Christopher Taylor

Renal histopathology in fatal cases of diarrhoea-associated haemolytic uraemic syndrome

Abstract.u2003Autopsy material was examined from British children dying early in the course of haemolytic uraemic syndrome (HUS). These presented after 1983, the period in which verocytotoxin-producing Escherichia coli (VTEC) infection was confirmed as the leading cause of diarrhoea-associated (D+HUS) in the United Kingdom. Of 18 cases referred for this study, 3 were found on review to have no history of a diarrhoeal prodrome (D-HUS). In the D+ patients, the median duration from onset of diarrhoea to death was 8 days (range 4–42 days). VTEC infection was confirmed in 6 cases. All had neutrophilia at presentation (median 21, range 15–49.8 × 109/l). The 15 cases had uniform pathological features, consisting of glomerular thromboses and congested rather than ischaemic glomeruli. Arteriolar thromboses were common at the hilum of glomeruli and were sometimes also seen proximally, including in interlobular arteries. There were cortical infarcts in 5 cases with extensive thrombosis. Cases were demonstrated to have significantly greater numbers of neutrophils expressed per 100 glomeruli than controls, when counted using immunohistological stains to neutrophil elastase and CD15. This study showed uniformity of the renal changes in D+ HUS and gave further evidence of the importance of neutrophils in the pathogenesis of the disease.

Guidelines for the diagnosis and management of distal intestinal obstruction syndrome in cystic fibrosis patients

Complete or incomplete intestinal obstruction by viscid faecal material in the terminal ileum and proximal colon - distal intestinal obstruction syndrome (DIOS) - is a common complication in cystic fibrosis. Estimates of prevalence range from 5 to 12 episodes per 1000 patients per year in children, with higher rates reported in adults. DIOS is mainly seen in patients with pancreatic insufficiency, positive history of meconium ileus and previous episodes of DIOS. DIOS is being described with increasing frequency following organ transplantation. Diagnosis is based on suggestive symptoms with a right lower quadrant mass confirmed on X-ray. The main differential is chronic constipation. Treatment consists of rehydration combined with stool softening laxatives or gut lavage with balanced electrolyte solutions. Rapid fluid shifts have been described following osmotic agents. Avoiding dehydration and optimizing pancreatic enzyme dosage may reduce the chance of further episodes. Prophylactic laxative therapy is widely used, but is not evidence-based.

Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq.

Previous studies have demonstrated the utility of microarray expression analysis to identify potential microRNA targets. Nevertheless, technical limitations intrinsic to this platform constrain its ability to fully exploit the potential of assessing transcript level changes to explore microRNA targetomes. High-throughput multiplexed Illumina-based next-generation sequencing (NGS) provides a digital readout of absolute transcript levels and imparts a higher level of accuracy and dynamic range than microarray platforms. We used Illumina NGS to analyze transcriptome changes induced by the human microRNA MIR155. This analysis resulted in a larger inferred targetome than similar studies carried out using microarray platforms. A comparison with 3 UTR reporter data demonstrated general concordance between NGS and corresponding 3 UTR reporter results. Nonharmonious results were investigated more deeply using transcript structure information assembled from the NGS data. This analysis revealed that transcript structure plays a substantial role in mitigated targeting and in frank targeting failures. With its high level of accuracy, its broad dynamic range, its utility in assessing transcript structure, and its capacity to accurately interrogate global direct and indirect transcriptome changes, NGS is a useful tool for investigating the biology and mechanisms of action of microRNAs.

Clinico-pathological findings in diarrhoea-negative haemolytic uraemic syndrome

This is a retrospective, national clinico-pathological study of past and current patients with haemolytic uraemic syndrome not associated with diarrhoea (D− HUS). Thirty-four patients were analysed and notified by members of the British Association for Paediatric Nephrology in 1998–1999. There was a 2:1 excess of males. Ten presented in infancy. The aetiology included 5 patients with complement abnormalities, 2 patients with complications of pneumococcal infection, and 2 with malignancies. Parental consanguinity was noted in 6 patients. Five children died, 9 developed chronic renal failure, and 10 end-stage renal failure. Only 7 made full recoveries. With a single exception, the pathological findings were unlike the previously reported glomerular thrombosis that is characteristic of diarrhoea-associated HUS, or HUS complicating verocytotoxin-producing Escherichia coli infection. Early and late glomerulopathy could be distinguished. Arteriolar and arterial disease was observed in 8 and 7 patients, respectively. Arterial disease correlated with a poor outcome. The pathology of D− HUS is of prognostic value, but this study was not powered to identify specific aetiological/pathological correlations.

Quantitative and Qualitative RNA-Seq-Based Evaluation of Epstein-Barr Virus Transcription in Type I Latency Burkitt's Lymphoma Cells

ABSTRACT RNA-seq provides a rich source of transcriptome information with high qualitative and quantitative value. Here, we provide a pipeline for Epstein-Barr virus (EBV) transcriptome analysis using RNA-seq and we apply it to two type I latency cell lines, Mutu I and Akata. This analysis revealed substantial average expression levels of many lytic genes in predominantly latent cell populations. The lytic transcripts BHLF1 and LF3 were expressed at levels greater than those for 98% of all cellular polyadenylated transcripts. Exon junction mapping accurately identified the Qp-derived EBNA1 splicing pattern, lytic gene splicing, and a complex splicing pattern within the BamHI A region.

Isoform-level microRNA-155 target prediction using RNA-seq

Computational prediction of microRNA targets remains a challenging problem. The existing rule-based, data-driven and expression profiling approaches to target prediction are mostly approached from the gene-level. The increasing availability of RNA-seq data provides a new perspective for microRNA target prediction on the isoform-level. We hypothesize that the splicing isoform is the ultimate effector in microRNA targeting and that the proposed isoform-level approach is capable of predicting non-dominant isoform targets as well as their targeting regions that are otherwise invisible to many existing approaches. To test the hypothesis, we used an iterative expectation maximization (EM) algorithm to quantify transcriptomes at the isoform-level. The performance of the EM algorithm in transcriptome quantification was examined in simulation studies using FluxSimulator. We used joint evidence from isoform-level down-regulation and seed enrichment to predict microRNA-155 targets. We validated our computational approach using results from 149 in-house performed in vitro 3′-UTR assays. We also augmented the splicing database using exon–exon junction evidence, and applied the EM algorithm to predict and quantify 1572 cell line specific novel isoforms. Combined with seed enrichment analysis, we predicted 51 novel microRNA-155 isoform targets. Our work is among the first computational studies advocating the isoform-level microRNA target prediction.

RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets

High-throughput RNA sequencing (RNA-seq) has become an instrumental assay for the analysis of multiple aspects of an organisms transcriptome. Further, the analysis of a biological specimens associated microbiome can also be performed using RNA-seq data and this application is gaining interest in the scientific community. There are many existing bioinformatics tools designed for analysis and visualization of transcriptome data. Despite the availability of an array of next generation sequencing (NGS) analysis tools, the analysis of RNA-seq data sets poses a challenge for many biomedical researchers who are not familiar with command-line tools. Here we present RNA CoMPASS, a comprehensive RNA-seq analysis pipeline for the simultaneous analysis of transcriptomes and metatranscriptomes from diverse biological specimens. RNA CoMPASS leverages existing tools and parallel computing technology to facilitate the analysis of even very large datasets. RNA CoMPASS has a web-based graphical user interface with intrinsic queuing to control a distributed computational pipeline. RNA CoMPASS was evaluated by analyzing RNA-seq data sets from 45 B-cell samples. Twenty-two of these samples were derived from lymphoblastoid cell lines (LCLs) generated by the infection of naïve B-cells with the Epstein Barr virus (EBV), while another 23 samples were derived from Burkitts lymphomas (BL), some of which arose in part through infection with EBV. Appropriately, RNA CoMPASS identified EBV in all LCLs and in a fraction of the BLs. Cluster analysis of the human transcriptome component of the RNA CoMPASS output clearly separated the BLs (which have a germinal center-like phenotype) from the LCLs (which have a blast-like phenotype) with evidence of activated MYC signaling and lower interferon and NF-kB signaling in the BLs. Together, this analysis illustrates the utility of RNA CoMPASS in the simultaneous analysis of transcriptome and metatranscriptome data. RNA CoMPASS is freely available at http://rnacompass.sourceforge.net/.

A case of neonatal Bartter’s syndrome

Abstract. We describe a child with a neonatal presentation of Bartter’s syndrome. Unlike infants previously described with a similar clinical presentation, the urinary excretion rate of prostaglandin E2 in this child was similar to normal children and Tamm-Horsfall protein was distributed normally in the thick ascending limb of the loop of Henle. The child failed to respond to indomethacin alone, but thrived after the addition of the angiotensin converting enzyme inhibitor, captopril.

Colonic and Duodenal Flat Adenomas in Children with Classical Familial Adenomatous Polyposis

Flat adenomas of the colon and duodenum have been described as associating with familial adenomatous polyposis (FAP), its attenuated variant, and the so-called hereditary nonpolyposis colorectal cancer. There seem to be no report on the occurrence of flat adenomas in pediatric patients with family history of FAP. We are reporting 4 children from 2 cancer-prone families in whom colonic and duodenal moderately dysplastic flat adenomas were found. Gastrointestinal endoscopy and biopsies were performed in 3 female siblings (7, 9, and 11 years old) and 1 male (9 years old) when referred for screening owing to familial history of bowel cancer (family 1) or evidence of bilateral congenital hypertrophy of the retinal pigment epithelium (CHRPE), which is known to be associated with FAP (family 2). Endoscopic visualization of the mucosa was improved by use of 0.2% indigo carmine solution spray. Biopsies were routinely processed for H&E and immunohistochemistry staining. Present patients were asymptomatic, with the exception of 2 weeks rectal bleeding in 1 of them. The colonic videoendoscopy showed in 2/3 siblings hundreds of flat or slightly raised plaques less than 1 cm in diameter as well as some classic polyps throughout the colon. The other sibling showed 40 flat-topped lesions with minimal elevation and central umbilication in the cecum. Upper endoscopy demonstrated a few flat lesions in the nonperiampullary area of the duodenum in 2/4 patients. The colonic videoendoscopy performed on the 9-year-old boy revealed multiple small sessile polyps. Microscopic study demonstrated tubular adenomas with a few neoplastic crypts, slight disarray of the overall architecture, and moderate (low-grade) dysplasia of the epithelium. These features were more obvious at the center and superficial areas of the adenomas. The 4 children had multiple flat adenomas of the colon and duodenum (2/4) matching with those described in adult patients. Flat adenomas in the context of FAP probably represent early stages of the adenoma development. Careful endoscopic-histologic correlation may result in increasing recognition of these lesions at the pediatric age.

NONINVASIVE MONITORING IN THE PEDIATRIC INTENSIVE CARE UNIT

The best ICU monitors are physicians and nurses, who integrate all of the physiologic parameters of patients with the known pathophysiology of the disease process. Over-reliance on raw electronic data, with their inherent errors, jeopardizes the safe and efficient care of patients. Data must be interpreted in the context of the history, repetitive physical examinations, response to therapy, and a background of experience. New modalities and the application of artificial intelligence may facilitate the interpretation of data, but the role of the bedside medical practitioner remains as the heart of pediatric critical care.