Volatile collections and gas chromatography revealed the presence of six male-specific compounds. These compounds were identified using chromatographic and spectral techniques as: (Z)-2-(3,3-dimethylcyclohexylidene)ethanol, (E)-2-(3,3-dimethylcyclohexylidene)ethanol, (Z)-(3,3-dimethylcyclohexylidene)acetaldehyde, (E)-(3,3-dimethylcyclohexylidene)acetaldehyde, (E)-3,7-dimethyl-2,6-octadienoic acid (geranic acid), and (E)-3,7-dimethyl-2,6-octadien-1-ol (geraniol). The emission rates of these compounds from feeding males were determined to be about: 7.2, 4.8, 0.45, 0.30, 2.0, and 0.30µg/male/day, respectively. Sticky traps baited with a synthetic blend of these compounds captured more pepper weevils (both sexes) than did unbaited control traps or pheromone-baited boll weevil traps. Commercial and laboratory formulations of the synthetic pheromone were both attractive. However, the commercial formulation did not release geranic acid properly, and geranic acid is necessary for full activity. The pheromones of the pepper weevil and the boll weevil are compared. Improvements for increasing trap efficiency and possible uses for the pepper weevil pheromone are discussed. A convenient method for purifying geranic acid is also described.