Shamir et al 15. Meresse B, Curran SA, Ciszewski C, et al. Reprogramming of CTLs into natural killer-like cells in celiac disease. J Exp Med 2006;203: 1343–55.
Celiac Disease Genetics: Past, Present and Future Challenges Cisca Wijmenga and Javier Gutierrez-Achury ABSTRACT In the past few years there has been enormous progress in unraveling the genetic basis of celiac disease (CD). Apart from the well-known association to HLA, there are currently 40 genomic loci associated to CD. Most of these loci show pleiotropic effects across many autoimmune diseases and highlight the importance of a dysregulated immune system in the predisposition to CD. It is still too early, however, to use genetics in clinical practice for predicting individual risk. The major challenge for the future is to translate genetic findings into a better understanding of the underlying disease mechanism and to design new ways to treat CD and prevent its development.
CELIAC DISEASE GENETICS: THE PAST
I
n the early 1970 s it was discovered that particular HLA molecules were involved in CD. With time it became evident that patients with CD more often carried particular HLA risk molecules. It is now widely recognized that the HLA-DQA105 and DQB102 alleles confer risk to CD (1). These HLA-associated alleles are not only frequently found in patients with CD (up to 95%) but also in the general population (up to 35%), implying that HLA is a necessary but not sufficient factor for CD pathogenesis. This prompted research into other genetic factors predisposing to CD. The first efforts were focused on linkage analysis in large pedigrees segregating the disease or in affected sibling pairs, and on investigating association with candidate genes in case-control cohorts. Both approaches were largely unsuccessful for different reasons: (1) the limited power, as most studies were too small; (2) the investigation of only a few candidate genes; and (3) the lack of comprehensive genetic markers across the entire human genome. By the turn of the century in 2000, the CD28-CTLA4-ICOS locus was the only other locus that was suggested to be associated with CD.
CELIAC DISEASE GENETICS: THE PRESENT The genetic landscape of CD changed completely after the discovery of SNPs (single nucleotide polymorphisms) and the development of array-based genotyping technology in 2006, which allowed for genome-wide association studies (GWAS) to be From the University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands. Address correspondence and reprint requests to Cisca Wijmenga, PhD, University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands (e-mail: cisca. [email protected]). Copyright # 2014 by European Society for Pediatric Gastroenterology, Hepatology, and Nutrition and North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition DOI: 10.1097/01.mpg.0000450392.23156.10
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conducted. CD was one of the first diseases for which a GWAS was performed. The initial study tested 310,605 SNPs for association in 778 cases and 1422 controls and yielded 13 new CDassociated loci (2–5). Many of these new loci contained genes related to the immune response and this became even more apparent after a much larger, second GWAS had been performed in close to 5000 cases and more than 10000 controls, which resulted in 26 CDassociated loci (4). Many of these loci suggested that T-cell development and the innate immune system were causally related to CD. An important result from the GWAS was the strong overlap seen in the association signals with other autoimmune diseases (6). This observation prompted the development of the Immunochip as a customized genotyping platform to refine the signals to single genes in loci that had already been significantly associated to CD, and to reveal more of the overlapping association signals. Immunochip genotyping in CD revealed another 13 non-HLA loci contributing risk to CD, resulting in 39 GWAS loci comprising 57 independent genetic SNP variants (7) (Fig. 1). Immunochip analysis has been performed for at least another 12 autoimmune diseases and shown that the majority of the 39 non-HLA CD GWAS-associated loci overlap with at least one of the other phenotypes (Fig. 2). HLA and the 39 non-HLA GWAS loci in CD can explain approximately 50% of the genetic variation of the disease. In order to find the remaining genetic variation it is necessary to collect many more samples; however, this has become a difficult task. Alternative approaches may include cross-disease metaanalysis, in other words, including other autoimmune diseases given their genetic overlap. A study of CD and rheumatoid arthritis has shown that this is feasible (8). Although it is difficult to estimate the total number of unique samples already genotyped with the Immunochip platform (given the possible overlap across studies), pooling all of these samples significantly improves the power. The genetic architecture of CD is likely to be polygenic (ie, many relatively common alleles with very modest effect sizes contribute to the phenotype). A recent study by Stahl et al suggested that at least another 2667 genetic variants could be involved in CD (9). If this proves to be true, large case-control studies will indeed be the only way to find such variants. Large families have been documented with CD, segregating across multiple generations (10). The association in such families could be consistent with a simpler genetic model than the polygenic one and could involve rare alleles with larger effect sizes. Sequencing all genes in the genome may be a powerful tool to identify such alleles, although a study by Szperl et al in 2011 was unable to reveal any rare coding variants with a strong effect to explain CD in a 3-generation family (11). Similarly, a resequencing study of the coding part of associated CD loci in large case-control cohorts only identified 1 additional rare coding variant in the NCF2 gene (12), bringing the total to 40 non-HLA loci and 58 SNPs associated with CD. It is becoming clear from further study of the GWAS findings, however, that it cannot be ruled out that the true causal variants are located outside the coding part of the genome. Kumar et al have shown that 81% of the GWAS variants in CD are located in noncoding regions of the genome (either intergenic or intronic) (13). This suggests that one of the mechanisms by which genetic variation could have an impact on phenotypic expression in CD is by affecting the levels of gene expression (4,7) rather than by changing the nature of the proteincoding genes. More recent evidence suggests that the great majority of the human genome is involved in gene regulation, in part by encoding www.jpgn.org
Copyright 2014 by ESPGHAN and NASPGHAN. Unauthorized reproduction of this article is prohibited.
JPGN
Volume 59, Supplement 1, July 2014
Celiac Disease: Past, Present, Future Challenges
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FIGURE 1. Timeline of celiac disease associations. Outside the human leukocyte antigen (HLA) region, there are currently 39 genome-wide association studies (GWAS) loci and 57 different single-nucleotide polymorphisms (SNP) that show association to celiac disease (CD) (data are based on references 2–5, and 7). For some loci, >1 independent SNP shows association. A resequencing study of the coding part of associated CD loci in large case-control cohorts recently identified 1 additional rare coding variant in the NCF2 gene (12), bringing the total to 40 non-HLA loci and 58 SNPs associated with CD.
so-called noncoding RNAs. A more detailed inspection of the CD GWAS loci showed that some of the genetic variants associated with the disease are in, or close to, long noncoding RNA genes (lncRNA), antisense RNA genes, or microRNAs (miRNAs) (14). This observation has implications for our understanding of CD. Because gene regulation is tissue specific and cell specific, future studies aimed at elucidating disease mechanisms should focus on the proper effector cell type. For CD this is likely to be the glutenrestricted T cell, which can only be found in intestinal biopsies from patients.
CELIAC DISEASE GENETICS: FUTURE CHALLENGES The challenge for the near future is to translate the genetic findings in CD research into risk prediction models and functional analyses towards unraveling disease mechanisms. For risk prediction it is clear that genetics alone is not, and never will be, sufficient to predict accurately the risk in the general population. Nevertheless, in high-risk groups this may be possible. The major genetic risk factor in CD (ie, carrying the determining HLA genotype) is already being used in clinical practice to identify potentially affected individuals. A recent study showed that the 57 nonHLA alleles could improve the positive predictive value of a model compared to using HLA alone, although the difference is not striking, with an area under the receiver operator characteristic curve of 0.854, compared with 0.823 for HLA only (15). This study showed, however, that 11.1% of individuals could be reclassified into a more accurate risk group. This information could be useful in the future, particularly if a more accurate risk classification has implications for treatment or intervention times. What will clearly boost our knowledge about the relation between genetic risk carriers and phenotypic outcome, are large, prospective cohort studies studying individuals from birth onward and monitoring clinical signs, food intake and microbiome patterns, epigenetic changes, and all kinds of other factors that may affect health and the development of disease. In this regard, it is extremely interesting to study the group of individuals who carry a high genetic risk for CD but remain www.jpgn.org
healthy, because they may provide new insights into how we can prevent disease development. With respect to disease mechanisms, genetic studies have provided novel insights into underlying pathways that were not well appreciated earlier. For example, we have seen that many of the genes located in the same loci as risk alleles are involved in the innate immunity, which may suggest an intricate relation between the adaptive and innate immune systems. How the innate immunity is triggered is unknown, although it is tempting to speculate that certain gliadin molecules play a role in the process. Future work should be directed towards a better understanding of these aspects.
CONCLUSIONS For a complete picture of CD genetics, thousands of additional genetic variants need to be identified, which will require cohorts of many thousands of individuals. Such studies can be conducted only by pooling within or between populations and within and between related phenotypes. In addition, to better understand the relation between genotype and phenotype, the clinical characterization of patients should be made as accurately as possible, in a standardized fashion, and they should be studied over time. In the future this may also allow for the development of better prediction models for disease development and progression. Studying healthy individuals who are at risk for CD (based on their genetic and family history) may provide insight into preventive factors. To determine how genetic variation changes the levels of gene expression and how that affects both protein-coding and noncoding RNA genes will require studies of the appropriate effector cell types. Eventually, unraveling the genetics of CD will reveal why the immune system becomes dysregulated and will provide leads to alternative ways to treat the disease. Acknowledgments: The authors thank Gosia Trynka for providing Figure 1 and Jackie Senior for editing the manuscript. Current work in the Wijmenga group is funded by the European Research Council under the European Union’s Seventh Framework
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Copyright 2014 by ESPGHAN and NASPGHAN. Unauthorized reproduction of this article is prohibited.
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FIGURE 2. Immunochip results of nonhuman leukocyte antigen loci shared across 13 other autoimmune diseases. Celiac disease (CD) shares at least 1 locus with each of 13 other diseases (red ribbons). The same is seen for the other 13 diseases analyzed. The numbers in the external ring represents the total number of shared loci per disease and each ribbon represents the absolute number of shared loci between any 2 specific diseases. Each locus can be shared with more than 1 disease, which results in a larger number of shared loci. The other loci represented in the figure include autoimmune thyroiditis (ATD), systemic sclerosis (SS), atopic dermatitis (AD), primary sclerosing cholangitis (PSCh), ulcerative colitis (UC), Crohn disease (CD), inflammatory bowel diseases (IBDs) with shared loci between UC and CD (sharedIBD), primary biliary cirrhosis (PBC), juvenile idiopathic arthritis (JIA), ankylosing spondylitis (AS), psoriasis (PS), rheumatoid arthritis (RA), and multiple sclerosis (MS). Only loci identified by immunochip analysis and reaching the genome-wide significance threshold P < 5 108, are included. Programme (FP/2007-2013)/ERC Grant Agreement no. 2012322698, and the Dutch Digestive Disease Research Foundation (MLDS, WO11-30).
REFERENCES 1. De Haas EC, Kumar V, Wijmenga C. Immunogenetics of celiac disease. In: Devi S, Mullin GE, eds. Clinical Gastroenterology. Totowa, NJ: Humana Press; 2013:1–16. 2. Van Heel DA, Franke L, Hunt KA, et al. A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21. Nat Genet 2007;39:827–9.
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3. Hunt KA, Zhernakova A, Turner G, et al. Newly identified genetic risk variants for celiac disease related to the immune response. Nat Genet 2008;40:395–402. 4. Dubois PC, Trynka G, Franke L, et al. Multiple common variants for celiac disease influencing immune gene expression. Nat Genet 2010; 42:295–302. 5. Trynka G, Zhernakova A, Romanos J, et al. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. Gut 2009;58:1078–83. 6. Zhernakova A, van Diemen CC, Wijmenga C. Detecting shared pathogenesis from the shared genetics of immune-related diseases. Nat Rev Genet 2009;10:43–55.
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7. Trynka G, Hunt KA, Bockett NA, et al. Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat Genet 2011;43:1193–201. 8. Zhernakova A, Stahl EA, Trynka G, et al. Meta-analysis of genomewide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. PLoS Genet 2011;7: e1002004. 9. Stahl EA, Wegmann D, Trynka G, et al. Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis. Nat Genet 2012;44:483–9. 10. van Belzen MJ, Vrolijk MM, Meijer JW, et al. A genomewide screen in a four-generation Dutch family with celiac disease: evidence for linkage to chromosomes 6 and 9. Am J Gastroenterol 2004;99:466– 71. 11. Szperl AM, Ricano-Ponce I, Li JK, et al. Exome sequencing in a family segregating for celiac disease. Clin Genet 2011;80:138–47. 12. Hunt KA, Mistry V, Bockett NA, et al. Negligible impact of rare autoimmune-locus coding-region variants on missing heritability. Nature 2012;498:232–5. 13. Kumar V, Wijmenga C, Withoff S. From genome-wide association studies to disease mechanisms: celiac disease as a model for autoimmune diseases. Semin Immunopathol 2012;34:567–80. 14. Ricano-Ponce I, Wijmenga C. Mapping of immune-mediated disease genes. Annu Rev Genomics Hum Genet 2013;14:325–53. 15. Romanos J, Rosen A, Kumar V, et al. Improving coeliac disease risk prediction by testing non-HLA variants additional to HLA variants. Gut 2014;63:415–22.
The New Epidemiology of Celiac Disease
Carlo Catassi, Simona Gatti, and yAlessio Fasano
ABSTRACT The prevalence of celiac disease (CD) varies greatly, but several reports have shown that CD is increasing in frequency in different geographic areas. The increase in prevalence can be partially attributed to the improvement in diagnostic techniques and disease awareness; however the equally well documented rise in incidence in the last 30–40 years cannot be so easily explained. The new epidemiology of CD is now characterized by an increase of new cases in the historical CD areas (northern Europe and the United States) and more interestingly in a spread of the disease in new regions (Asian countries). A significant change in diet habits, particularly in gluten consumption as well as in infant feeding patterns are probably the main factors that can account for these new trends in CD epidemiology.
C
eliac disease (CD) occurs in a genetically susceptible host that is exposed to the necessary environmental factor— dietary gluten. Historically, CD was first described in areas where gluten containing grains were staple food. Over time, an increasing From the Department of Pediatrics, Universita` Politecnica delle Marche, 60121, Ancona, Italy, and the yCenter for Celiac Research, Massachustetts General Hospital for Children and Celiac Program at Harvard Medical School, Boston, MA. Address correspondence and reprint requests to Carlo Catassi, Department of Pediatrics, Universita` Politecnica delle Marche, via Corridoni 11, 60123 Ancona, Italy (e-mail: [email protected]). Copyright # 2014 by European Society for Pediatric Gastroenterology, Hepatology, and Nutrition and North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition DOI: 10.1097/01.mpg.0000450393.23156.59
www.jpgn.org
Celiac Disease: Past, Present, Future Challenges incidence of CD has been observed in areas that were previously considered CD-free due to global changes in the diet, mostly related to higher consumption of wheat-based products (eg, pasta, pizza). In Western countries several recent studies evaluated the overall prevalence of CD in the general population, usually by counting the number of clinically diagnosed CD patients plus those detected by serological screening of a population sample. In Europe and the United States, the mean frequency of CD in the general population is approximately 1% (1,2), with some regional differences, the reasons for which remain elusive. The prevalence of CD is as high as 2% to 3% in Finland and Sweden, whereas it is only 0.2% in Germany, although these areas share a similar distribution of causal factors (level of gluten intake and frequency of HLA-DQ2 and -DQ8) (1,3). Although the incidence of clinically diagnosed CD cases is increasing, still the larger part of the ‘‘celiac iceberg’’ remains undetected, with a ratio of 1:3 to 1:5 between diagnosed and undiagnosed cases (1,3). A 6.4-fold increase in incidence has been recently described in Scotland from 1990 to 2009 and particularly classical cases of CD are increasing, indicating a true rise in the incidence of pediatric CD (4). In Western countries the overall prevalence of CD is on the rise as well. A recent US study showed that CD prevalence was only 0.2% in the year 1975, and increased 5-fold during the following 25 years (5). The reasons for these changes are unclear, but have to do with the environmental components of CD (changes in the quantity and quality of ingested gluten, infant feeding patterns, the spectrum of intestinal infections, gut microbiota colonization, etc). Variation in the pattern of infant nutrition could influence the prevalence of CD at the population level, as suggested by the analysis of an epidemic of early-onset CD observed in Sweden during the 1980–1990s. The Swedish data indicated that the disease risk was substantially lower in infants introducing small amount of gluten when still breast-fed (3). The protective role of breastfeeding has been supported by other observational, retrospective studies and summarized in a meta-analysis (6). As far as weaning, an increased risk of CD has been reported in infants introducing gluten-containing food either before the age of 4 months or after 6 months, supporting the view of the ‘‘window’’ period of facilitated tolerance (4–6 months) (7). These observations have recently been challenged by a large epidemiological survey performed in Norway (8). The major results of this study performed on a large population sample (324 CD cases and 81,843 cohort controls), were somewhat shocking: (a) breast-feeding did not exert any protection against development of CD. Instead, mean duration of breastfeeding had been significantly longer in CD children (10.4 months) than controls (9.9 months) and the disease risk was significantly higher in infants breast-fed for more than 12 months; (b) gluten introduction under continued breast-feeding was not protective; (c) in the adjusted analysis, only delayed (>6 months) but not early (
Celiac Disease Genetics: Past, Present and Future Challenges Cisca Wijmenga and Javier Gutierrez-Achury ABSTRACT In the past few years there has been enormous progress in unraveling the genetic basis of celiac disease (CD). Apart from the well-known association to HLA, there are currently 40 genomic loci associated to CD. Most of these loci show pleiotropic effects across many autoimmune diseases and highlight the importance of a dysregulated immune system in the predisposition to CD. It is still too early, however, to use genetics in clinical practice for predicting individual risk. The major challenge for the future is to translate genetic findings into a better understanding of the underlying disease mechanism and to design new ways to treat CD and prevent its development.
CELIAC DISEASE GENETICS: THE PAST
I
n the early 1970 s it was discovered that particular HLA molecules were involved in CD. With time it became evident that patients with CD more often carried particular HLA risk molecules. It is now widely recognized that the HLA-DQA105 and DQB102 alleles confer risk to CD (1). These HLA-associated alleles are not only frequently found in patients with CD (up to 95%) but also in the general population (up to 35%), implying that HLA is a necessary but not sufficient factor for CD pathogenesis. This prompted research into other genetic factors predisposing to CD. The first efforts were focused on linkage analysis in large pedigrees segregating the disease or in affected sibling pairs, and on investigating association with candidate genes in case-control cohorts. Both approaches were largely unsuccessful for different reasons: (1) the limited power, as most studies were too small; (2) the investigation of only a few candidate genes; and (3) the lack of comprehensive genetic markers across the entire human genome. By the turn of the century in 2000, the CD28-CTLA4-ICOS locus was the only other locus that was suggested to be associated with CD.
CELIAC DISEASE GENETICS: THE PRESENT The genetic landscape of CD changed completely after the discovery of SNPs (single nucleotide polymorphisms) and the development of array-based genotyping technology in 2006, which allowed for genome-wide association studies (GWAS) to be From the University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands. Address correspondence and reprint requests to Cisca Wijmenga, PhD, University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands (e-mail: cisca. [email protected]). Copyright # 2014 by European Society for Pediatric Gastroenterology, Hepatology, and Nutrition and North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition DOI: 10.1097/01.mpg.0000450392.23156.10
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conducted. CD was one of the first diseases for which a GWAS was performed. The initial study tested 310,605 SNPs for association in 778 cases and 1422 controls and yielded 13 new CDassociated loci (2–5). Many of these new loci contained genes related to the immune response and this became even more apparent after a much larger, second GWAS had been performed in close to 5000 cases and more than 10000 controls, which resulted in 26 CDassociated loci (4). Many of these loci suggested that T-cell development and the innate immune system were causally related to CD. An important result from the GWAS was the strong overlap seen in the association signals with other autoimmune diseases (6). This observation prompted the development of the Immunochip as a customized genotyping platform to refine the signals to single genes in loci that had already been significantly associated to CD, and to reveal more of the overlapping association signals. Immunochip genotyping in CD revealed another 13 non-HLA loci contributing risk to CD, resulting in 39 GWAS loci comprising 57 independent genetic SNP variants (7) (Fig. 1). Immunochip analysis has been performed for at least another 12 autoimmune diseases and shown that the majority of the 39 non-HLA CD GWAS-associated loci overlap with at least one of the other phenotypes (Fig. 2). HLA and the 39 non-HLA GWAS loci in CD can explain approximately 50% of the genetic variation of the disease. In order to find the remaining genetic variation it is necessary to collect many more samples; however, this has become a difficult task. Alternative approaches may include cross-disease metaanalysis, in other words, including other autoimmune diseases given their genetic overlap. A study of CD and rheumatoid arthritis has shown that this is feasible (8). Although it is difficult to estimate the total number of unique samples already genotyped with the Immunochip platform (given the possible overlap across studies), pooling all of these samples significantly improves the power. The genetic architecture of CD is likely to be polygenic (ie, many relatively common alleles with very modest effect sizes contribute to the phenotype). A recent study by Stahl et al suggested that at least another 2667 genetic variants could be involved in CD (9). If this proves to be true, large case-control studies will indeed be the only way to find such variants. Large families have been documented with CD, segregating across multiple generations (10). The association in such families could be consistent with a simpler genetic model than the polygenic one and could involve rare alleles with larger effect sizes. Sequencing all genes in the genome may be a powerful tool to identify such alleles, although a study by Szperl et al in 2011 was unable to reveal any rare coding variants with a strong effect to explain CD in a 3-generation family (11). Similarly, a resequencing study of the coding part of associated CD loci in large case-control cohorts only identified 1 additional rare coding variant in the NCF2 gene (12), bringing the total to 40 non-HLA loci and 58 SNPs associated with CD. It is becoming clear from further study of the GWAS findings, however, that it cannot be ruled out that the true causal variants are located outside the coding part of the genome. Kumar et al have shown that 81% of the GWAS variants in CD are located in noncoding regions of the genome (either intergenic or intronic) (13). This suggests that one of the mechanisms by which genetic variation could have an impact on phenotypic expression in CD is by affecting the levels of gene expression (4,7) rather than by changing the nature of the proteincoding genes. More recent evidence suggests that the great majority of the human genome is involved in gene regulation, in part by encoding www.jpgn.org
Copyright 2014 by ESPGHAN and NASPGHAN. Unauthorized reproduction of this article is prohibited.
JPGN
Volume 59, Supplement 1, July 2014
Celiac Disease: Past, Present, Future Challenges
HLA and 40 loci (58 independent SNPs) Dense genotyping (Immunochip)
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FIGURE 1. Timeline of celiac disease associations. Outside the human leukocyte antigen (HLA) region, there are currently 39 genome-wide association studies (GWAS) loci and 57 different single-nucleotide polymorphisms (SNP) that show association to celiac disease (CD) (data are based on references 2–5, and 7). For some loci, >1 independent SNP shows association. A resequencing study of the coding part of associated CD loci in large case-control cohorts recently identified 1 additional rare coding variant in the NCF2 gene (12), bringing the total to 40 non-HLA loci and 58 SNPs associated with CD.
so-called noncoding RNAs. A more detailed inspection of the CD GWAS loci showed that some of the genetic variants associated with the disease are in, or close to, long noncoding RNA genes (lncRNA), antisense RNA genes, or microRNAs (miRNAs) (14). This observation has implications for our understanding of CD. Because gene regulation is tissue specific and cell specific, future studies aimed at elucidating disease mechanisms should focus on the proper effector cell type. For CD this is likely to be the glutenrestricted T cell, which can only be found in intestinal biopsies from patients.
CELIAC DISEASE GENETICS: FUTURE CHALLENGES The challenge for the near future is to translate the genetic findings in CD research into risk prediction models and functional analyses towards unraveling disease mechanisms. For risk prediction it is clear that genetics alone is not, and never will be, sufficient to predict accurately the risk in the general population. Nevertheless, in high-risk groups this may be possible. The major genetic risk factor in CD (ie, carrying the determining HLA genotype) is already being used in clinical practice to identify potentially affected individuals. A recent study showed that the 57 nonHLA alleles could improve the positive predictive value of a model compared to using HLA alone, although the difference is not striking, with an area under the receiver operator characteristic curve of 0.854, compared with 0.823 for HLA only (15). This study showed, however, that 11.1% of individuals could be reclassified into a more accurate risk group. This information could be useful in the future, particularly if a more accurate risk classification has implications for treatment or intervention times. What will clearly boost our knowledge about the relation between genetic risk carriers and phenotypic outcome, are large, prospective cohort studies studying individuals from birth onward and monitoring clinical signs, food intake and microbiome patterns, epigenetic changes, and all kinds of other factors that may affect health and the development of disease. In this regard, it is extremely interesting to study the group of individuals who carry a high genetic risk for CD but remain www.jpgn.org
healthy, because they may provide new insights into how we can prevent disease development. With respect to disease mechanisms, genetic studies have provided novel insights into underlying pathways that were not well appreciated earlier. For example, we have seen that many of the genes located in the same loci as risk alleles are involved in the innate immunity, which may suggest an intricate relation between the adaptive and innate immune systems. How the innate immunity is triggered is unknown, although it is tempting to speculate that certain gliadin molecules play a role in the process. Future work should be directed towards a better understanding of these aspects.
CONCLUSIONS For a complete picture of CD genetics, thousands of additional genetic variants need to be identified, which will require cohorts of many thousands of individuals. Such studies can be conducted only by pooling within or between populations and within and between related phenotypes. In addition, to better understand the relation between genotype and phenotype, the clinical characterization of patients should be made as accurately as possible, in a standardized fashion, and they should be studied over time. In the future this may also allow for the development of better prediction models for disease development and progression. Studying healthy individuals who are at risk for CD (based on their genetic and family history) may provide insight into preventive factors. To determine how genetic variation changes the levels of gene expression and how that affects both protein-coding and noncoding RNA genes will require studies of the appropriate effector cell types. Eventually, unraveling the genetics of CD will reveal why the immune system becomes dysregulated and will provide leads to alternative ways to treat the disease. Acknowledgments: The authors thank Gosia Trynka for providing Figure 1 and Jackie Senior for editing the manuscript. Current work in the Wijmenga group is funded by the European Research Council under the European Union’s Seventh Framework
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Copyright 2014 by ESPGHAN and NASPGHAN. Unauthorized reproduction of this article is prohibited.
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FIGURE 2. Immunochip results of nonhuman leukocyte antigen loci shared across 13 other autoimmune diseases. Celiac disease (CD) shares at least 1 locus with each of 13 other diseases (red ribbons). The same is seen for the other 13 diseases analyzed. The numbers in the external ring represents the total number of shared loci per disease and each ribbon represents the absolute number of shared loci between any 2 specific diseases. Each locus can be shared with more than 1 disease, which results in a larger number of shared loci. The other loci represented in the figure include autoimmune thyroiditis (ATD), systemic sclerosis (SS), atopic dermatitis (AD), primary sclerosing cholangitis (PSCh), ulcerative colitis (UC), Crohn disease (CD), inflammatory bowel diseases (IBDs) with shared loci between UC and CD (sharedIBD), primary biliary cirrhosis (PBC), juvenile idiopathic arthritis (JIA), ankylosing spondylitis (AS), psoriasis (PS), rheumatoid arthritis (RA), and multiple sclerosis (MS). Only loci identified by immunochip analysis and reaching the genome-wide significance threshold P < 5 108, are included. Programme (FP/2007-2013)/ERC Grant Agreement no. 2012322698, and the Dutch Digestive Disease Research Foundation (MLDS, WO11-30).
REFERENCES 1. De Haas EC, Kumar V, Wijmenga C. Immunogenetics of celiac disease. In: Devi S, Mullin GE, eds. Clinical Gastroenterology. Totowa, NJ: Humana Press; 2013:1–16. 2. Van Heel DA, Franke L, Hunt KA, et al. A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21. Nat Genet 2007;39:827–9.
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3. Hunt KA, Zhernakova A, Turner G, et al. Newly identified genetic risk variants for celiac disease related to the immune response. Nat Genet 2008;40:395–402. 4. Dubois PC, Trynka G, Franke L, et al. Multiple common variants for celiac disease influencing immune gene expression. Nat Genet 2010; 42:295–302. 5. Trynka G, Zhernakova A, Romanos J, et al. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. Gut 2009;58:1078–83. 6. Zhernakova A, van Diemen CC, Wijmenga C. Detecting shared pathogenesis from the shared genetics of immune-related diseases. Nat Rev Genet 2009;10:43–55.
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7. Trynka G, Hunt KA, Bockett NA, et al. Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat Genet 2011;43:1193–201. 8. Zhernakova A, Stahl EA, Trynka G, et al. Meta-analysis of genomewide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. PLoS Genet 2011;7: e1002004. 9. Stahl EA, Wegmann D, Trynka G, et al. Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis. Nat Genet 2012;44:483–9. 10. van Belzen MJ, Vrolijk MM, Meijer JW, et al. A genomewide screen in a four-generation Dutch family with celiac disease: evidence for linkage to chromosomes 6 and 9. Am J Gastroenterol 2004;99:466– 71. 11. Szperl AM, Ricano-Ponce I, Li JK, et al. Exome sequencing in a family segregating for celiac disease. Clin Genet 2011;80:138–47. 12. Hunt KA, Mistry V, Bockett NA, et al. Negligible impact of rare autoimmune-locus coding-region variants on missing heritability. Nature 2012;498:232–5. 13. Kumar V, Wijmenga C, Withoff S. From genome-wide association studies to disease mechanisms: celiac disease as a model for autoimmune diseases. Semin Immunopathol 2012;34:567–80. 14. Ricano-Ponce I, Wijmenga C. Mapping of immune-mediated disease genes. Annu Rev Genomics Hum Genet 2013;14:325–53. 15. Romanos J, Rosen A, Kumar V, et al. Improving coeliac disease risk prediction by testing non-HLA variants additional to HLA variants. Gut 2014;63:415–22.
The New Epidemiology of Celiac Disease
Carlo Catassi, Simona Gatti, and yAlessio Fasano
ABSTRACT The prevalence of celiac disease (CD) varies greatly, but several reports have shown that CD is increasing in frequency in different geographic areas. The increase in prevalence can be partially attributed to the improvement in diagnostic techniques and disease awareness; however the equally well documented rise in incidence in the last 30–40 years cannot be so easily explained. The new epidemiology of CD is now characterized by an increase of new cases in the historical CD areas (northern Europe and the United States) and more interestingly in a spread of the disease in new regions (Asian countries). A significant change in diet habits, particularly in gluten consumption as well as in infant feeding patterns are probably the main factors that can account for these new trends in CD epidemiology.
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eliac disease (CD) occurs in a genetically susceptible host that is exposed to the necessary environmental factor— dietary gluten. Historically, CD was first described in areas where gluten containing grains were staple food. Over time, an increasing From the Department of Pediatrics, Universita` Politecnica delle Marche, 60121, Ancona, Italy, and the yCenter for Celiac Research, Massachustetts General Hospital for Children and Celiac Program at Harvard Medical School, Boston, MA. Address correspondence and reprint requests to Carlo Catassi, Department of Pediatrics, Universita` Politecnica delle Marche, via Corridoni 11, 60123 Ancona, Italy (e-mail: [email protected]). Copyright # 2014 by European Society for Pediatric Gastroenterology, Hepatology, and Nutrition and North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition DOI: 10.1097/01.mpg.0000450393.23156.59
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Celiac Disease: Past, Present, Future Challenges incidence of CD has been observed in areas that were previously considered CD-free due to global changes in the diet, mostly related to higher consumption of wheat-based products (eg, pasta, pizza). In Western countries several recent studies evaluated the overall prevalence of CD in the general population, usually by counting the number of clinically diagnosed CD patients plus those detected by serological screening of a population sample. In Europe and the United States, the mean frequency of CD in the general population is approximately 1% (1,2), with some regional differences, the reasons for which remain elusive. The prevalence of CD is as high as 2% to 3% in Finland and Sweden, whereas it is only 0.2% in Germany, although these areas share a similar distribution of causal factors (level of gluten intake and frequency of HLA-DQ2 and -DQ8) (1,3). Although the incidence of clinically diagnosed CD cases is increasing, still the larger part of the ‘‘celiac iceberg’’ remains undetected, with a ratio of 1:3 to 1:5 between diagnosed and undiagnosed cases (1,3). A 6.4-fold increase in incidence has been recently described in Scotland from 1990 to 2009 and particularly classical cases of CD are increasing, indicating a true rise in the incidence of pediatric CD (4). In Western countries the overall prevalence of CD is on the rise as well. A recent US study showed that CD prevalence was only 0.2% in the year 1975, and increased 5-fold during the following 25 years (5). The reasons for these changes are unclear, but have to do with the environmental components of CD (changes in the quantity and quality of ingested gluten, infant feeding patterns, the spectrum of intestinal infections, gut microbiota colonization, etc). Variation in the pattern of infant nutrition could influence the prevalence of CD at the population level, as suggested by the analysis of an epidemic of early-onset CD observed in Sweden during the 1980–1990s. The Swedish data indicated that the disease risk was substantially lower in infants introducing small amount of gluten when still breast-fed (3). The protective role of breastfeeding has been supported by other observational, retrospective studies and summarized in a meta-analysis (6). As far as weaning, an increased risk of CD has been reported in infants introducing gluten-containing food either before the age of 4 months or after 6 months, supporting the view of the ‘‘window’’ period of facilitated tolerance (4–6 months) (7). These observations have recently been challenged by a large epidemiological survey performed in Norway (8). The major results of this study performed on a large population sample (324 CD cases and 81,843 cohort controls), were somewhat shocking: (a) breast-feeding did not exert any protection against development of CD. Instead, mean duration of breastfeeding had been significantly longer in CD children (10.4 months) than controls (9.9 months) and the disease risk was significantly higher in infants breast-fed for more than 12 months; (b) gluten introduction under continued breast-feeding was not protective; (c) in the adjusted analysis, only delayed (>6 months) but not early (
