Comparison of two multi-trait association testing methods and sequence-based fine mapping of six additive QTL in Swiss Large White pigs

BACKGROUND

Genetic correlations between complex traits suggest that pleiotropic variants contribute to trait variation. Genome-wide association studies (GWAS) aim to uncover the genetic underpinnings of traits. Multivariate association testing and the meta-analysis of summary statistics from single-trait GWAS enable detecting variants associated with multiple phenotypes. In this study, we used array-derived genotypes and phenotypes for 24 reproduction, production, and conformation traits to explore differences between the two methods and used imputed sequence variant genotypes to fine-map six quantitative trait loci (QTL).

RESULTS

We considered genotypes at 44,733 SNPs for 5,753 pigs from the Swiss Large White breed that had deregressed breeding values for 24 traits. Single-trait association analyses revealed eleven QTL that affected 15 traits. Multi-trait association testing and the meta-analysis of the single-trait GWAS revealed between 3 and 6 QTL, respectively, in three groups of traits. The multi-trait methods revealed three loci that were not detected in the single-trait GWAS. Four QTL that were identified in the single-trait GWAS, remained undetected in the multi-trait analyses. To pinpoint candidate causal variants for the QTL, we imputed the array-derived genotypes to the sequence level using a sequenced reference panel consisting of 421 pigs. This approach provided genotypes at 16 million imputed sequence variants with a mean accuracy of imputation of 0.94. The fine-mapping of six QTL with imputed sequence variant genotypes revealed four previously proposed causal mutations among the top variants.

CONCLUSIONS

Our findings in a medium-size cohort of pigs suggest that multivariate association testing and the meta-analysis of summary statistics from single-trait GWAS provide very similar results. Although multi-trait association methods provide a useful overview of pleiotropic loci segregating in mapping populations, the investigation of single-trait association studies is still advised, as multi-trait methods may miss QTL that are uncovered in single-trait GWAS.

Exploring barriers to vaccine delivery in adult migrants: a qualitative study in primary care

Background

The COVID-19 pandemic has highlighted shortfalls in the delivery of vaccine programmes to older migrant groups. Guidelines exist, however, little is known around care pathways and engagement of these older cohorts in routine vaccinations in primary care, including catch-up programmes. We explored the views of primary care professionals around barriers and facilitators to catch-up vaccination in adult migrants (defined as foreign born; 18+ years) with incomplete or uncertain vaccination status.

Methods

We did a qualitative interview study with purposive sampling and thematic analysis in UK primary care (50 practices included nationally; 1 hour qualitative interviews) with 64 primary care professionals (PCPs): 48 clinical staff including GPs, Practice Nurses and healthcare assistants (HCAs); 16 administrative staff including practice managers and receptionists (mean age 45 years; 84.4% female; a range of ethnicities).

Results

Participants highlighted direct and indirect barriers to catch-up vaccines in adult migrants who may have missed vaccines as children, missed boosters, and not be aligned with the UK's vaccine schedule, from both a personal and service-delivery level, with themes including: lack of training and knowledge of guidance around catch-up vaccination among staff; unclear or incomplete vaccine records; and lack of incentivization (including financial reimbursement) and dedicated time and care pathways. Adult migrants were reported as being excluded from many vaccination initiatives, most of which focus exclusively on children. PCPs noted that migrants expressed to them a range of views around vaccines, from positivity to uncertainty, to refusal.

Conclusions

Vaccine uptake in adult migrants could be improved through implementing new financial incentives, strengthening care pathways and training, and working directly with local community groups to improve understanding around the benefits of vaccination at all ages.

Key messages

Clinical correlation and assessment of olfactory dysfunction with n-butanol in COVID-19 patients: our experience

Background: Studies showed olfactory disturbances in COVID patients. This has attracted focus of clinicians as an easy clinical screening tool in suspected population. Material and methods: 70 mild and moderate category COVID-19 RT-PCR positive patients, more than 10 years of age were tested on day of admission for olfaction with serial dilution of n-butanol and asked to grade severity of their olfactory dysfunction according to visual analogue score from 1-10. Results: Fatigue 42 (93.33%), sore throat 37 (82.22%), fever 36 (80%) and dyspnea 23 (51.11%) were the most common symptoms in moderate patients. Diabetes, hypertension and allergy were the three prominent risk factors. At time of admission, n-butanol diagnosed 20 patients having olfactory dysfunction compared to 11 by VAS. Patients tend to grade their dysfunction higher on VAS whereas the n-butanol test classified their olfactory dysfunction lower. Viral load and high CRP were not found to be significantly related with olfactory dysfunction. d-Dimer and LDH levels were found statistically associated with higher grading of olfactory dysfunction detected by n-butanol. Conclusion: The majority of cases developed hyposmia before they were admitted to hospital even before they realized that they were having hyposmia as revealed by n-butanol testing. We should go for objective tests of olfaction.

Characterisation and comparison of immune response mechanisms in an indigenous and a commercial pig breed after classical swine fever vaccination

The live attenuated classical swine fever (CSF) vaccine has been successfully used to prevent and control CSF outbreaks for 6 decades. However, the immune response mechanisms against the vaccine remain poorly understood. Moreover, very few reports exist regarding the breed differences in the response to CSF vaccine. In this study, we generated the peripheral blood mononuclear cell transcriptomes of indigenous Ghurrah and commercial Landrace pig breeds, before and 7 days after CSF vaccination. Subsequently, between and within-breed differential gene expression analyses were carried out. Results revealed large differences in pre-vaccination peripheral blood mononuclear cell transcriptome profiles of the two breeds, which were homogenised 7 days after vaccination. Before vaccination, gene set enrichment analysis showed that pathways related to antigen sensing and innate immune response were enriched in Ghurrah, while pathways related to adaptive immunity were enriched in Landrace. Ghurrah exhibited greater immunomodulation compared to Landrace following the vaccination. In Ghurrah, cell-cycle processes and T-cell response pathways were upregulated after vaccination. However, no pathways were upregulated in Landrace after vaccination. Pathways related to inflammation were downregulated in both the breeds after vaccination. Key regulators of inflammation such as IL1A, IL1B, NFKBIA and TNF genes were strongly downregulated in both the breeds after vaccination. Overall, our results have elucidated the mechanisms of host immune response against CSF vaccination in two distinct breeds and revealed common key genes instrumental in the global immune response to the vaccine.

Peritransplant eculizumab does not prevent delayed graft function in deceased donor kidney transplant recipients: Results of two randomized controlled pilot trials

Animal models and observational human data indicate that complement, including C5a, pathogenically participates in ischemia reperfusion (IR) injury that manifests as delayed graft function (DGF) following deceased donor kidney transplantation. We report on the safety/efficacy of anti-C5 monoclonal antibody eculizumab (Ecu) administered in the operating room prior to reperfusion, to prevent DGF in recipients of deceased donor kidney transplants in two related, investigator-sponsored, randomized controlled trials. Eight recipients from a single center were enrolled in a pilot study that led to a 19-subject multicenter trial. Together, 27 deceased donor kidney transplant recipients, 16 Ecu-treated and 11 controls, were treated with rabbit antithymocyte globulin, tacrolimus, mycophenolate mofetil with or without glucocorticoids, and followed for 6 months. Data analysis showed no epidemiological or transplant-related differences between study arms. Ecu was well tolerated with a similar severe adverse event incidence between groups. The DGF rate did not differ between Ecu-treated (44%) and control (45%, P = 1.0) subjects. Serum creatinine reduction in the first week after transplantation, and graft function up to 180-days post-transplant, were also similar. Ecu administration was safe but did not reduce the rate of DGF in a high-risk population of deceased donor recipients.

Measures of Neural Similarity

One fundamental question is what makes two brain states similar. For example, what makes the activity in visual cortex elicited from viewing a robin similar to a sparrow? One common assumption in fMRI analysis is that neural similarity is described by Pearson correlation. However, there are a host of other possibilities, including Minkowski and Mahalanobis measures, with each differing in its mathematical, theoretical, and neural computational assumptions. Moreover, the operable measures may vary across brain regions and tasks. Here, we evaluated which of several competing similarity measures best captured neural similarity. Our technique uses a decoding approach to assess the information present in a brain region, and the similarity measures that best correspond to the classifier’s confusion matrix are preferred. Across two published fMRI datasets, we found the preferred neural similarity measures were common across brain regions but differed across tasks. Moreover, Pearson correlation was consistently surpassed by alternatives.

Krüppel-like factor 4 is a negative regulator of STAT3-induced glomerular epithelial cell proliferation

Pathologic glomerular epithelial cell (GEC) hyperplasia is characteristic of both rapidly progressive glomerulonephritis (RPGN) and subtypes of focal segmental glomerulosclerosis (FSGS). Although initial podocyte injury resulting in activation of STAT3 signals GEC proliferation in both diseases, mechanisms regulating this are unknown. Here, we show that the loss of Krüppel-like factor 4 (KLF4), a zinc-finger transcription factor, enhances GEC proliferation in both RPGN and FSGS due to dysregulated STAT3 signaling. We observed that podocyte-specific knockdown of Klf4 (C57BL/6J) increased STAT3 signaling and exacerbated crescent formation after nephrotoxic serum treatment. Interestingly, podocyte-specific knockdown of Klf4 in the FVB/N background alone was sufficient to activate STAT3 signaling, resulting in FSGS with extracapillary proliferation, as well as renal failure and reduced survival. In cultured podocytes, loss of KLF4 resulted in STAT3 activation and cell-cycle reentry, leading to mitotic catastrophe. This triggered IL-6 release into the supernatant, which activated STAT3 signaling in parietal epithelial cells. Conversely, either restoration of KLF4 expression or inhibition of STAT3 signaling improved survival in KLF4-knockdown podocytes. Finally, human kidney biopsy specimens with RPGN exhibited reduced KLF4 expression with a concomitant increase in phospho-STAT3 expression as compared with controls. Collectively, these results suggest the essential role of KLF4/STAT3 signaling in podocyte injury and its regulation of aberrant GEC proliferation.

Telenephrology: Providing Healthcare to Remotely Located Patients with Chronic Kidney Disease

BACKGROUND

Chronic kidney disease (CKD) patients who live far (>30 miles) from their nephrologist experience lower rates of clinic visit adherence, limited access to treatment, and higher rates of hospitalization and mortality than patients who live in close proximity to their nephrologist. Strategies to minimize disparities between urban and remotely located CKD patients are needed. The purpose of this study was to determine whether adherence to clinic visits and clinical outcomes in the remote management of CKD via telenephrology is comparable to in-person conventional care.

METHODS

Renal clinic adherence and composite outcomes of death, end-stage renal disease (ESRD), or doubling of serum creatinine (Cr) were measured in geographically remote Hudson Valley VA Medical Center (HVVAMC) CKD patients enrolled in telenephrology (n = 112) and CKD patients enrolled in the Bronx VAMC renal clinic (n = 116).

RESULTS

Prior to implementing the telenephrology service, 53.1% of scheduled visits of rural HVVAMC patients to the Bronx VAMC renal clinic were either cancelled or were "no-shows." This was reduced by nearly half (28.5%) after instituting telenephrology (p < 0.001). Moreover, the frequency of attending appointments was greater in the telenephrology (71.9%) vs. in-person Bronx VA cohort (61.0%). The incidence of the composite outcome of death, ESRD, or doubling of Cr was similar between both groups (p = 0.96) over 2 years of follow-up.

CONCLUSIONS

Remote CKD care delivered through telenephrology improves renal clinic visit adherence while delivering comparable renal outcomes. Application of this technology is a promising method to provide access to care to rural CKD patients and to minimize the disparity between urban/rural patients.

A systematic review of left unilateral electroconvulsive therapy

OBJECTIVE

To systematically review the published clinical trials, case series, and case reports on left unilateral (LUL) electrode placement for clinical electroconvulsive therapy (ECT).

METHOD

PubMed, Ovid Medline, and the Cochrane Library were searched for articles concerning LUL ECT. Number of patients, efficacy, and cognitive outcomes were extracted from the papers that met our inclusion criteria.

RESULTS

A total of 52 articles were included in this review, consisting of 33 clinical trials, seven case series, and 12 case reports.

CONCLUSION

Overall, the efficacy of LUL electrode placement for the treatment of depression and psychosis is similar to that of right unilateral (RUL) and bilateral (BL) electrode placements. Patients receiving LUL ECT tend to experience more verbal memory impairment than patients receiving RUL ECT, but less verbal impairment than patients receiving BL ECT. In contrast, patients receiving LUL ECT tended to experience the least visual and nonverbal memory impairment, compared to patients receiving RUL or BL ECT.

Who and how in the regulation of mitochondrial cristae shape and function

Mitochondrial adaptation to different physiological conditions highly relies on the regulation of mitochondrial ultrastructure, particularly at the level of cristae compartment. Cristae represent the membrane hub where most of the respiratory complexes embed to account for OXPHOS and energy production in the form of adenosine triphosphate (ATP). Changes in cristae number and shape define the respiratory capacity as well as cell viability. The identification of key regulators of cristae morphology and the understanding of their contribution to the mitochondrial ultrastructure and function have become an strategic goal to understand mitochondrial disorders and to exploit as therapeutic targets. This review summarizes the known regulators of cristae ultrastructure and discusses their contribution and implications for mitochondrial dysfunction.

A Retrospective Study in Adults with Metabolic Syndrome: Diabetic Risk Factor Response to Daily Consumption of Agaricus bisporus (White Button Mushrooms)

Adults with metabolic syndrome from different race/ethnicities are often predisposed to developing type 2 diabetes (T2D); however, growing evidence suggests that healthy diets and lifestyle choices can significantly slow or prevent progression to T2D. This poorly understood relationship to healthy dietary patterns and prevention of T2D motivated us to conduct a retrospective analysis to determine the potential impact of a minor dietary lifestyle change (daily mushroom consumption) on known T2D risk factors in racially diverse adults with confirmed features of the metabolic syndrome. Retrospectively, we studied 37 subjects who had participated in a dietary intervention focused on vitamin D bioavailability from white button mushrooms (WBM). All 37 had previously completed a 16-week study where they consumed 100 g of WBM daily and were then followed-up for one month during which no mushrooms were consumed. We analyzed differences in serum risk factors from baseline to 16-week, and from baseline to one-month follow-up. Measurement of serum diabetic risk factors included inflammatory and oxidative stress markers and the antioxidant component naturally rich in mushrooms, ergothioneine. Significant beneficial health effects were observed at 16-week with the doubling of ergothioneine from baseline, increases in the antioxidant marker ORAC (oxygen radical absorption capacity) and anti-inflammatory hormone, adiponectin and significant decreases in serum oxidative stress inducing factors, carboxymethyllysine (CML) and methylglyoxal (MG), but no change in the lipid oxidative stress marker 8-isoprostane, leptin or measures of insulin resistance or glucose metabolism. We conclude that WBM contain a variety of compounds with potential anti-inflammatory and antioxidant health benefits that can occur with frequent consumption over time in adults predisposed to T2D. Well-controlled studies are needed to confirm these findings and identify the specific mushroom components beneficial to health.

Timing of Pregnancy After Kidney Transplantation and Risk of Allograft Failure

The optimal timing of pregnancy after kidney transplantation remains uncertain. We determined the risk of allograft failure among women who became pregnant within the first 3 posttransplant years. Among 21 814 women aged 15-45 years who received a first kidney-only transplant between 1990 and 2010 captured in the United States Renal Data System, n = 729 pregnancies were identified using Medicare claims. The probability of allograft failure from any cause including death (ACGL) at 1, 3, and 5 years after pregnancy was 9.6%, 25.9%, and 36.6%. In multivariate analyses, pregnancy in the first posttransplant year was associated with an increased risk of ACGL (hazard ratio [HR]: 1.18; 95% confidence interval [CI] 1.00, 1.40) and death censored graft loss (DCGL) (HR:1.25; 95% CI 1.04, 1.50), while pregnancy in the second posttransplant year was associated with an increased risk of DCGL (HR: 1.26; 95% CI 1.06, 1.50). Pregnancy in the third posttransplant year was not associated with an increased risk of ACGL or DCGL. These findings demonstrate a higher incidence of allograft failure after pregnancy than previously reported and that the increased risk of allograft failure extends to pregnancies in the second posttransplant year.

Krüppel-Like Factor 15 Mediates Glucocorticoid-Induced Restoration of Podocyte Differentiation Markers

Podocyte injury is the inciting event in primary glomerulopathies, such as minimal change disease and primary FSGS, and glucocorticoids remain the initial and often, the primary treatment of choice for these glomerulopathies. Because inflammation is not readily apparent in these diseases, understanding the direct effects of glucocorticoids on the podocyte, independent of the immunomodulatory effects, may lead to the identification of targets downstream of glucocorticoids that minimize toxicity without compromising efficacy. Several studies showed that treatment with glucocorticoids restores podocyte differentiation markers and normal ultrastructure and improves cell survival in murine podocytes. We previously determined that Krüppel-like factor 15 (KLF15), a kidney-enriched zinc finger transcription factor, is required for restoring podocyte differentiation markers in mice and human podocytes under cell stress. Here, we show that in vitro treatment with dexamethasone induced a rapid increase of KLF15 expression in human and murine podocytes and enhanced the affinity of glucocorticoid receptor binding to the promoter region of KLF15 In three independent proteinuric murine models, podocyte-specific loss of Klf15 abrogated dexamethasone-induced podocyte recovery. Furthermore, knockdown of KLF15 reduced cell survival and destabilized the actin cytoskeleton in differentiated human podocytes. Conversely, overexpression of KLF15 stabilized the actin cytoskeleton under cell stress in human podocytes. Finally, the level of KLF15 expression in the podocytes and glomeruli from human biopsy specimens correlated with glucocorticoid responsiveness in 35 patients with minimal change disease or primary FSGS. Thus, these studies identify the critical role of KLF15 in mediating the salutary effects of glucocorticoids in the podocyte.

Decontamination of heavy metal laden sewage sludge with simultaneous solids reduction using thermophilic sulfur and ferrous oxidizing species

A possibility of using simultaneous sewage sludge digestion and metal leaching (SSDML) process at the thermophilic temperature to remove heavy metals and suspended solids from sewage sludge is explored in this study. Though thermophilic sludge digestion efficiently produces a stable sludge, its inability to remove heavy metals requires it to be used in tandem with another process like bioleaching for metal reduction. Previously, different temperature optima were known for the heterotrophs (thermophilic) responsible for the sludge digestion and the autotrophs involved in bioleaching (mesophilic), because of which the metal concentration was brought down separately in a different reactor. In our study, SSDML process was carried out at 50 °C (thermophilic) by using ferrous sulfate (batch-1) and sulfur (batch-2) as the energy source in two reactors. The concentration of volatile suspended solids reduced by >40% in both batches, while that of heavy metals zinc, copper, chromium, cadmium and nickel decreased by >50% in both batch-1 and batch-2. Lead got leached out only in batch-1. Using 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis analysis, Alicyclobacillus tolerans was found to be the microorganism responsible for lowering the pH in both the reactors at thermophilic temperature. The indicator organism count was also below the maximum permissible limit making sludge suitable for agricultural use. Our results indicate that SSDML at thermophilic temperature can be effectively used for reduction of heavy metals and suspended solids from sewage sludge.

Getting England to be more physically active: are the Public Health Responsibility Deal's physical activity pledges the answer?

BACKGROUND

The Public Health Responsibility Deal (RD) in England is a public-private partnership involving voluntary pledges between government, industry, and other organisations to improve public health by addressing alcohol, food, health at work, and physical activity. This paper analyses the RD physical activity (PA) pledges in terms of the evidence of their potential effectiveness, and the likelihood that they have motivated actions among organisations that would not otherwise have taken place.

METHODS

We systematically reviewed evidence of the effectiveness of interventions proposed in four PA pledges of the RD, namely, those on physical activity in the community; physical activity guidelines; active travel; and physical activity in the workplace. We then analysed publically available data on RD signatory organisations' plans and progress towards achieving the physical activity pledges, and assessed the extent to which activities among organisations could be attributed to the RD.

RESULTS

Where combined with environmental approaches, interventions such as mass media campaigns to communicate the benefits of physical activity, active travel in children and adults, and workplace-related interventions could in principle be effective, if fully implemented. However, most activities proposed by each PA pledge involved providing information or enabling choice, which has limited effectiveness. Moreover, it was difficult to establish the extent of implementation of pledges within organisations, given that progress reports were mostly unavailable, and, where provided, it was difficult to ascertain their relevance to the RD pledges. Finally, 15 % of interventions listed in organisations' delivery plans were judged to be the result of participation in the RD, meaning that most actions taken by organisations were likely already under way, regardless of the RD.

CONCLUSIONS

Irrespective of the nature of a public health policy to encourage physical activity, targets need to be evidence-based, well-defined, measurable and encourage organisations to go beyond business as usual. RD physical activity targets do not adequately fulfill these criteria.

"Out of Sight, Out of Mind": The Failed Renal Allograft as a Cause of ESA Resistance

Approximately 10% of patients treated with erythropoiesis‐stimulating agents (ESAs) for the anemia of chronic kidney disease are unresponsive or relatively resistant to therapy. The etiology of this is usually linked to iron deficiency or an independent underlying illness. We describe a hemodialysis patient with a failed renal transplant 1.5 years earlier, who developed progressive erythropoietin resistance and anemia without an apparent cause. He simultaneously developed nonspecific malaise and fatigue. By exclusion, the only possible cause of these signs and symptoms was inflammation from acute and chronic rejection in the retained failed renal allograft. Following pulse steroids and transplant nephrectomy, the patient's symptoms resolved and both his hemoglobin improved and his erythropoietin requirements decreased significantly. The patient never required a blood transfusion and was successfully relisted for a deceased donor renal transplant. Hence, inflammation from a retained transplant allograft may be an under‐recognized cause of erythropoietin resistance in dialysis patients. Although transplant nephrectomy remains a controversial practice due to concerns of alloantibody production, it may be considered in patients with failed renal allografts and anemia refractory to treatment with ESAs.

Nutritional vitamin D supplementation and health-related outcomes in hemodialysis patients: a protocol for a systematic review and meta-analysis

BACKGROUND

The prevalence of vitamin D deficiency in hemodialysis patients is high. While most hemodialysis patients are treated with activated vitamin D (1,25[OH]2D) to prevent renal osteodystrophy, clinical practices of the screening and treatment of 25(OH)2D deficiency are highly variable. It is unclear if nutritional vitamin D supplementation with D2 or D3 provides an additional clinical benefit beyond that provided by activated vitamin D treatment in this population.

METHODS/DESIGN

We will conduct a systematic review of nutritional vitamin D (D2/D3) supplementation and health-related outcomes in hemodialysis patients according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The primary objective is to assess the impact of nutritional vitamin D supplementation on clinical outcomes relevant in hemodialysis patients, such as mortality, cardiovascular events, infections, and fractures. Secondary outcomes will include anemia, hyperparathyroidism, medication use (erythrocyte-stimulating agents, activated vitamin D), and quality of life. We will search MEDLINE, Scopus, Web of Science, and ClinicalTrials.gov for randomized, controlled trials of nutritional vitamin D supplementation (ergocalciferol/D2 or cholecalciferol/D3) in chronic hemodialysis patients. The Cochrane Risk Assessment Tool will be used to assess the quality of eligible studies. We will perform meta-analyses using standard techniques for the outcomes listed above if pooling is deemed appropriate/sufficient. The results of this systematic review may highlight gaps in our knowledge of the relevance of nutritional vitamin D in end-stage renal disease, allowing for the informed design of clinical trials assessing the impact of nutritional vitamin D therapy in the hemodialysis population in the future.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO CRD42014013931.

Assessment and management of hypertension in transplant patients

Hypertension in renal transplant recipients is common and ranges from 50% to 80% in adult recipients and from 47% to 82% in pediatric recipients. Cardiovascular morbidity and mortality and shortened allograft survival are important consequences of inadequate control of hypertension. In this review, we examine the epidemiology, pathophysiology, and management considerations of post-transplant hypertension. Donor and recipient factors, acute and chronic allograft injury, and immunosuppressive medications may each explain some of the pathophysiology of post-transplant hypertension. As observed in other patient cohorts, renal artery stenosis and adrenal causes of hypertension may be important contributing factors. Notably, BP treatment goals for renal transplant recipients remain an enigma because there are no adequate randomized controlled trials to support a benefit from targeting lower BP levels on graft and patient survival. The potential for drug-drug interactions and altered pharmacokinetics and pharmacodynamics of the different antihypertensive medications need to be carefully considered. To date, no specific antihypertensive medications have been shown to be more effective than others at improving either patient or graft survival. Identifying the underlying pathophysiology and subsequent individualization of treatment goals are important for improving long-term patient and graft outcomes in these patients.

SWI/SNF chromatin remodeling enzymes in melanocyte differentiation and melanoma

Epidermal melanocytes are pigment-producing cells derived from the neural crest that protects skin from the damaging effects of solar radiation. Malignant melanoma, a highly aggressive cancer, arises from melanocytes. SWI/SNF enzymes are multiprotein complexes that remodel chromatin structure and have extensive roles in cellular differentiation. Components of the complex have been found to be mutated or lost in several human cancers. This review focuses on studies that implicate SWI/SNF enzymes in melanocyte differentiation and in melanoma.

Monitoring T cell alloreactivity

Currently, immunosuppressive therapy in kidney transplant recipients is center-specific, protocol-driven, and adjusted according to functional or histological evaluation of the allograft and/or signs of drug toxicity or infection. As a result, a large fraction of patients receive too much or too little immunosuppression, exposing them to higher rates of infection, malignancy and drug toxicity, or increased risk of acute and chronic graft injury from rejection, respectively. The individualization of immunosuppression requires the development of assays able to reliably quantify and/or predict the magnitude of the recipient's immune response toward the allograft. As alloreactive T cells are central mediators of allograft rejection, monitoring T cell alloreactivity has become a priority for the transplant community. Among available assays, flow cytometry based phenotyping, T cell proliferation, T cell cytokine secretion, and ATP release (ImmuKnow), have been the most thoroughly tested. While numerous cross-sectional studies have found associations between the results of these assays and the presence of clinically relevant post-transplantation outcomes, data from prospective studies are still scanty, thereby preventing widespread implementation in the clinic. Future studies are required to test the hypothesis that tailoring immunosuppression on the basis of results offered by these biomarkers leads to better outcomes than current standard clinical practice.

The Kidney Donor Profile Index (KDPI) of marginal donors allocated by standardized pretransplant donor biopsy assessment: distribution and association with graft outcomes

Pretransplant donor biopsy (PTDB)-based marginal donor allocation systems to single or dual renal transplantation could increase the use of organs with Kidney Donor Profile Index (KDPI) in the highest range (e.g. >80 or >90), whose discard rate approximates 50% in the United States. To test this hypothesis, we retrospectively calculated the KDPI and analyzed the outcomes of 442 marginal kidney transplants (340 single transplants: 278 with a PTDB Remuzzi score<4 [median KDPI: 87; interquartile range (IQR): 78-94] and 62 with a score=4 [median KDPI: 87; IQR: 76-93]; 102 dual transplants [median KDPI: 93; IQR: 86-96]) and 248 single standard transplant controls (median KDPI: 36; IQR: 18-51). PTDB-based allocation of marginal grafts led to a limited discard rate of 15% for kidneys with KDPI of 80-90 and of 37% for kidneys with a KDPI of 91-100. Although 1-year estimated GFRs were significantly lower in recipients of marginal kidneys (-9.3, -17.9 and -18.8 mL/min, for dual transplants, single kidneys with PTDB score<4 and =4, respectively; p<0.001), graft survival (median follow-up 3.3 years) was similar between marginal and standard kidney transplants (hazard ratio: 1.20 [95% confidence interval: 0.80-1.79; p=0.38]). In conclusion, PTDB-based allocation allows the safe transplantation of kidneys with KDPI in the highest range that may otherwise be discarded.

Immunosuppressive effects of erythropoietin on human alloreactive T cells

Correction of anemia with erythropoietin (EPO) is associated with improved kidney transplant outcomes. Emerging evidence, predominantly from animal models, indicates that these observations may be erythropoiesis-independent and that EPO exhibits immunosuppressive properties. We examined the effects of EPO on human T-cell alloimmunity by first documenting that CD4(+) and CD8(+) T cells express EPO receptor (EPO-R) on their surfaces. In mixed lymphocyte reactions, EPO induced a dose-dependent decrease in allogeneic CD4(+) T-cell proliferation (EPO 1000 U/ml: 44.6%±22.9% of vehicle, P<0.05; 2000 U/ml: 11.1%±4% of vehicle, P<0.001) without inducing cell death. The effects required signals transmitted directly through the EPO-R expressed on T cells, resulting in diminished Th1 differentiation without effects on regulatory T-cell induction. Mechanistic studies revealed that EPO prevented IL-2-induced proliferation by uncoupling IL-2 receptor signaling, inhibiting phosphorylation of the intracellular intermediaries AKT and extracellular signal-regulated kinase that are known to mediate T-cell expansion. EPO treatment reduced expansion of human naïve CD4(+) T cells after adoptive transfer into NOD scid γc(null) mouse recipients, verifying the effects in vivo. Although activated T cells expressed CD131, an alternative EPO receptor, addition of a specific CD131 agonist peptide, ARA290, did not alter T-cell proliferation or cytokine production. Our findings link EPO-R signaling on T cells to inhibition of T-cell immunity, providing one mechanism that could explain the observed protective effects of EPO in kidney transplant recipients.

Diabetic nephropathy in a nonobese mouse model of type 2 diabetes mellitus

A large body of research has contributed to our understanding of the pathophysiology of diabetic nephropathy. Yet, many questions remain regarding the progression of a disease that accounts for nearly half the patients entering dialysis yearly. Several murine models of diabetic nephropathy secondary to Type 2 diabetes mellitus (T2DM) do exist, and some are more representative than others, but all have limitations. In this study, we aimed to identify a new mouse model of diabetic nephropathy secondary to T2DM in a previously described T2DM model, the MKR (MCK-KR-hIGF-IR) mouse. In this mouse model, T2DM develops as a result of functional inactivation of insulin-like growth factor-1 receptor (IGF-1R) in the skeletal muscle. These mice are lean, with marked insulin resistance, hyperinsulinemia, hyperglycemia, and dyslipidemia and thus are representative of nonobese human T2DM. We show that the MKR mice, when under stress (high-fat diet or unilateral nephrectomy), develop progressive diabetic nephropathy with marked albuminuria and meet the histopathological criteria as defined by the Animal Models of Diabetic Complications Consortium. Finally, these MKR mice are fertile and are on a common background strain, making it a novel model to study the progression of diabetic nephropathy.

Low Dietary Intake of Vitamin D and Vitamin D Deficiency in Hemodialysis Patients

BACKGROUND

The purpose of this study was to test the hypothesis that decreased dietary intake of Vitamin D contributes to Vitamin D deficiency in end-stage renal disease (ESRD) patients on hemodialysis (HD).

METHODS

We performed a cross-sectional study of 58 hemodialysis outpatients from two Mount Sinai Medical Center (MSMC)-affiliated outpatient HD units in New York City and 648 outpatients at MSMC with CKD stages I-IV. Serum 25(OH)D concentrations were measured from August 2010 to July of 2011 in recruited hemodialysis patients (n=58) and linked with results of dietary and lifestyle surveys. The Mount Sinai Data Warehouse (electronic medical record) was used to capture 25(OH) Vitamin D levels for outpatients with CKD stages I-IV who had Vitamin D testing during the same time period.

RESULTS

The prevalence of Vitamin D insufficiency/deficiency in the HD cohort was 96.6%. Mean (SD) and median (IQR) 25(OH)D concentrations were 15.65 (6.82) and 13.55 (10.15) ng/mL, respectively. Dietary surveys showed a median weekly Vitamin D intake of 1044 IU (IQR=808, vs. a recommended weekly allowance of 4200 IU) and specific avoidance of foods containing both Vitamin D and phosphorus. In contrast, mean and median 25(OH)D concentrations in patients with CKD stages I-IV were 25.66 (13.44) and 23.60 (15.48) ng/mL (p<0.001 vs. HD patients).

CONCLUSIONS

Vitamin D deficiency is more prevalent in HD patients than in pre-dialysis patients with CKD and is associated with decreased dietary intake of Vitamin D. Dialysis restrictions imposed to reduce dietary phosphorus intake likely contributes to the development of hypovitaminosis D in ESRD patients.

The association of IL28B polymorphism and graft survival in patients with hepatitis C undergoing liver transplantation

Hepatitis C virus (HCV) infection is the leading cause of liver transplantation (LT) in Western countries. Polymorphism in the IL28B gene region has a major impact on the natural history and response to antiviral treatment in HCV. We investigated whether IL28B polymorphism was associated with graft survival in patients with or without HCV undergoing LT. 1,060 adult patients (age >18 years) underwent LT between years 2000 and 2008. Patients with previous LT, living donor LT and patients dying or requiring retransplants within 30 days of LT were excluded. DNA samples of 620 (84%) recipients and 377 (51%) donors were available for genotyping of IL28B rs12979860C>T. Donor IL28B genotypes had no significant differences in graft survival irrespective of HCV status. There was no difference in graft outcome in the non-HCV cohort (n = 293) based on recipient IL28B genotype. In the HCV group (n = 327), recipients with CC or CT genotype had better graft survival compared to TT genotype (62% vs. 48%, p = 0.02). HCV recipients with CC or CT genotype had delayed time to clinically relevant HCV recurrence compared to TT (10.4 vs. 6.7 months, p = 0.002). The beneficial effect of the CC/CT genotype on HCV recurrence and graft survival was independent of antiviral treatment. In conclusion, our study demonstrated that in contrast to donor IL28B genotype recipient IL28B was associated with graft survival and clinically relevant HCV recurrence in HCV infected recipients. No effect of IL28B genotype was manifest in non-HCV LT recipients.

Congenital paediatric atlantoaxial dislocation: clinico-radiological profile and surgical outcome

INTRODUCTION

Congenital atlantoaxial dislocation (AAD) is the most common bony abnormality affecting the craniovertebral junction. The paediatric population has specific problems like preoperative diagnostic difficulties, precise neurological examination, radiological diagnosis, surgical problems including physical fitness to tolerate surgery (including problems of anaesthesia), technical difficulties in surgery and problems related to immobilization.

MATERIAL AND METHODS

A total of 229 consecutive paediatric (≤18 years) patients of AAD visited our centre from the period of January 1997 to August 2011. Twenty-nine cases were excluded from the study as these cases were diagnosed as CVJ tuberculosis, 31 cases were excluded as they were traumatic and the remaining 169 cases were retrospectively analysed. These patients were operated by a single experienced surgeon (the senior author) at the Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow. The preoperative and the postoperative clinical evaluation of the patient was done by the Kumar and Kalra myelopathic scoring system. The score was recorded in the preoperative period, at the time of discharge, at 3 months follow-up and at 6 months follow-up.

RESULTS

Ninety-four were males and 75 were females. The age range was 4 to 18 years with mean age 9.96±3.78 years. The follow-up ranged from 3 to 120 months with mean follow-up being 39.03±13.38 months. One hundred five cases were of fixed/irreducible AAD, and 64 were cases of mobile/reducible AAD. Majority of these cases presented with features of pyramidal tract involvement, and 108 cases had compromised pulmonary function test. One hundred thirty-seven cases had improved outcome, and 18 cases were in the same grade in the postoperative period with only 14 cases either deteriorated or died.

CONCLUSIONS

Congenital paediatric AAD are a different subset of abnormalities and have a satisfactory outcome. Preoperative evaluation must also include identification of various syndromes associated with paediatric AAD and respiratory reserve. Cormack-Lehane grade can be helpful in selecting borderline cases for postoperative need of tracheostomy. Majority of the cases have a good outcome, and therefore, surgery should be offered even in severe grade.

Deterministic characterization of phase noise in biomolecular oscillators

On top of the many external perturbations, cellular oscillators also face intrinsic perturbations due the randomness of chemical kinetics. Biomolecular oscillators, distinct in their parameter sets or distinct in their architecture, show different resilience with respect to such intrinsic perturbations. Assessing this resilience can be done by ensemble stochastic simulations. These are computationally costly and do not permit further insights into the mechanistic cause of the observed resilience. For reaction systems operating at a steady state, the linear noise approximation (LNA) can be used to determine the effect of molecular noise. Here we show that methods based on LNA fail for oscillatory systems and we propose an alternative ansatz. It yields an asymptotic expression for the phase diffusion coefficient of stochastic oscillators. Moreover, it allows us to single out the noise contribution of every reaction in an oscillatory system. We test the approach on the one-loop model of the Drosophila circadian clock. Our results are consistent with those obtained through stochastic simulations with a gain in computational efficiency of about three orders of magnitude.

Anticardiac myosin immunity and chronic allograft vasculopathy in heart transplant recipients

Chronic allograft vasculopathy (CAV) contributes to heart transplant failure, yet its pathogenesis is incompletely understood. Although cellular and humoral alloimmunity are accepted pathogenic mediators, animal models suggest that T cells and Abs reactive to graft-expressed autoantigens, including cardiac myosin (CM), could participate. To test the relationship between CAV and anti-CM autoimmunity in humans, we performed a cross-sectional study of 72 heart transplant recipients: 40 with CAV and 32 without. Sera from 65% of patients with CAV contained anti-CM Abs, whereas <10% contained Abs to other autoantigens (p < 0.05), and only 18% contained anti-HLA Abs (p < 0.05 versus anti-CM). In contrast, 13% of sera from patients without CAV contained anti-CM Abs (p < 0.05; odds ratio [OR], associating CAV with anti-CM Ab = 13, 95% confidence interval [CI] 3.79-44.6). Multivariable analysis confirmed the association to be independent of time posttransplant and the presence of anti-HLA Abs (OR = 28, 95% CI 5.77-133.56). PBMCs from patients with CAV responded more frequently to, and to a broader array of, CM-derived peptides than those without CAV (p = 0.01). Detection of either CM-peptide-reactive T cells or anti-CM Abs was highly and independently indicative of CAV (OR = 45, 95% CI 4.04-500.69). Our data suggest detection of anti-CM immunity could be used as a biomarker for outcome in heart transplantation recipients and support the need for further studies to assess whether anti-CM immunity is a pathogenic mediator of CAV.

Antibodies reactive to non-HLA antigens in transplant glomerulopathy

Although T and B cell alloimmunity contribute to transplant injury, autoimmunity directed at kidney-expressed, non-HLA antigens may also participate. Because the specificity, prevalence, and importance of antibodies to non-HLA antigens in late allograft injury are poorly characterized, we used a protein microarray to compare antibody repertoires in pre- and post-transplant sera from several cohorts of patients with and without transplant glomerulopathy. Transplantation routinely induced changes in antibody repertoires, but we did not identify any de novo non-HLA antibodies common to patients with transplant glomerulopathy. The screening studies identified three reactivities present before transplantation that persisted after transplant and strongly associated with transplant glomerulopathy. ELISA confirmed that reactivity against peroxisomal-trans-2-enoyl-coA-reductase strongly associated with the development of transplant glomerulopathy in independent validation sets. In addition to providing insight into effects of transplantation on non-HLA antibody repertoires, these results suggest that pretransplant serum antibodies to peroxisomal-trans-2-enoyl-coA-reductase may predict prognosis in kidney transplantation.

Late post-transplant erythrocytosis in a hepatitis C-positive allograft recipient on sirolimus

Hematological complications in renal transplant recipients include anemia, leukopenia, and post-transplant erythrocytosis (PTE). There are numerous causes for these which include immunosuppressive drugs, viral infections, etc. We report here a hepatitis C (HCV)-positive case who developed PTE while receiving rapamycin. As both HCV infection and rapamycin through different mechanisms can produce anemia, this case report highlights the rarity of erythrocytosis.

Complement component C3 allotypes and outcomes in liver transplantation

The complement system has been implicated in the pathogenesis of liver diseases. Human complement component C3 (C3) exists as 2 allotypes, fast (F) and slow (S). We conducted a study to address the influence of these alleles on ischemia-reperfusion (IR) injury and graft survival in liver transplant recipients. Four hundred thirty patients receiving liver transplants from 2000 to 2004 were included. C3 allotypes of 296 donor-recipient pairs were determined and correlated with clinical outcomes. Four groups were analyzed according to the C3 genotype: C3 SS donor and recipient, C3 FS or C3 FF donor and C3 SS recipient, C3 SS donor and C3 FS or C3 FF recipient, and C3 FS or C3 FF donor and recipient. Baseline characteristics of the 4 groups were similar. The mean follow-up time was 4.3 +/- 2.2 years. The 4 groups had similar rates of IR injury (P = 0.16). The hazard ratios for liver allograft survival in the C3 SS donor and recipient group in comparison with the other 3 groups (C3 FS or C3 FF donor and C3 SS recipient, C3 SS donor and C3 FS or C3 FF recipient, and C3 FS or C3 FF donor and recipient) were not significantly different: 1.13 (P = 0.60), 0.99 (P = 0.97), and 1.02 (P = 0.95), respectively. In conclusion, donor and recipient C3 genotypes are not associated with liver transplantation outcomes.

Trastuzumab (Herceptin)-associated lung injury

We report a case of trastuzumab pneumonitis in a patient with metastatic breast cancer. Bronchoalveolar lavage showed marked neutrophilia. A CT scan of the chest showed diffuse ground-glass opacities. The patient was treated with corticosteroids with a partial response. Trastuzumab-associated pneumonitis is not well described, and data in the literature is sparse. We describe the clinical and radiographical findings of trastuzumab-associated pneumonitis.