Coeliac disease : investigation of the genetic factors underlying coeliac disease

Coeliac disease is a common food intolerance with a complex genetic aetiology. It is caused by ingestion of gluten peptides from wheat and related proteins from barley and rye in genetically susceptible individuals. The disease affects the small intestine and leads to abnormalities ranging from the infiltration of the villous epithelium by lymphocytes to total villous atrophy. Clinical symptoms include gastrointestinal complaints such as diarrhoea and abdominal pain but also fatigue, weight loss, anaemia, osteopenia, growth retardation and failure to thrive. Coeliac disease is treated by a life-long gluten-free diet; there is no drug therapy available. One important genetic factor contributing to coeliac disease is the human leukocyte antigen (HLA) DQ locus. The majority of patients are positive for DQ2, and almost all of the remaining patients are positive for DQ8. However, the contribution of the HLA region comprises at most half of the total genetic risk. Therefore, non-HLA genes must also play an important role in coeliac disease pathogenesis, but little is known about the location and identity of these genes. This thesis describes the first localisation of susceptibility loci for coeliac disease in the Dutch population, in a well-characterized set of affected sibpairs. Linkage analysis revealed that a major locus was located at 19p13.1. This is the first locus to reach genome-wide significance in coeliac disease in an outbred population. Another locus, showing genome-wide suggestive linkage, was identified at 6q21-22. This region is also implicated in other autoimmune disorders and it may therefore harbour a general susceptibility gene for autoimmunity. Both the 19p13.1 and 6q21-22 loci present novel susceptibility loci for coeliac disease. A second genome-wide screen was performed in a four-generation Dutch family with 17 coeliac disease patients. Surprisingly, a third locus, located at 9p21-13, was identified as the major locus in this family. This locus had also been implicated in Scandinavian families with coeliac disease, and probably presents a locus with a small risk to coeliac disease in general. The 19p13.1 candidate region of 3 Mb, containing 92 genes, was subjected to systematic fine-mapping. Association analysis using microsatellite markers narrowed-down the region to 450 kb and only 12 genes. Subsequent typing of single nucleotide polymorphisms pinpointed the location of the gene to the final 150 kb of this region, with eight possible candidate genes left. Furthermore, the contribution of three functional candidate genes to coeliac disease risk was evaluated: 1. tissue transglutaminase, which modifies gluten peptides into epitopes with strong affinity for HLA-DQ2 and DQ8, resulting in a greatly enhanced T cell response, 2. the cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), which has been implicated as a general susceptibility gene for autoimmunity, 3. the cytokine interferon-?, which plays an important role in the pathogenesis of coeliac disease. However, none of these genes showed association with coeliac disease. Finally, an extensive scan of the HLA region was performed to search additional HLA risk loci for coeliac disease, acting independently of DQ2. The results indicated that the contribution of the HLA region is mainly attributable to DQ2 and that a significant contribution of other HLA genes is unlikely

Vegetation recovery in tidal marshes reveals critical slowing down under increased inundation

A declining rate of recovery following disturbance has been proposed as an important early warning for impending tipping points in complex systems. Despite extensive theoretical and laboratory studies, this \u27critical slowing down\u27 remains largely untested in the complex settings of real-world ecosystems. Here, we provide both observational and experimental support of critical slowing down along natural stress gradients in tidal marsh ecosystems. Time series of aerial images of European marsh development reveal a consistent lengthening of recovery time as inundation stress increases. We corroborate this finding with transplantation experiments in European and North American tidal marshes. In particular, our results emphasize the power of direct observational or experimental measures of recovery over indirect statistical signatures, such as spatial variance or autocorrelation. Our results indicate that the phenomenon of critical slowing down can provide a powerful tool to probe the resilience of natural ecosystems

CREBBP mutations in individuals without Rubinstein-Taybi syndrome phenotype

Item does not contain fulltextMutations in CREBBP cause Rubinstein-Taybi syndrome. By using exome sequencing, and by using Sanger in one patient, CREBBP mutations were detected in 11 patients who did not, or only in a very limited manner, resemble Rubinstein-Taybi syndrome. The combined facial signs typical for Rubinstein-Taybi syndrome were absent, none had broad thumbs, and three had only somewhat broad halluces. All had apparent developmental delay (being the reason for molecular analysis); five had short stature and seven had microcephaly. The facial characteristics were variable; main characteristics were short palpebral fissures, telecanthi, depressed nasal ridge, short nose, anteverted nares, short columella, and long philtrum. Six patients had autistic behavior, and two had self-injurious behavior. Other symptoms were recurrent upper airway infections (n = 5), feeding problems (n = 7) and impaired hearing (n = 7). Major malformations occurred infrequently. All patients had a de novo missense mutation in the last part of exon 30 or beginning of exon 31 of CREBBP, between base pairs 5,128 and 5,614 (codons 1,710 and 1,872). No missense or truncating mutations in this region have been described to be associated with the classical Rubinstein-Taybi syndrome phenotype. No functional studies have (yet) been performed, but we hypothesize that the mutations disturb protein-protein interactions by altering zinc finger function. We conclude that patients with missense mutations in this specific CREBBP region show a phenotype that differs substantially from that in patients with Rubinstein-Taybi syndrome, and may prove to constitute one (or more) separate entities. (c) 2016 Wiley Periodicals, Inc

Predictive testing of minors for Huntington's disease: The UK and Netherlands experiences

A consistent feature of predictive testing guidelines for Huntington's disease (HD) is the recommendation not to undertake predictive tests on those < 18 years. Exceptions are made but the extent of, and reasons for, deviation from the guidelines are unknown. The UK Huntington's Prediction Consortium has collected data annually on predictive tests undertaken from the 23 UK genetic centers. DNA analysis for HD in the Netherlands is centralized in the Laboratory for Diagnostic Genome Analysis in Leiden. In the UK, 60 tests were performed on minors between 1994 and 2015 representing 0.63% of the total number of tests performed. In the Netherlands, 23 tests were performed on minors between 1997 and 2016. The majority of the tests were performed on those aged 16 and 17 years for both countries (23% and 57% for the UK, and 26% and 57% for the Netherlands). Data on the reasons for testing were identified for 36 UK and 22 Netherlands cases and included: close to the age of 18 years, pregnancy, currently in local authority care and likely to have less support available after 18 years, person never having the capacity to consent and other miscellaneous reasons. This study documents the extent of HD testing of minors in the UK and the Netherlands and suggests that, in general, the recommendation is being followed. We provide some empirical evidence as to reasons why clinicians have departed from the recommendation. We do not advise changing the recommendation but suggest that testing of minors continues to be monitored

Reply: Late onset Huntington's disease with 29 CAG repeat expansion

Neurological Motor Disorder

Maternal intermediate repeat expansion into the affected range in Huntington's disease

Background: Intermediate repeat alleles are usually stable when transmitted to the next generation. However, in a small percentage of transmissions these repeats expand into the affected range, leading to a new mutation and a sporadic patient. Until now, expansions of intermediate alleles into the affected range have only been documented in paternal transmission. Case History: The index patient is a 40-year-old female with a clinical diagnosis of Huntington's disease. Symptoms started around the age of 30. The two older siblings of the patient are symptom free. CAG repeat analysis revealed the presence of a normal allele (17 repeats) and an expanded allele of 48 repeats, thereby confirming the clinical diagnosis. Her father died at 87-years-old father and had no signs of the disease. Her mother has died of sclerodermia and (vascular) dementia at the age of 70. DNA of both parents was available: blood of the father and paraffin embedded colon tissue of the mother. The father tested homozygous for an allele in the normal range (17 repeats), while the mother carried a normal allele (17 repeats) and an intermediate allele of 33 repeats. Paternity testing confirmed that they are the biological parents of the index case. The 6 siblings of the mother do not have Huntington's disease. Conclusions: The expanded repeat in our patient has originated from the intermediate repeat allele carried by her mother. This is the first documented case in Huntington's disease of expansion of an intermediate CAG repeat allele into the affected range that has occurred in maternal transmission

Parent-of-origin differences of mutant HTT CAG repeat instability in Huntington's disease

Background: Huntington's disease (HD) is a progressive autosomal dominant neurodegenerative disorder caused by a CAG repeat expansion in the HD gene (HTT). The CAG domain of mutant HTT is unstable upon intergenerational transmission, however, little is known about the underlying mechanisms. Methods: From the HD archives of the Leiden University Medical Centre DNA samples from all parent-offspring pairs involving 36 CAG repeats or more were selected. To minimize procedural variability, CAG repeat lengths in both mutant and normal HTT were reassessed using the same standardized protocol, which resulted in the identification of 337 parent-offspring transmissions. The effects of both parental (mutant and normal CAG repeat size, age and gender) and offspring (gender and season of conception) characteristics on CAG repeat instability were assessed. Results: Paternal transmissions were often associated with CAG repeat expansion, whereas maternal transmissions mainly resulted in CAG repeat contraction (mean change: +1.76 vs. -0.07, p < 0.001). Only in paternal transmissions larger mutant CAG repeat size was associated with a greater degree of CAG repeat expansion (beta = 0.73; p < 0.001). Conversely, only in maternal transmissions larger CAG repeat size of the normal allele was associated with a greater degree of CAG repeat contraction (beta = -0.07; p = 0.029). Parental age, offspring gender and season of conception were not related to CAG repeat instability. Conclusion: Our findings suggest a slight maternal contraction bias as opposed to a paternal expansion bias of the mutant HTT CAG repeat during intergenerational transmission, which only in the maternal line is associated with normal HTT CAG repeat size. (C) 2011 Elsevier Masson SAS. All rights reserved.Neurological Motor Disorder

A probabilistic framework for windows of opportunity: the role of temporal variability in critical transitions

The establishment of young organisms in harsh environments often requires a window of opportunity (WoO). That is, a short time window in which environmental conditions drop long enough below the hostile average level, giving the organism time to develop tolerance and transition into stable existence. It has been suggested that this kind of establishment dynamics is a noise-induced transition between two alternate states. Understanding how temporal variability (i.e. noise) in environmental conditions affects establishment of organisms is therefore key, yet not well understood or included explicitly in the WoO framework. In this paper, we develop a coherent theoretical framework for understanding when the WoO open or close based on simple dichotomous environmental variation. We reveal that understanding of the intrinsic timescales of both the developing organism and the environment is fundamental to predict if organisms can or cannot establish. These insights have allowed us to develop statistical laws for predicting establishment probabilities based on the period and variance of the fluctuations in naturally variable environments. Based on this framework, we now get a clear understanding of how changes in the timing and magnitude of climate variability or management can mediate establishment chances

A probabilistic framework for windows of opportunity: the role of temporal variability in critical transitions

The establishment of young organisms in harsh environments often requires a window of opportunity (WoO). That is, a short time window in which environmental conditions drop long enough below the hostile average level, giving the organism time to develop tolerance and transition into stable existence. It has been suggested that this kind of establishment dynamics is a noise-induced transition between two alternate states. Understanding how temporal variability (i.e. noise) in environmental conditions affects establishment of organisms is therefore key, yet not well understood or included explicitly in the WoO framework. In this paper, we develop a coherent theoretical framework for understanding when the WoO open or close based on simple dichotomous environmental variation. We reveal that understanding of the intrinsic timescales of both the developing organism and the environment is fundamental to predict if organisms can or cannot establish. These insights have allowed us to develop statistical laws for predicting establishment probabilities based on the period and variance of the fluctuations in naturally variable environments. Based on this framework, we now get a clear understanding of how changes in the timing and magnitude of climate variability or management can mediate establishment chances.</p