Choosing Wisely: The Canadian Rheumatology Association Pediatric Committee's List of Items Physicians and Patients Should Question

OBJECTIVE

To develop a list of tests or treatments frequently used in pediatric rheumatology practice that may be unnecessary based on existing evidence.

METHODS

A Choosing Wisely (CW) working group composed of 16 pediatric rheumatologists, 1 allied health professional, 1 parent, and 1 patient used the Delphi method to generate, rank, and refine a list of tests and treatments that may be unnecessary or harmful. The items with the highest content agreement and perceived impact were presented in a survey to all Canadian Rheumatology Association (CRA) physicians who practice pediatric rheumatology. Respondents were asked to rate their agreement and impact, and to rank the items. Five items with the highest composite scores and 2 additional items selected by the CW working group were put forward for literature review.

RESULTS

The initial Delphi procedure generated 80 items. After 3 rounds, the list was narrowed to 13 items. The survey was completed by 41/81 (51%) CRA pediatric members across Canada. Respondent characteristics were similar to those of the CRA pediatric membership for self-reported gender, geographical location, and career stage. The highest composite score items were antinuclear antibody testing, drug toxicity monitoring, HLA-B27 testing, rheumatoid factor/anticyclic citrullinated peptide testing, and Lyme serology testing. Two additional items (numerous or repeated intraarticular corticosteroid injections, and autoinflammatory diseases genetic testing) were also selected. Literature review was performed for these 7 highest priority items.

CONCLUSION

We have identified areas for quality improvement in the evaluation and treatment of rheumatic diseases in Canadian children.

Hemophagocytic Lymphohistiocytosis Gene Variants in Childhood-Onset SLE with Macrophage Activation Syndrome

OBJECTIVE

Macrophage activation syndrome (MAS), a life-threatening complication of SLE, resembles familial hemophagocytic lymphohistiocytosis (fHLH), an inherited disorder of hyperinflammation. We compared the proportion of childhood-onset SLE (cSLE) patients with and without MAS, who carried low-frequency HLH non-synonymous variants.

METHODS

We enrolled patients from the Lupus Clinic at SickKids, Toronto. Demographic and clinical features were extracted from the lupus database and ancestry was genetically inferred using multiethnic genotyping array data. Patients with MAS (based on expert diagnosis) underwent either paired-end whole exome sequencing (read-depth:70-118X) or whole-genome sequencing. Non-MAS patients had whole-genome sequencing (read-depth:37-40X). In 16 HLH genes we prioritized low-frequency (minor allele frequency (MAF) <0.05) exonic nonsynonymous variants. We compared the proportion of patients with and without MAS carrying HLH variants (Fisher's exact test, P<0.05). MAFs were compared to an ancestrally-matched general population (TOPMed and gnomAD).

RESULTS

The study included 81 patients, 19 with MAS. We identified 47 unique low-frequency non-synonymous HLH variants. There was no difference in the proportion of MAS and non-MAS patients carrying ≥1 HLH variants (37% versus 47%, P=0.44). The MAS cohort did not carry more HLH variants when compared to an ancestrally-matched general population.

CONCLUSION

In a single-center multiethnic cSLE cohort, we found no difference in the proportion of MAS patients carrying non-synonymous HLH genetic variants compared to patients without MAS. This is the first study to examine the frequency of HLH genetic variants in relation to MAS among cSLE patients. Future studies are required to validate our findings.

A novel ICK mutation causes ciliary disruption and lethal endocrine-cerebro-osteodysplasia syndrome

Background

Endocrine-cerebro-osteodysplasia (ECO) syndrome [MIM:612651] caused by a recessive mutation (p.R272Q) in Intestinal cell kinase (ICK) shows significant clinical overlap with ciliary disorders. Similarities are strongest between ECO syndrome, the Majewski and Mohr-Majewski short-rib thoracic dysplasia (SRTD) with polydactyly syndromes, and hydrolethalus syndrome. In this study, we present a novel homozygous ICK mutation in a fetus with ECO syndrome and compare the effect of this mutation with the previously reported ICK variant on ciliogenesis and cilium morphology.

Results

Through homozygosity mapping and whole-exome sequencing, we identified a second variant (c.358G > T; p.G120C) in ICK in a Turkish fetus presenting with ECO syndrome. In vitro studies of wild-type and mutant mRFP-ICK (p.G120C and p.R272Q) revealed that, in contrast to the wild-type protein that localizes along the ciliary axoneme and/or is present in the ciliary base, mutant proteins rather enrich in the ciliary tip. In addition, immunocytochemistry revealed a decreased number of cilia in ICK p.R272Q-affected cells.

Conclusions

Through identification of a novel ICK mutation, we confirm that disruption of ICK causes ECO syndrome, which clinically overlaps with the spectrum of ciliopathies. Expression of ICK-mutated proteins result in an abnormal ciliary localization compared to wild-type protein. Primary fibroblasts derived from an individual with ECO syndrome display ciliogenesis defects. In aggregate, our findings are consistent with recent reports that show that ICK regulates ciliary biology in vitro and in mice, confirming that ECO syndrome is a severe ciliopathy.

Electronic supplementary material

The online version of this article (doi:10.1186/s13630-016-0029-1) contains supplementary material, which is available to authorized users.

Exome sequencing identifies NFS1 deficiency in a novel Fe-S cluster disease, infantile mitochondrial complex II/III deficiency

Iron-sulfur (Fe-S) clusters are a class of highly conserved and ubiquitous prosthetic groups with unique chemical properties that allow the proteins that contain them, Fe-S proteins, to assist in various key biochemical pathways. Mutations in Fe-S proteins often disrupt Fe-S cluster assembly leading to a spectrum of severe disorders such as Friedreich's ataxia or iron-sulfur cluster assembly enzyme (ISCU) myopathy. Herein, we describe infantile mitochondrial complex II/III deficiency, a novel autosomal recessive mitochondrial disease characterized by lactic acidemia, hypotonia, respiratory chain complex II and III deficiency, multisystem organ failure and abnormal mitochondria. Through autozygosity mapping, exome sequencing, in silico analyses, population studies and functional tests, we identified c.215G>A, p.Arg72Gln in NFS1 as the likely causative mutation. We describe the first disease in man likely caused by deficiency in NFS1, a cysteine desulfurase that is implicated in respiratory chain function and iron maintenance by initiating Fe-S cluster biosynthesis. Our results further demonstrate the importance of sufficient NFS1 expression in human physiology.

A mutation in the serine protease TMPRSS4 in a novel pediatric neurodegenerative disorder

Background

To elucidate the genetic basis of a novel neurodegenerative disorder in an Old Order Amish pedigree by combining homozygosity mapping with exome sequencing.

Methods and results

We identified four individuals with an autosomal recessive condition affecting the central nervous system (CNS). Neuroimaging studies identified progressive global CNS tissue loss presenting early in life, associated with microcephaly, seizures, and psychomotor retardation; based on this, we named the condition Autosomal Recessive Cerebral Atrophy (ARCA). Using two unbiased genetic approaches, homozygosity mapping and exome sequencing, we narrowed the candidate region to chromosome 11q and identified the c.995C > T (p.Thr332Met) mutation in the TMPRSS4 gene. Sanger sequencing of additional relatives confirmed that the c.995C > T genotype segregates with the ARCA phenotype. Residue Thr332 is conserved across species and among various ethnic groups. The mutation is predicted to be deleterious, most likely due to a protein structure alteration as demonstrated with protein modelling.

Conclusions

This novel disease is the first to demonstrate a neurological role for a transmembrane serine proteases family member. This study demonstrates a proof-of-concept whereby combining exome sequencing with homozygosity mapping can find the genetic cause of a rare disease and acquire better understanding of a poorly described protein in human development.

Transcriptional profiling of endocrine cerebro-osteodysplasia using microarray and next-generation sequencing

Background

Transcriptome profiling of patterns of RNA expression is a powerful approach to identify networks of genes that play a role in disease. To date, most mRNA profiling of tissues has been accomplished using microarrays, but next-generation sequencing can offer a richer and more comprehensive picture.

Methodology/Principal Findings

ECO is a rare multi-system developmental disorder caused by a homozygous mutation in ICK encoding intestinal cell kinase. We performed gene expression profiling using both cDNA microarrays and next-generation mRNA sequencing (mRNA-seq) of skin fibroblasts from ECO-affected subjects. We then validated a subset of differentially expressed transcripts identified by each method using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Finally, we used gene ontology (GO) to identify critical pathways and processes that were abnormal according to each technical platform. Methodologically, mRNA-seq identifies a much larger number of differentially expressed genes with much better correlation to qRT-PCR results than the microarray (r² = 0.794 and 0.137, respectively). Biologically, cDNA microarray identified functional pathways focused on anatomical structure and development, while the mRNA-seq platform identified a higher proportion of genes involved in cell division and DNA replication pathways.

Conclusions/Significance

Transcriptome profiling with mRNA-seq had greater sensitivity, range and accuracy than the microarray. The two platforms generated different but complementary hypotheses for further evaluation.

Phenomics: expanding the role of clinical evaluation in genomic studies

With advances in high-throughput genotyping technologies, the rate-limiting step of large-scale genetic investigations has become the collection of sensitive and specific phenotype information in large samples of study participants. Clinicians play a pivotal role for successful genetic studies because sound clinical acumen can substantially increase study power by reducing measurement error and improving diagnostic precision for translational research. Phenomics is the systematic measurement and analysis of qualitative and quantitative traits, including clinical, biochemical, and imaging methods, for the refinement and characterization of a phenotype. Phenomics requires deep phenotyping, the collection of a wide breadth of phenotypes with fine resolution, and phenomic analysis, composed of constructing heat maps, cluster analysis, text mining, and pathway analysis. In this article, we review the components of phenomics and provide examples of their application to genomic studies, specifically for implicating novel disease processes, reducing sample heterogeneity, hypothesis generation, integration of multiple types of data, and as an extension of Mendelian randomization studies.

Kinase mutations in human disease: interpreting genotype-phenotype relationships

Protein kinases are one of the largest families of evolutionarily related proteins and comprise one of the most abundant gene families in humans. Here we survey kinase gene mutations from the perspective of human disease phenotypes and further analyse the structural features of mutant kinases, including mutational hotspots. Our evaluation of the genotype-phenotype relationship across 915 human kinase mutations - that underlie 67 single-gene diseases, mainly inherited developmental and metabolic disorders and also certain cancers - enhances our understanding of the role of kinases in development, kinase dysfunction in pathogenesis and kinases as potential targets for therapy.

APOC1 T45S polymorphism is associated with reduced obesity indices and lower plasma concentrations of leptin and apolipoprotein C-I in aboriginal Canadians

Apolipoprotein (apo) C-I is a constituent of chylomicrons, very low density lipoprotein, and high density lipoprotein. The role of apo C-I in human metabolism is incompletely defined. We took advantage of a naturally occurring amino acid polymorphism that is present in aboriginal North Americans, namely apo C-I T45S. We assessed the hypothesis that metabolic traits, including obesity-related and lipoprotein-related traits, would differ between carriers and noncarriers of apo C-I T45S. A genotyping assay was developed for APOC1 T45S and genotypes were determined in a sample of 410 Canadian Oji-Cree subjects. The allele frequency of the apo C-I S45 allele was approximately 8% in this sample. We observed the apo C-I S45 allele was significantly associated with 1) lower percent body fat (P < 0.05), 2) lower waist circumference (P = 0.058), 3) lower serum leptin levels (P < 0.05), and 4) lower plasma apo C-I levels (P < 0.0001), using a newly developed ELISA-based method. Taken together, these results suggest that at the whole human phenotype level, apo C-I is associated with the complex metabolic trait of obesity as well as with serum leptin levels.

A multiplex human syndrome implicates a key role for intestinal cell kinase in development of central nervous, skeletal, and endocrine systems

Six infants in an Old Order Amish pedigree were observed to be affected with endocrine-cerebro-osteodysplasia (ECO). ECO is a previously unidentified neonatal lethal recessive disorder with multiple anomalies involving the endocrine, cerebral, and skeletal systems. Autozygosity mapping and sequencing identified a previously unknown missense mutation, R272Q, in ICK, encoding intestinal cell kinase (ICK). Our results established that R272 is conserved across species and among ethnicities, and three-dimensional analysis of the protein structure suggests protein instability due to the R272Q mutation. We also demonstrate that the R272Q mutant fails to localize at the nucleus and has diminished kinase activity. These findings suggest that ICK plays a key role in the development of multiple organ systems.

Genetics of metabolic syndrome

Metabolic syndrome (MetS) is a common phenotype, affecting about 24% of the US population. It is associated with an increased risk for type 2 diabetes and cardiovascular disease. Although there is no universally accepted definition for MetS, affected individuals commonly have a cluster of features, including abdominal obesity, hypertension, dyslipidemia, and dysglycemia. Recently, there has been extensive interest in potential genetic contributions to MetS. At present, no single gene or cluster of genes has been consistently replicated for MetS among different populations, likely due to the complex interplay between gene and environment necessary for expression of this phenotype. We review recent studies regarding the genetic contributions to MetS.

Common variants APOC3, APOA5, APOE and PON1 are associated with variation in plasma lipoprotein traits in Greenlanders

OBJECTIVES

We undertook studies of the association between common genomic variations in APOC3, APOA5, APOE and PON1 genes and variation in biochemical phenotypes in a sample of Greenlanders.

STUDY DESIGN

Genetic association study of quantitative lipoprotein traits.

METHODS

In a sample of 1,310 adult Greenlanders, fasting plasma lipid, lipoprotein and apolipoprotein (apo) concentrations were assessed for association with known functional genomic variants of APOC3, APOA5, APOE and PON1. For significantly associated polymorphisms, between-genotype differences were examined in closer detail.

RESULTS

We found that (1) the APOE restriction isotype was associated with variation in plasma total and LDL cholesterol and apo B (all p < .0001); (2) the APOC3 promoter genotype was associated with variation in plasma triglycerides, HDL cholesterol and apo A-I (all p < .002); (3) the APOA5 codon 19 genotype was associated with variation in plasma triglycerides (p = .027); and (4) the PON1 codon 192 genotype was associated with variation in total and LDL cholesterol and apo B (all p < .05).

CONCLUSIONS

Taken together, our results suggest that common genetic variations in APOC3, APOA5, APOE and PON1 are associated with significant variation in intermediate traits in plasma lipoprotein metabolism in Greenlanders; the associations are similar to those observed for these variants in other populations.

Uncloaking the genetic determinants of metabolic syndrome

The metabolic syndrome (MetS) is a commonly encountered cluster of clinical phenotypes, including central obesity, hypertension, hyperglycemia, and dyslipidemia. Identifying genetic determinants of MetS will lead to better understanding of its progression and pathogenesis. To further the knowledge of MetS it is important to not only study the candidate genes for each individual component but to also investigate patients with rare monogenic disorders who express a cluster of the phenotypes commonly observed in MetS, however defined. In addition, certain genetic variants have been observed to increase or decrease the risk of developing the entire syndrome. It is apparent that only through complete understanding of the gene-gene, gene-gender and gene-nutrition interactions underlying MetS, will it become possible to determine or minimize the principal complications, namely type 2 diabetes and cardiovascular disease. In this review, we focus on the current evidence for common gene polymorphisms that predispose to or protect from the development of MetS.

Genetic characterization of two autosomal recessive disorders, Majewski-like and cerebral atrophy syndromes

Introduction: We recently identified two lethal recessive disorders segregating within the same Old Order Amish pedigree. The first disorder, Majewski-like syndrome (MLS), has features that overlap with both Majewski short rib-polydactyly syndrome and hydrolethalus syndrome. MLS is a lethal multi-system disorder that affects the development of the brain, adrenal glands, pituitary gland and bone. The second disorder, cerebral atrophy syndrome (CAS), is characterized by progressive and global loss of brain tissue. Affected children present early in life with microcephaly, seizures, and psychomotor retardation, and possess distinctive MRI findings. The objective of this study was to identify the genetic bases of these disorders to provide prompt and reliable diagnosis for families. Methods: Assuming recessive inheritance and mutation homogeneity (autozygosity), we used Affymetrix 10,000-single nucleotide polymorphism (10K-SNP) to genotype all affected individuals and identify candidate regions. SNP data were analyzed using Agilent GT autozygosity mapping software. LOD scores were used to identify candidate regions, and genes within these regions were prioritized for sequencing. Results and Conclusion: Because the Ontario Anabaptist population is relatively small, genetically isolated, and historically young, we were able to robustly map candidate regions using relatively low marker density and only a few affected individuals. Our preliminary data is consistent with the clinical observation that MLS and CAS segregate independently, as recessive conditions, within the pedigree. Thus far, we have sequenced 12 genes within the MLS locus, all of which were normal. For CAS, autozygosity mapping yielded two loci with comparable linkage scores, one of which contained no observable mutations. Once the causative mutations have been identified for MLS and CAS, we intend to study their population frequencies and also to pursue in vitro studies of gene and protein functions.

Micromethods for the characterization of lipid A-core and O-antigen lipopolysaccharide

Methods for rapid and simple analysis of lipopolysaccharide (LPS) from bacterial whole-cell lysates or membrane preparations have contributed to advancing our knowledge of the genetics of the LPS biogenesis. LPS, a major constituent of the outer membranes in Gram-negative bacteria, has a complex mechanism of synthesis and assembly that requires the coordinated participation of many genes and gene products. This chapter describes a collection of methods routinely used in our laboratory for the characterization of LPS in Escherichia coli and other bacteria.