Deep learning on electronic medical records identifies distinct subphenotypes of diabetic kidney disease driven by genetic variations in the Rho pathway

Kidney disease affects 50% of all diabetic patients; however, prediction of disease progression has been challenging due to inherent disease heterogeneity. We use deep learning to identify novel genetic signatures prognostically associated with outcomes. Using autoencoders and unsupervised clustering of electronic health record data on 1,372 diabetic kidney disease patients, we establish two clusters with differential prevalence of end-stage kidney disease. Exome-wide associations identify a novel variant in ARHGEF18, a Rho guanine exchange factor specifically expressed in glomeruli. Overexpression of ARHGEF18 in human podocytes leads to impairments in focal adhesion architecture, cytoskeletal dynamics, cellular motility, and RhoA/Rac1 activation. Mutant GEF18 is resistant to ubiquitin mediated degradation leading to pathologically increased protein levels. Our findings uncover the first known disease-causing genetic variant that affects protein stability of a cytoskeletal regulator through impaired degradation, a potentially novel class of expression quantitative trait loci that can be therapeutically targeted.

Derivation and validation of genome-wide polygenic score for urinary tract stone diagnosis

Urinary tract stones have high heritability indicating a strong genetic component. However, genome-wide association studies (GWAS) have uncovered only a few genome wide significant single nucleotide polymorphisms (SNPs). Polygenic risk scores (PRS) sum cumulative effect of many SNPs and shed light on underlying genetic architecture. Using GWAS summary statistics from 361,141 participants in the United Kingdom Biobank, we generated a PRS and determined association with stone diagnosis in 28,877 participants in the Mount Sinai BioMe Biobank. In BioMe (1,071 cases and 27,806 controls), for every standard deviation increase, we observed a significant increment in adjusted odds ratio of a factor of 1.2 (95% confidence interval 1.13-1.26). In comparison, a risk score comprised of GWAS significant SNPs was not significantly associated with diagnosis. After stratifying individuals into low and high-risk categories on clinical risk factors, there was a significant increment in adjusted odds ratio of 1.3 (1.12-1.6) in the low- and 1.2 (1.1-1.2) in the high-risk group for every standard deviation increment in PRS. In a 14,348-participant validation cohort (Penn Medicine Biobank), every standard deviation increment was associated with a significant adjusted odds ratio of 1.1 (1.03 - 1.2). Thus, a genome-wide PRS is associated with urinary tract stones overall and in the absence of known clinical risk factors and illustrates their complex polygenic architecture.

Early clinical experiences with nintedanib in three UK tertiary interstitial lung disease centres

Background

Nintedanib has been shown to slow disease progression in patients with idiopathic pulmonary fibrosis (IPF). It was approved by the National Institute for Health and Care Excellence (NICE) in January 2016 for IPF patients with a forced vital capacity (FVC) of 50–80% in the United Kingdom (UK).

Aim

To report real world data about our early clinical experience using nintedanib in 187 patients with a multi-disciplinary (MDT) diagnosis of IPF in a manufacturer funded patient in need scheme (three UK centres) prior to NICE approval.

Methods

All patients with a MDT diagnosis of IPF from December 2014 to January 2016 commenced on nintedanib were included. Demographic details, adverse events (AEs) and where available lung function results were retrospectively collected from clinical letters.

Results

187 patients (76% males) with a median age of 72 years (49–89) were treated with nintedanib. The average pre-treatment FVC was 81.1 ± 19.8% and diffusion capacity of the lungs for carbon monoxide was 43.9 ± 15% (n = 82). Fifty percent of patients started nintedanib because they were ineligible for pirfenidone due to an FVC > 80%. The median treatment course was 8 ± 4 months. The majority of patients experienced 1–3 AEs with nintedanib (52%, n = 97). The most frequent AEs were diarrhoea (50%), nausea (36%), reduced appetite (24%), tiredness (20%) and gastro-oesophageal reflux (18%). The majority of AEs resulted in no change in treatment (64%, n = 461). 21% (n = 150) of AEs resulted in a dose reduction and 13% (n = 94) necessitated discontinuation of treatment. 1 in 5 patients discontinued treatment either temporarily or on a permanent basis during the monitoring period. In a select cohort of patients, a statistically significant greater proportion of patients remained stable or improved and a lower proportion declined, as depicted by FVC changes of > 5% after nintedanib commencement (P < 0.05 using Chi squared test).

Conclusions

Nintedanib is well tolerated and has an acceptable safety profile. Only 8% of those reporting diarrhoea discontinued treatment either on a temporary or permanent basis. There were no signals with respect to increased cardiovascular morbidity or major bleeding risk. This is in keeping with the INPULSIS clinical trial findings but in a real world cohort.

Nontuberculous mycobacteria in gastrostomy fed patients with cystic fibrosis

Multi-drug resistant Mycobacterium abscessus complex (MABSC) is a form of Nontuberculous mycobacteria (NTM) of special, international concern in Cystic Fibrosis (CF). We hypothesised that gastric juice and percutaneous endoscopic gastrostomy (PEG) feeding devices might yield MABSC isolates. Gastric juice and sputa from sixteen adult PEG fed CF patients and five replaced PEG tubes were studied. Bacterial and fungal isolates were cultured. Mycobacterium were identified by rpoB, sodA and hsp65 gene sequencing and strain typed using variable number tandem repeat. Bacteria and/or fungi grew from all gastric juice, sputa and PEG samples. MABSC were detected in 7 patients. Five had MABSC in their sputum. Two had an identical MABSC strain in their sputum and gastric juice and one had the same strain isolated from their PEG tube and sputum. Two patients who were sputum sample negative had MABSC isolated in their gastric juice or PEG tube. MABSC were therefore identified for the first time from a gastric sample in a minority of patients. We conclude that gastric juice and PEG-tubes may be a potential source of MABSC isolates in CF patients, and these findings warrant further study.

Assessing the function of homologous recombination DNA repair in malignant pleural effusion (MPE) samples

Background:

Patients with malignant pleural effusions (MPEs) generally have advanced disease with poor survival and few therapeutic options. Cells within MPEs may be used to stratify patients for targeted therapy. Targeted therapy with poly(ADP ribose) polymerase inhibitors (PARPi) depends on identifying homologous recombination DNA repair (HRR)-defective cancer cells. We aimed to determine the feasibility of assaying HRR status in MPE cells.

Methods:

A total of 15 MPE samples were collected from consenting patients with non-small-cell lung cancer (NSCLC), mesothelioma and ovarian and breast cancer. Primary cultures were confirmed as epithelial by pancytokeratin, and HRR status was determined by the detection of γH2AX and RAD51 foci following a 24-h exposure to rucaparib, by immunofluorescence microscopy. Massively parallel next-generation sequencing of DNA repair genes was performed on cultured MPE cells.

Results:

From 15 MPE samples, 13 cultures were successfully established, with HRR function successfully determined in 12 cultures. Four samples – three NSCLC and one mesothelioma – were HRR defective and eight samples – one NSCLC, one mesothelioma, one sarcomatoid, one breast and four ovarian cancers – were HRR functional. No mutations in DNA repair genes were associated with HRR status, but there was probable loss of heterozygosity of FANCG, RPA1 and PARP1.

Conclusions:

HRR function can be successfully detected in MPE cells demonstrating the potential to stratify patients for targeted therapy with PARPi.

A study of the prevalence of systemic sclerosis in northeast England

OBJECTIVES

We aimed to obtain an estimate of the prevalence and demographics of systemic sclerosis (SSc) and its subtypes at the turn of the millennium.

METHODS

Case finding from multiple sources from a defined geographical area. Diagnosis confirmed by clinical examination.

RESULTS

The crude prevalence of SSc in northeast England was 8.8 (95% CI: 6.8-10.8) per 100,000. The prevalence when adjusted for the entire UK is 8.2 (95% CI: 6.2-9.8) per 100,000. The ratio of women to men was 5.2:1. The median age of patients was 57.1 yr. The ratio of limited cutaneous SSc to diffuse cutaneous SSc was 4.7:1. Limited cutaneous SSc is associated with the presence of anticentromere antibodies; diffuse cutaneous SSc is associated with anti-Scl 70 antibodies, but either antibody was found in either form of SSc.

CONCLUSIONS

SSc appears to be more common in northeast England than was found in the West Midlands in 1986. This may reflect changes in the diagnostic definition of SSc.

Preliminary findings of quorum signal molecules in clinically stable lung allograft recipients

BACKGROUND

Infection with bacteria such as Pseudomonas is common in lung allograft recipients, particularly during chronic rejection. Analysis of sputum samples from patients with cystic fibrosis infected with Pseudomonas aeruginosa or Burkholderia cepacia has indicated the presence of bacterial N-acylhomoserine lactones (AHLs) quorum sensing signalling molecules. AHLs not only control the expression of bacterial virulence genes but are also involved in stimulating the maturation of antibiotic resistant biofilms and host chemokine release. It was hypothesised that AHLs may be detected even in clinically stable lung transplant recipients free of clinical infection or rejection.

METHODS

Three 60 ml samples of bronchoalveolar lavage (BAL) fluid were taken from nine stable lung transplant recipients 3-12 months after transplantation. Detection of AHLs was carried out on dichloromethane extracted supernatants using the bioluminescence based AHL reporter plasmid pSB1075. This responds to the presence of AHLs with long acyl chains (C10-C14), generating light. Synthetic AHLs were included as positive controls.

RESULTS

Five of the nine BAL fluid supernatants exhibited AHL activity, suggesting the presence of AHLs with long N-acyl chains. There was no correlation between the levels of AHLs detected or their absence and BAL fluid microbiology or diagnosis before transplantation.

CONCLUSIONS

This is the first evidence for the presence of AHL quorum sensing signals in human lung allograft recipients, even in subjects with no rejection or apparent infection. Further longitudinal follow up of these preliminary findings is required to elucidate potential links with infection, rejection, and allograft deterioration.

The genetic structures of a range of Douglas-fir provenance collections after planting in different European countries, assessed with two biochemical marker systems

Genetic diversities of Douglas-fir provenance trials planted on several European sites were compared using both isozyme and terpene markers. A principal coordinate analysis based on similarity coefficients calculated from isozyme data indicated that, with the exception of two populations, differences between populations were small. There were no consistent trends in the variation in allele frequencies between populations. Most populations contained an excess of homozygotes, perhaps due to high selection pressure. Terpene composition was analysed in two resin systems, and showed a decreasing level of population diversity by planting site in the order: Spain-France-England-Scotland-Italy. Thus isozymes, which are generally considered to be neutral markers, indicated a modest degree of genetic drift due to sampling effects, while terpenes showed that some reduction in genetic diversity had occurred due to local selective pressures.

Quantitation of skeletal muscle necrosis using 99Tcm-pyrophosphate with SPECT in a canine model

Patients with acute arterial occlusion may suffer from significant muscle necrosis. It is important to determine the amount of regional muscle necrosis for prognostic purposes and evaluation of therapy. We have used technetium-99m-pyrophosphate (PPi) with single photon emission computed tomography (SPECT) to quantitate muscle necrosis. A canine gracilis muscle ischaemia model was used. PPi was injected 1.5 h before the muscle preparation was removed from the dog. SPECT was performed on the muscle preparations. An automatic edge detection program using the threshold technique determined the number of pixels with significant PPi activity in each transaxial section. Volume was calculated by summing the number of pixels with significant PPi activity and multiplying by the voxel size. The results were compared with quantitation using computerized planimetry with nitroblue tetrazolium staining (correlation coefficient = 0.93). PPi with SPECT is an accurate method for quantiating muscle necrosis.

The rate and distribution of muscle blood flow after prolonged ischemia

The magnitude and distribution of muscle blood flow in the lower extremity after relief of an acute arterial occlusion may influence the extent of the resulting necrosis. The object of this study was to document the distribution of blood flow in the resting state and after prolonged periods of complete ischemia, and to assess the relationship between the degree of reactive hyperemia and subsequent necrosis. The isolated bilateral canine gracilis muscle preparation that we have previously characterized was used for microsphere studies. Total blood flow was measured by means of timed venous collections, and the distribution of flow was determined by means of a multiple microsphere injection technique. Measurements of microsphere distribution and blood flow were made before ischemia and during the initial 48 minutes of reperfusion after both 4 and 5 hours of normothermic ischemia, which resulted in 46.7% +/- 6% and 71.2% +/- 7% necrosis, respectively. The muscle was harvested and sectioned transversely into six slices approximately 1.5 cm thick, and the extent of necrosis was quantified by means of nitroblue tetrazolium staining 48 hours after reperfusion. Blood flow distribution during the early reperfusion phase was determined in each muscle slice and in both the alive and dead portions of each slice by use of the microsphere injection technique. Preischemic blood flow was distributed homogeneously throughout the muscle and was 4.5 +/- 0.8 ml/100 gm/min (mean +/- SEM, n = 8). On reperfusion total flow was 6 to 10 times higher than it was before ischemia and was distributed predominantly to the middle slices (p less than 0.05, n = 12).(ABSTRACT TRUNCATED AT 250 WORDS)

Identification of clinically significant skeletal muscle necrosis by single photon emission computed tomography

Ischemia-reperfusion damage to skeletal muscle may cause serious local as well as systemic complications, its impact predominantly related to the quantity of ischemic muscle in the lower extremity. To date, there has been no noninvasive method of estimating that quantity. The authors used single photon emission computed tomography (SPECT) to quantify the volume of muscle that takes up technetium-99 pyrophosphate above a baseline threshold. Compared with the standard technique of staining slices of the muscle with nitroblue tetrazolium they found a close correlation using SPECT (r = 0.88, p less than 0.01, n = 19) in the canine model. In humans, this clinically applicable noninvasive technique may allow the surgeon to document accurately the extent of muscle necrosis in the lower extremity, to anticipate the impact of an ischemia-reperfusion injury and evaluate methods of reducing the extent of post-ischemic skeletal muscle necrosis.

Management education and training of nurses: research study

The model of more pro-active management with a more analytical and deliberative approach has considerable implications for the roles of all managers within the National Health Service today. Nurse managers, in particular, will now be faced with developing different managerial roles than they have had in the years since the 1974 reorganization. Nurse management courses in the past were more concerned with the overt training of behavioural skills and less concerned with the quantitative and analytical aspects of management. This paper investigates in what areas nurse managers perceived their training to have been deficient and argues for a continuous process of education, as opposed to the existing intermittent 'hurdle process' which, in the main, is the basis of nurse management development at the present time.