Defining the Celiac Disease Transcriptome using Clinical Pathology Specimens Reveals Biologic Pathways and Supports Diagnosis

Abstract

Celiac disease is provoked by gluten exposure, but the complete pathogenic process in the duodenum and the loss of tolerance to gluten is not well understood. We aimed to define the core celiac transcriptomic signature and pathologic pathways in pre-treatment formalin-fixed paraffin-embedded (FFPE) duodenum biopsies used for clinical diagnosis. We use mRNAseq to define pre-treatment diagnostic duodenum gene expression in 54 pediatric celiac patients and non-celiac controls, and we validate our key findings in two independent cohorts of 67 adults and pediatric participants that used fresh frozen biopsies. We further define similar and divergent genes and pathways in 177 small bowel Crohn disease patients and controls. We observe a marked suppression of mature epithelial metabolic functions in celiac patients, overlapping substantially with the Crohn disease signature. A marked adaptive immune response was noted for the up-regulated signature including interferon response, alpha-beta, and gamma-delta T-cells that overlapped to some extent with the Crohn disease signature. However, we also identified a celiac disease specific signature linked to increased cell proliferation, nuclear division, and cell cycle activity that was localized primarily to the epithelia as noted by CCNB1 and Ki67 staining. Lastly, we demonstrate the utility of the transcriptomic date to correctly classify disease or healthy states in the discovery and validation cohorts. Our data supplement recently published datasets providing insights into celiac pathogenesis using clinical pathology FFPE samples, and can stimulate new approaches to address this highly prevalent condition.

Deciphering the Transcriptomic Heterogeneity of Duodenal Coeliac Disease Biopsies

“…Next, we ask about potential expression markers distinguishing between CD- and non-CD-cases independent of their group membership. First we discovered previous prognostic signatures of CD [ 51 ], Crohn’s disease [ 52 ] and of Ulcerative Colitis [ 27 ] in terms of their expression profiles and gene maps ( Figure 6 A). The genes of the UP (upregulated in CD) and DN (downregulated in CD) sets accumulate in or near spots D/E in the left upper corner and in or near spot A in the right lower corner of the map, respectively (red circles in Figure 6 A).…”

Genome-Wide Transcriptomic Analysis of Intestinal Mucosa in Celiac Disease Patients on a Gluten-Free Diet and Postgluten Challenge

“…This has also been shown in other studies where active celiac disease patients were compared with healthy control subjects or celiac patients on a GFD in a nonpaired manner. 16 , 18 Deficient enterocyte differentiation has been suggested to be ascribed to hyperactive Wnt signaling in the disease, as Wnt signaling needs to be inhibited for enterocyte differentiation to occur. 45 In fact, the number of cells expressing nuclear beta-catenin in the crypt, as a proxy for active Wnt signaling, has been shown to be increased along with expression of a few studied Wnt target genes in active celiac disease.…”

“… 24 Also, other attempts to build a molecular model for grouped mucosal injury classification have been presented. 18 , 63 In our study, we modeled the behavior of continuous metric parameters (VH:CrD and the density of CD3 + IELs), which were assigned to each endoscopic biopsy, and a multiple regression analysis was applied. In conclusion, we show that by using transcriptomic data one may predict histomorphological parameters with a high accuracy.…”

“…We believe that discovering the molecular mechanisms responsible for thwarting the differentiation program of the intestinal epithelial cells could lead to a better understanding of the mechanisms of celiac disease development and the consequent deterioration of the small intestinal mucosal morphology. Transcriptomic studies using microarray 15 or RNA-sequencing (RNA-Seq) technologies 16 , 17 , 18 and proteomic 19 and epigenomic 20 analyses were conducted on celiac disease patient biopsies. The majority of these studies used untreated patient samples, samples from patients on a GFD, and non–celiac disease samples as a control group.…”

Future of paediatric gastroenterology

“…Mostly they will facilitate diagnosis and when plugged into the diagnostic algorithms they will concertina diagnostic time. If a diagnosis is not achieved using gene panels or whole exome or whole genome sequencing we will, depending on the clinical phenotype, employ the patient's transcriptome, 5 proteome, 6 metabolome 7 or lipidome 8 to make a diagnosis. Having established a diagnosis we will be able to precisely elucidate a defect, and design therapies.…”