Establishing a celiac disease (CD) diagnosis can be difficult, such as when CD-specific antibody levels are just above cutoff or when small intestinal biopsies show low-grade injuries. To investigate the biological pathways involved in CD and select potential biomarkers to aid in CD diagnosis, RNA sequencing of duodenal biopsies from subjects with either confirmed Active CD (n = 20) or without any signs of CD (n = 20) was performed. Gene enrichment and pathway analysis highlighted contexts, such as immune response, microbial infection, phagocytosis, intestinal barrier function, metabolism, and transportation. Twenty-nine potential CD biomarkers were selected based on differential expression and biological context. The biomarkers were validated by real-time polymerase chain reaction of eight RNA sequencing study subjects, and further investigated using an independent study group (n = 43) consisting of subjects not affected by CD, with a clear diagnosis of CD on either a gluten-containing or a gluten-free diet, or with low-grade intestinal injury. Selected biomarkers were able to classify subjects with clear CD/non-CD status, and a subset of the biomarkers (CXCL10, GBP5, IFI27, IFNG, and UBD) showed differential expression in biopsies from subjects with no or low-grade intestinal injury that received a CD diagnosis based on biopsies taken at a later time point. A large number of pathways are involved in CD pathogenesis, and gene expression is affected in CD mucosa already in low-grade intestinal injuries. RNA sequencing of low-grade intestinal injuries might discover pathways and biomarkers involved in early stages of CD pathogenesis.Electronic supplementary materialThe online version of this article (10.1007/s00018-018-2898-5) contains supplementary material, which is available to authorized users.

Celiac disease (CD) is identified by histopathologic changes in the small intestine which normalize during a gluten-free diet. The histopathologic assessment of duodenal biopsies is usually routine but can be difficult. This study investigated gene expression profiling as a diagnostic tool. A total of 109 genes were selected to reflect alterations in crypt-villi architecture, inflammatory response, and intestinal permeability and were examined for differential expression in normal mucosa compared with CD mucosa in pediatric patients. Biopsies were classified using discriminant analysis of gene expression. Fifty genes were differentially expressed, of which eight (APOC3, CYP3A4, OCLN, MAD2L1, MKI67, CXCL11, IL17A, and CTLA4) discriminated normal mucosa from CD mucosa without classification errors using leave-one-out cross-validation (n ϭ 39) and identified the degree of mucosal damage. Validation using an independent set of biopsies (n ϭ 27) resulted in four discrepant cases. Biopsies from two of these cases showed a patchy distribution of lesions, indicating that discriminant analysis based on single biopsies failed to identify CD mucosa. In the other two cases, serology support class according to discriminant analysis and histologic specimens were judged suboptimal but assessable. Gene expression profiling shows promise as a diagnostic tool and for follow-up of CD, but further evaluation is needed. (Pediatr Res 69: 530-537, 2011) C eliac disease (CD) is an inflammatory condition of the small intestine with a diverse range of symptoms (1), and a prevalence of approximately 1% in Western European populations (2). CD is triggered by gliadin peptides derived from gluten-containing cereals, and the inflamed small intestinal mucosa is characterized by villous atrophy, crypt hyperplasia, and infiltration of lymphocytes in the epithelium (1). In addition, patients with CD have increased permeability over the epithelial layer of the small intestine, and an altered structure of the tight junction has been demonstrated in children with CD (3).A positive serological test for antibodies against tissue transglutaminase and/or gliadin may indicate CD (4). However, a histopathologic assessment (HA) of small intestinal biopsies regarding abnormalities characteristic of CD is required to establish a diagnosis (5,6). Diagnostic criteria also require that the patient should have a clinical remission when on a strict gluten-free diet (GFD). The mucosal damage is often graded histologically, using such established measures as the modified Marsh scale (7). The interobserver reproducibility between pathologists assessing the same small intestinal biopsy specimens shows fair to substantial agreement (8,9), with most of the disagreements found in Marsh 1-3B lesions (8) and with some of the interpathologist assessments transgressing the boundary between normal mucosa and CD mucosa (8).Gene expression profiling shows a potential as a robust test for classification purposes, with a high interlaboratory reproducibility (10,11). A ...

No abstract

Eighty-seven children with short stature (height more than 2 SD below the mean for age and sex) were investigated by small intestinal biopsy. There was no obvious reason for their growth retardation found by routine examination and they had no gastrointestinal symptoms. Coeliac disease was found in two children and probable coeliac disease in two children. Although the prevalence of coeliac disease was comparatively low in this study of Swedish children with short stature, it emphasizes the fact that coeliac disease must be considered in a child with short stature even in the absence of gastrointestinal symptoms.