Immunology Letters 158 (2014) 116–119
Contents lists available at ScienceDirect
Immunology Letters journal homepage: www.elsevier.com/locate/immlet
Review
Genetics of autoimmunity: An update Rosa Sorrentino ∗ Department of Biology and Biotechnology “Charles Darwin” and Istituto Pasteur-Cenci Bolognetti, Sapienza University, Rome, Italy
a r t i c l e
i n f o
Article history: Received 22 October 2013 Received in revised form 3 December 2013 Accepted 4 December 2013 Available online 24 December 2013 Keywords: Autoimmunity Genetics Polymorphisms
a b s t r a c t The advent of genome-wide association studies (GWAS) has produced tremendous insights into the genetics of immune-mediated diseases allowing to identify hundreds of associated variants, some of which disease-specific and some others shared by groups of diseases. However, each variant usually accounts for a small genetic risk and all together they explain a relatively small portion of heritability for each disease. In addition, many of the associated variants map in regions of still undisclosed functions. This opens up to a new era of studies in search of the “missing heritability” which might partially be explained by gene–gene interactions and/or additive effects impacting on biochemical pathways relevant for the disease pathogenesis. The introduction of the immunochip analysis that allows to analyze thousands of patients for variations more strictly correlated with the immune/inflammatory functions is now allowing to single out relevant pathways shared by different diseases. Finally, great expectations are brought about from the studies on the effects that epigenetic modifications can have on the tuning of the expression of single allele/s in myeloid cells as well as in target tissues. Some of these topics have been discussed at the 15th International Congress of Immunology. © 2013 Elsevier B.V. All rights reserved.
The occurrence of autoimmunity represents a big challenge for the immunologists since it entails that something has gone wrong with the tuning of the immune response but, given the heterogeneity of the clinical manifestations leading to such large number of different diseases, determining the heart of the matter has proved to be quite difficult. Can the genetics help to untangle this task? Autoimmune diseases show a variable degree of heritability based on polygenic variants and the new era of the genetics has given hope to pinpoint the major variants that could impact on the disease course. It must be pointed out however, that, in autoimmune diseases, as well as in other polygenic diseases, the heritability is usually higher than what can be explained by the associated variants emerging from the GWAS. This “missing heritability” is a highly debated topic for which not necessarily a unique explanation does exist. It is possible that, due to the limitations of GWAS that mostly rely on not very dense common variants, we are indeed missing rare causal variations sharing a moderate degree of linkage disequilibrium with the analyzed markers, and thus shortening the distance from monogenic diseases. Part of this missing heritability might also be explained by gene–gene interactions which require the analysis of very large cohorts of patients and which, again, remind the effect of modifier genes in monogenic diseases [1–5]. In any case, heterogeneous groups of patients are often collected under a single disease, hiding different
∗ Tel.: +39 0649917706. E-mail address: [email protected] 0165-2478/$ – see front matter © 2013 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.imlet.2013.12.005
aetiological causes and complicating the matter. During this workshop, several examples of the state of art in the field have been discussed attesting the contribution of the genetics to the comprehension of the mechanisms responsible for the aberrant immune responses (Table 1). A provocative news coming from the GWAS, is that the number of variants found to be associated to each disease is increasing everyday, in parallel with the technical improvements that allow to analyze larger cohorts of patients. A direct relationship between the number of cases analyzed by GWAS and the growing list of associated variants has been recently illustrated [6]. However, all together these allelic variants account for a relatively small risk, explaining between 20% and 50% of heritability, increasing the skepticism of the non-geneticists on the real value of such a large and costly amount of data. The recent introduction of the immunochips that spot immune-related variants, represents a step forward since it allows to identify those genes more strictly related to the immune/inflammatory pathways. From these data, pathways shared by apparently different diseases and epistatic interactions among these genes, are beginning to emerge [6]. Moreover, specific genetic variants can now be associated with different clinical features allowing to split cohorts of patients in more homogenous groups. An intriguing and innovative message emerging from animal models in which the functional impact of these variants is studied, is that, while so far the attention has been focused on myeloid cells as key players in the inflammatory network, it is now time to go back to tissues and to ask what is the primum movens in the cross-talk
R. Sorrentino / Immunology Letters 158 (2014) 116–119 Table 1 Examples of genes associated with more than two immune-mediated diseases. Gene (chromosome region)
Disease
Refs.
ERAP1 (5q15)
AS Behc¸et’s disease Psoriasis
9 10 11
IRF5-TNPO3 (7q32)
LES Sjogren’s disease RA Systemic sclerosis Primary biliary cirrhosis IBD
15, 16 14 27 17 12 27
STAT3 (17q21)
IBD Psoriasis MS
6 6 6
STAT4 (2q32)
IBD RA Primary biliary cirrhosis Coeliac disease LES Behc¸et’s disease
6 6 6 6 6 6
IL12A (3q25)
MS Primary biliary cirrhosis Coeliac disease
6 6 6
IL-12R (1p31)
AS IBD Primary biliary cirrhosis Behc¸et’s disease
6 6 6 6
IL-23R (1p31)
AS IBD Psoriasis
6 6 6
TYK2 (19p13)
AS IBD Psoriasis MS T1D RA Primary biliary cirrhosis
6 6 6 6 6 6 6
PTPN22 (1p13)
RA T1D SLE
28 28 28
CTLA4 (2q33)
Coeliac disease T1D Graves’ disease
29 30 30
AS, ankylosing spondylitis; RA, rheumatoid arthritis; SLE, systemic lupus erythematosus; T1D, type I diabetes; IBD, inflammatory bowel disease; CD, coeliac disease, MS, multiple sclerosis.
between immune cells and target tissues. There are some lessons coming from the workshop held at the ICI 2013 meeting. To start from the beginning however, the best known and undeniable hallmark of autoimmune diseases is their association with the HLA region, that refers to the involvement of an adaptive immune response which has been indeed demonstrated to play a direct role with both its cellular and humoral arms. This association in the majority of cases involves the HLA-class II region, with the exception of a subgroup of diseases associated with the HLAclass I alleles [7]. The case of HLA-B27 in Ankylosing Spondylitis has been discussed and it has been shown how a single amino acid substitution (D116H) in the two subtypes, the disease-associated B*2705 and the non-associated B*2709, dictates a strong difference in the flexibility of the peptide-binding groove. This confers to the disease-associated B*2705 specific properties that can influence its folding as well as its peptidome [8]. Strong support for a direct role played by the HLA-class I molecules in the pathogenesis of the associated autoimmune diseases is coming from GWAS.
117
Thanks to the large cohorts of patients that can now be analyzed, it has been possible to define the association of three of these diseases, namely Ankylosing Spondylitis, Psoriasis and Behc¸et disease, with ERAP1 gene on chromosome 5 [9–11]. This gene encodes for an ER-resident aminopeptidase involved in the refining of peptides bound to the HLA-class I molecules. Interestingly, this association holds true only in those cases positive respectively for HLA-B*27, HLA-Cw6 and HLA-B*51, indicating a gene–gene interaction that strengthens the role of antigen presentation in the pathogenesis of these diseases. What about the HLA-B27/Cw6/B51 negative cases in AS, Psoriasis and Behc¸et, respectively? Do these patients suffer from a different disease? In practice, what these data tell us is that, while it would make sense to target ERAP1 activity in the HLA-associated cases, it wouldn’t in the negative ones, giving an example of how the genetics can help us to design more specific therapeutic approaches. Defining gene–gene interactions is of paramount relevance since it would allow to infer from a list of genes, pathways of higher penetrance. A second crucial question to which the genetics can contribute, is the finding of a common ground shared by different autoimmune diseases. To this regard, besides ERAP1 in HLA-class I-associated diseases discussed above, many other connections are emerging. In this workshop the role played by the IRF5-TNPO3 region on chromosome 17 has been discussed. This is a complex region found to be associated with different autoimmune diseases such as SLE, Sjogren’s syndrome, systemic sclerosis and primary biliary cirrhosis. However, it is not clear which function is associated with each disease. The Harley’s group in Cincinnati has made an effort to identify the causal variants in SLE over a region of 85.5 kb and reported a strong association with age of onset (variants in the haplotype) and the presence of anti-Ro and anti-dsDNA autoantibodies (variants in the IRF-5 promoter) involving the IRF-5 gene directly in the B cellmediated response and a less defined region in the triggering of the different diseases [12–19]. A further illustration of how different clinical aspects can be associated with different subsets of genes comes from Rheumatoid Arthritis as illustrated by Chovanova, who reported that allelic variants at different genes correlate with a higher proportion of different myeloid cell types and, consequently, with a different array of cytokines. As an example, a higher proportion of memory B cells correlates with risk alleles in PTPN22, AFF3, PAD14 and TRAF1/C5 genes whereas a higher proportion of CD8+ T cells correlates with risk alleles in IRF5, STAT4 and CTLA4 genes indicating that the long list of factors conferring susceptibility to RA represents a continuum in which, depending on the genetic background of the single patients, one or the other pathogenic aspect can prevail. Another examples of the link between associated variants and altered functions was reported by Fossati-Jimack who showed how the Arg to His substitution at position 77 of the CD11b, one of the genes more strongly associated with SLE, results in a defect of C3mediated phagocytosis in different cell types [20]. A further aspect complicating the genetics of autoimmune diseases, is that the association between a SNP and a disease can be restricted to some ethnic groups, depending on the allelic frequency and on the evolutionary history of the population. This is the case of the PXK (PX domain containing serine/threonine kinase) for which Vaughn reported an independent effect occurring in women with SLE of European ancestry only. He also showed that the risk allele correlates with a more rapid internalization of the B cell receptor (BCR) with which it co-localizes [21]. This is not surprising since a complex disease is the result of many different factors and the lack of one of them is never crucial, not even the absence of the HLA allele/s conferring the highest risk. Interestingly however, when disease associated variations are analyzed in isolated contexts, they often show a striking
118
R. Sorrentino / Immunology Letters 158 (2014) 116–119
functional effect that badly correlates with the low risk conferred to the disease. More advanced techniques to study the functional variations at single cell level in contexts in which the two alleles are not over-expressed are needed. This appears now to be possible [22]. A relevant question also discussed during the workshop, is in which cell/tissue context the altered function is pathogenic. In this framework, Okuma reported the impressive case of Sjogren’s disease. His group set up a mouse model in which the diseaseassociated IkB- gene, a transcriptional factor belonging to the NF-kB family involved in inflammation, was knocked-out. These mice developed a disease very similar to Sjogren’s, characterized by leukocyte infiltration and presence of autoantibodies. The surprise however was that the inflammation was not due to an altered function of the myeloid cells but to the enhanced apoptosis of the epithelial cells. Accordingly, the clinical symptoms were partially reverted by the use of caspase inhibitors. This group took a step forward and analyzed STAT3-deficient mice that showed symptoms very similar to those previously observed in the case of IkB- deficiency. Also under these circumstances, the clinical dysfunction was reported as due to a lack of function of STAT3-mediated IkB- function in which dysfunction of the epithelia cells elicited the activation of self-reactive lymphocytes [23,24]. Several questions remain open: why this happens in specific epithelial cells only? How do lymphocytes are activated? Is this due to the crosspresentation of specific antigens? But, more intriguingly, to what extent this model can be extrapolated to humans and/or to other autoimmune diseases? How much a knock-out model recapitulates the effect of genetic variants? Do we have to move more of our attention to the target tissue/s? Finally, another interesting report has been focused on Themis. Themis is a fine-tuner of the TCR signaling acting in thymus and influencing thymic selection as pointed out by Acuto during his lecture at ICI 2013 [25]. However, its function has also been linked to the maturation of T regulatory cells in a model of BN rats that had a frameshift mutation in Themis gene and developed an inflammatory bowel disease. Interestingly, Pedros reported that Themis deficiency in LEW rats does not impair T regulatory function neither correlates with any pathological phenotype unless a constitutive active VAV1 variant was present. These data indicate the VAV1/Themis co-operation as crucial for the regulation of the suppressive functions of Treg and point, not surprisingly, to the maturation/function of Treg as a pivotal event in autoimmunity [26]. In conclusion, the genetics of the autoimmune diseases is still a flourishing field and it is now approaching the second line of research. GWAS of thousands of patients have shown us that a high number of genes are associated with autoimmunity and research is in progress to attribute subsets of these genes to the different disease traits, such as age of onset, clinical course. The most relevant pathways are likely to be spotted thanks also to the identification of gene–gene interactions that should allow to focus on more personalized therapeutic approaches, and help to reconcile the functional differences enlightened by molecular studies with the small risk associated with each genetic variant. Finally, tremendous insights are expected from the study of the epigenetic interactions that could contribute to the expression of single alleles in relevant tissues. The genetics can tell us where to start by indicating which genes and pathways are relevant for each disease to occur, but how their expression can be modulated by epigenetic events, possibly under the control of environmental stimuli, represents the next challenging, long step. Next years will be very exciting and the next ICI congress will give us more insights into the connection between the genetics and the epigenetics events in the pathogenesis of autoimmune diseases.
References [1] Maher B. Personal genomes: the case of the missing heritability. Nature 2008;456:18–21. [2] Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, et al. Finding the missing heritability of complex diseases. Nature 2009;461: 747–53. [3] Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB. Rare variants create synthetic genome-wide associations. PLoS Biol 2010;8: e1000294. [4] Zuk O, Hechter E, Sunyaev SR, Lander ES. The case of the missing heritability: genetics interactions create phantom heritability. Proc Natl Acad Sci USA 2012;109:1193–8. [5] Hemani G, Knott S, Haley C. An evolutionary perspective on epistasis and the missing heritability. PLoS Genet 2013;9:e1003295. [6] Parkes M, Cortes A, van Heel DA, Brown M. Genetic insights into common pathways and complex relationships among immune-mediated diseases. Nat Rev Genet 2013;14:661–73. [7] Fernando MM, Stevens CR, Walsh EC, De Jager PL, Goyette P, Plenge RM, et al. Defining the role of the MHC in autoimmunity: a review and pooled analysis. PLoS Genet 2008;4:e1000024. [8] Sorrentino R, Böckmann RA, Fiorillo MT. HLA-B27 and antigen presentation: at the crossroads between immune defense and autoimmunity. Mol Immunol 2014;57:22–7. [9] Evans DM, Spencer CC, Pointon JJ, Su Z, Harvey D, Kochan G, et al. Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility. Nat Genet 2011;43:761–7. [10] Kirino Y, Bertsias G, Ishigatsubo Y, Mizuki N, Tugal-Tutkun I, Seyahi E, et al. Genome-wide association analysis identifies new susceptibility loci for Behc¸et’s disease and epistasis between HLA-B*51 and ERAP1. Nat Genet 2013;45:202–7. [11] Genetic Analysis of Psoriasis Consortium & the Wellcome Trust Case Control Consortium 2, Strange A, Capon F, Spencer CC, Knight J, Weale ME, et al. A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1. Nat Genet 2010;42: 985–90. [12] Hirschfield GM, Liu X, Han Y, Gorlov IP, Lu Y, Xu C, et al. Variants at IRF5-TNPO3, 17q12-21 and MMEL1 are associated with primary biliary cirrhosis. Nat Genet 2010;42:655–7. [13] Liu X, Invernizzi P, Lu Y, Kosoy R, Lu Y, Bianchi I, et al. Genome-wide metaanalyses identify three loci associated with primary biliary cirrhosis. Nat Genet 2010;42:658–60. [14] Miceli-Richard C, Gestermann N, Ittah M, Comets E, Loiseau P, Puechal X, et al. The CGGGG insertion/deletion polymorphism of the IRF5 promoter is a strong risk factor for primary Sjögren’s syndrome. Arthritis Rheum 2009;60(6):1991–7. [15] Kozyrev SV, Lewén S, Reddy PM, Pons-Estel B, Argentine Collaborative Group, Witte T, et al. Structural insertion/deletion variation in IRF5 is associated with a risk haplotype and defines the precise IRF5 isoforms expressed in systemic lupus erythematosus. Arthritis Rheum 2007;56:1234–41. [16] Graham RR, Kozyrev SV, Baechler EC, Reddy MV, Plenge RM, Bauer JW, et al. A common haplotype of interferon regulatory factor 5 (IRF5) regulates splicing and expression and is associated with increased risk of systemic lupus erythematosus. Nat Genet 2006;38:550–5. [17] Carmona FD, Martin JE, Beretta L, Simeón CP, Carreira PE. The systemic lupus erythematosus IRF5 risk haplotype is associated with systemic sclerosis. PLoS ONE 2013;8:e54419. [18] Stone RC, Du P, Feng D, Dhawan K, Rönnblom L. RNA-Seq for enrichment and analysis of IRF5 transcript expression in SLE. PLoS ONE 2013;8: e54487. [19] Dieudé P, Guedj M, Wipff J, Avouac J, Fajardy I. Association between the IRF5 rs2004640 functional polymorphism and systemic sclerosis: a new perspective for pulmonary fibrosis. Arthritis Rheum 2009;60:225–33. [20] Fossati-Jimack L, Ling GS, Cortini A, Szajna M, Malik TH. Phagocytosis is the main CR3-mediated function affected by the lupus-associated variant of CD11b in human myeloid cells. PLoS ONE 2013;8:e57082. [21] International Consortium for Systemic Lupus Erythematosus Genetics (SLEGEN), Harley JB, Alarcón-Riquelme ME, Criswell LA, Jacob CO, Kimberly RP, et al. Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet 2008;40:204–10. [22] Wills QF, Livak KJ, Tipping AJ, Enver T, Goldson AJ, Sexton DV. Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments. Nat Biotechnol 2013;31:748–52. [23] Okuma A, Hoshino K, Ohba T, Fukushi S, AibaS., Akira S, et al. Enhanced apoptosis by disruption of the STAT3-IB- signaling pathway in epithelial cells induces Sjögren’s syndrome-like autoimmune disease. Immunity 2013;38: 450–60. [24] Brendecke SM, Prinz M. IB- deficiency leaves epithelial cells high and dry. Immunity 2013;38:404–6. ˜ A, et al. [25] Paster W, Brockmeyer C, Fu G, Simister PC, de Wet B, Martinez-Riano GRB2-mediated recruitment of THEMIS to LAT is essential for thymocyte development. J Immunol 2013;190:3749–56. [26] Chabod M, Pedros C, Lamouroux L, Colacios C, Bernard I, Lagrange D, et al. A spontaneous mutation of the rat Themis gene leads to impaired
R. Sorrentino / Immunology Letters 158 (2014) 116–119 function of regulatory T cells linked to inflammatory bowel disease. PLoS Genet 2012;8:e1002461. [27] Lees CW, Barrett JC, Parkes M, Satsangi J. New IBD genetics: common pathways with other diseases. Gut 2011;60:1739–53. [28] Burn GL, Svensson L, Sanchez-Blanco C, Saini M, Cope AP. Why is PTPN22 a good candidate susceptibility gene for autoimmune disease? FEBS Lett 2011;585:3689–98.
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[29] Song GG, Kim JH, Kim YH, Lee YH. Association between CTLA-4 polymorphisms and susceptibility to celiac disease: a meta analysis. Hum Immunol 2013;74:1214–8. [30] Ueda H, Howson JM, Esposito L, Heward J, Snook X, Chamberlain G, et al. Association of the T regulatory gene CTLA4 with susceptibility to autoimmune disease. Nature 2003;423:506–11.
Contents lists available at ScienceDirect
Immunology Letters journal homepage: www.elsevier.com/locate/immlet
Review
Genetics of autoimmunity: An update Rosa Sorrentino ∗ Department of Biology and Biotechnology “Charles Darwin” and Istituto Pasteur-Cenci Bolognetti, Sapienza University, Rome, Italy
a r t i c l e
i n f o
Article history: Received 22 October 2013 Received in revised form 3 December 2013 Accepted 4 December 2013 Available online 24 December 2013 Keywords: Autoimmunity Genetics Polymorphisms
a b s t r a c t The advent of genome-wide association studies (GWAS) has produced tremendous insights into the genetics of immune-mediated diseases allowing to identify hundreds of associated variants, some of which disease-specific and some others shared by groups of diseases. However, each variant usually accounts for a small genetic risk and all together they explain a relatively small portion of heritability for each disease. In addition, many of the associated variants map in regions of still undisclosed functions. This opens up to a new era of studies in search of the “missing heritability” which might partially be explained by gene–gene interactions and/or additive effects impacting on biochemical pathways relevant for the disease pathogenesis. The introduction of the immunochip analysis that allows to analyze thousands of patients for variations more strictly correlated with the immune/inflammatory functions is now allowing to single out relevant pathways shared by different diseases. Finally, great expectations are brought about from the studies on the effects that epigenetic modifications can have on the tuning of the expression of single allele/s in myeloid cells as well as in target tissues. Some of these topics have been discussed at the 15th International Congress of Immunology. © 2013 Elsevier B.V. All rights reserved.
The occurrence of autoimmunity represents a big challenge for the immunologists since it entails that something has gone wrong with the tuning of the immune response but, given the heterogeneity of the clinical manifestations leading to such large number of different diseases, determining the heart of the matter has proved to be quite difficult. Can the genetics help to untangle this task? Autoimmune diseases show a variable degree of heritability based on polygenic variants and the new era of the genetics has given hope to pinpoint the major variants that could impact on the disease course. It must be pointed out however, that, in autoimmune diseases, as well as in other polygenic diseases, the heritability is usually higher than what can be explained by the associated variants emerging from the GWAS. This “missing heritability” is a highly debated topic for which not necessarily a unique explanation does exist. It is possible that, due to the limitations of GWAS that mostly rely on not very dense common variants, we are indeed missing rare causal variations sharing a moderate degree of linkage disequilibrium with the analyzed markers, and thus shortening the distance from monogenic diseases. Part of this missing heritability might also be explained by gene–gene interactions which require the analysis of very large cohorts of patients and which, again, remind the effect of modifier genes in monogenic diseases [1–5]. In any case, heterogeneous groups of patients are often collected under a single disease, hiding different
∗ Tel.: +39 0649917706. E-mail address: [email protected] 0165-2478/$ – see front matter © 2013 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.imlet.2013.12.005
aetiological causes and complicating the matter. During this workshop, several examples of the state of art in the field have been discussed attesting the contribution of the genetics to the comprehension of the mechanisms responsible for the aberrant immune responses (Table 1). A provocative news coming from the GWAS, is that the number of variants found to be associated to each disease is increasing everyday, in parallel with the technical improvements that allow to analyze larger cohorts of patients. A direct relationship between the number of cases analyzed by GWAS and the growing list of associated variants has been recently illustrated [6]. However, all together these allelic variants account for a relatively small risk, explaining between 20% and 50% of heritability, increasing the skepticism of the non-geneticists on the real value of such a large and costly amount of data. The recent introduction of the immunochips that spot immune-related variants, represents a step forward since it allows to identify those genes more strictly related to the immune/inflammatory pathways. From these data, pathways shared by apparently different diseases and epistatic interactions among these genes, are beginning to emerge [6]. Moreover, specific genetic variants can now be associated with different clinical features allowing to split cohorts of patients in more homogenous groups. An intriguing and innovative message emerging from animal models in which the functional impact of these variants is studied, is that, while so far the attention has been focused on myeloid cells as key players in the inflammatory network, it is now time to go back to tissues and to ask what is the primum movens in the cross-talk
R. Sorrentino / Immunology Letters 158 (2014) 116–119 Table 1 Examples of genes associated with more than two immune-mediated diseases. Gene (chromosome region)
Disease
Refs.
ERAP1 (5q15)
AS Behc¸et’s disease Psoriasis
9 10 11
IRF5-TNPO3 (7q32)
LES Sjogren’s disease RA Systemic sclerosis Primary biliary cirrhosis IBD
15, 16 14 27 17 12 27
STAT3 (17q21)
IBD Psoriasis MS
6 6 6
STAT4 (2q32)
IBD RA Primary biliary cirrhosis Coeliac disease LES Behc¸et’s disease
6 6 6 6 6 6
IL12A (3q25)
MS Primary biliary cirrhosis Coeliac disease
6 6 6
IL-12R (1p31)
AS IBD Primary biliary cirrhosis Behc¸et’s disease
6 6 6 6
IL-23R (1p31)
AS IBD Psoriasis
6 6 6
TYK2 (19p13)
AS IBD Psoriasis MS T1D RA Primary biliary cirrhosis
6 6 6 6 6 6 6
PTPN22 (1p13)
RA T1D SLE
28 28 28
CTLA4 (2q33)
Coeliac disease T1D Graves’ disease
29 30 30
AS, ankylosing spondylitis; RA, rheumatoid arthritis; SLE, systemic lupus erythematosus; T1D, type I diabetes; IBD, inflammatory bowel disease; CD, coeliac disease, MS, multiple sclerosis.
between immune cells and target tissues. There are some lessons coming from the workshop held at the ICI 2013 meeting. To start from the beginning however, the best known and undeniable hallmark of autoimmune diseases is their association with the HLA region, that refers to the involvement of an adaptive immune response which has been indeed demonstrated to play a direct role with both its cellular and humoral arms. This association in the majority of cases involves the HLA-class II region, with the exception of a subgroup of diseases associated with the HLAclass I alleles [7]. The case of HLA-B27 in Ankylosing Spondylitis has been discussed and it has been shown how a single amino acid substitution (D116H) in the two subtypes, the disease-associated B*2705 and the non-associated B*2709, dictates a strong difference in the flexibility of the peptide-binding groove. This confers to the disease-associated B*2705 specific properties that can influence its folding as well as its peptidome [8]. Strong support for a direct role played by the HLA-class I molecules in the pathogenesis of the associated autoimmune diseases is coming from GWAS.
117
Thanks to the large cohorts of patients that can now be analyzed, it has been possible to define the association of three of these diseases, namely Ankylosing Spondylitis, Psoriasis and Behc¸et disease, with ERAP1 gene on chromosome 5 [9–11]. This gene encodes for an ER-resident aminopeptidase involved in the refining of peptides bound to the HLA-class I molecules. Interestingly, this association holds true only in those cases positive respectively for HLA-B*27, HLA-Cw6 and HLA-B*51, indicating a gene–gene interaction that strengthens the role of antigen presentation in the pathogenesis of these diseases. What about the HLA-B27/Cw6/B51 negative cases in AS, Psoriasis and Behc¸et, respectively? Do these patients suffer from a different disease? In practice, what these data tell us is that, while it would make sense to target ERAP1 activity in the HLA-associated cases, it wouldn’t in the negative ones, giving an example of how the genetics can help us to design more specific therapeutic approaches. Defining gene–gene interactions is of paramount relevance since it would allow to infer from a list of genes, pathways of higher penetrance. A second crucial question to which the genetics can contribute, is the finding of a common ground shared by different autoimmune diseases. To this regard, besides ERAP1 in HLA-class I-associated diseases discussed above, many other connections are emerging. In this workshop the role played by the IRF5-TNPO3 region on chromosome 17 has been discussed. This is a complex region found to be associated with different autoimmune diseases such as SLE, Sjogren’s syndrome, systemic sclerosis and primary biliary cirrhosis. However, it is not clear which function is associated with each disease. The Harley’s group in Cincinnati has made an effort to identify the causal variants in SLE over a region of 85.5 kb and reported a strong association with age of onset (variants in the haplotype) and the presence of anti-Ro and anti-dsDNA autoantibodies (variants in the IRF-5 promoter) involving the IRF-5 gene directly in the B cellmediated response and a less defined region in the triggering of the different diseases [12–19]. A further illustration of how different clinical aspects can be associated with different subsets of genes comes from Rheumatoid Arthritis as illustrated by Chovanova, who reported that allelic variants at different genes correlate with a higher proportion of different myeloid cell types and, consequently, with a different array of cytokines. As an example, a higher proportion of memory B cells correlates with risk alleles in PTPN22, AFF3, PAD14 and TRAF1/C5 genes whereas a higher proportion of CD8+ T cells correlates with risk alleles in IRF5, STAT4 and CTLA4 genes indicating that the long list of factors conferring susceptibility to RA represents a continuum in which, depending on the genetic background of the single patients, one or the other pathogenic aspect can prevail. Another examples of the link between associated variants and altered functions was reported by Fossati-Jimack who showed how the Arg to His substitution at position 77 of the CD11b, one of the genes more strongly associated with SLE, results in a defect of C3mediated phagocytosis in different cell types [20]. A further aspect complicating the genetics of autoimmune diseases, is that the association between a SNP and a disease can be restricted to some ethnic groups, depending on the allelic frequency and on the evolutionary history of the population. This is the case of the PXK (PX domain containing serine/threonine kinase) for which Vaughn reported an independent effect occurring in women with SLE of European ancestry only. He also showed that the risk allele correlates with a more rapid internalization of the B cell receptor (BCR) with which it co-localizes [21]. This is not surprising since a complex disease is the result of many different factors and the lack of one of them is never crucial, not even the absence of the HLA allele/s conferring the highest risk. Interestingly however, when disease associated variations are analyzed in isolated contexts, they often show a striking
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functional effect that badly correlates with the low risk conferred to the disease. More advanced techniques to study the functional variations at single cell level in contexts in which the two alleles are not over-expressed are needed. This appears now to be possible [22]. A relevant question also discussed during the workshop, is in which cell/tissue context the altered function is pathogenic. In this framework, Okuma reported the impressive case of Sjogren’s disease. His group set up a mouse model in which the diseaseassociated IkB- gene, a transcriptional factor belonging to the NF-kB family involved in inflammation, was knocked-out. These mice developed a disease very similar to Sjogren’s, characterized by leukocyte infiltration and presence of autoantibodies. The surprise however was that the inflammation was not due to an altered function of the myeloid cells but to the enhanced apoptosis of the epithelial cells. Accordingly, the clinical symptoms were partially reverted by the use of caspase inhibitors. This group took a step forward and analyzed STAT3-deficient mice that showed symptoms very similar to those previously observed in the case of IkB- deficiency. Also under these circumstances, the clinical dysfunction was reported as due to a lack of function of STAT3-mediated IkB- function in which dysfunction of the epithelia cells elicited the activation of self-reactive lymphocytes [23,24]. Several questions remain open: why this happens in specific epithelial cells only? How do lymphocytes are activated? Is this due to the crosspresentation of specific antigens? But, more intriguingly, to what extent this model can be extrapolated to humans and/or to other autoimmune diseases? How much a knock-out model recapitulates the effect of genetic variants? Do we have to move more of our attention to the target tissue/s? Finally, another interesting report has been focused on Themis. Themis is a fine-tuner of the TCR signaling acting in thymus and influencing thymic selection as pointed out by Acuto during his lecture at ICI 2013 [25]. However, its function has also been linked to the maturation of T regulatory cells in a model of BN rats that had a frameshift mutation in Themis gene and developed an inflammatory bowel disease. Interestingly, Pedros reported that Themis deficiency in LEW rats does not impair T regulatory function neither correlates with any pathological phenotype unless a constitutive active VAV1 variant was present. These data indicate the VAV1/Themis co-operation as crucial for the regulation of the suppressive functions of Treg and point, not surprisingly, to the maturation/function of Treg as a pivotal event in autoimmunity [26]. In conclusion, the genetics of the autoimmune diseases is still a flourishing field and it is now approaching the second line of research. GWAS of thousands of patients have shown us that a high number of genes are associated with autoimmunity and research is in progress to attribute subsets of these genes to the different disease traits, such as age of onset, clinical course. The most relevant pathways are likely to be spotted thanks also to the identification of gene–gene interactions that should allow to focus on more personalized therapeutic approaches, and help to reconcile the functional differences enlightened by molecular studies with the small risk associated with each genetic variant. Finally, tremendous insights are expected from the study of the epigenetic interactions that could contribute to the expression of single alleles in relevant tissues. The genetics can tell us where to start by indicating which genes and pathways are relevant for each disease to occur, but how their expression can be modulated by epigenetic events, possibly under the control of environmental stimuli, represents the next challenging, long step. Next years will be very exciting and the next ICI congress will give us more insights into the connection between the genetics and the epigenetics events in the pathogenesis of autoimmune diseases.
References [1] Maher B. Personal genomes: the case of the missing heritability. Nature 2008;456:18–21. [2] Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, et al. Finding the missing heritability of complex diseases. Nature 2009;461: 747–53. [3] Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB. Rare variants create synthetic genome-wide associations. PLoS Biol 2010;8: e1000294. [4] Zuk O, Hechter E, Sunyaev SR, Lander ES. The case of the missing heritability: genetics interactions create phantom heritability. Proc Natl Acad Sci USA 2012;109:1193–8. [5] Hemani G, Knott S, Haley C. An evolutionary perspective on epistasis and the missing heritability. PLoS Genet 2013;9:e1003295. [6] Parkes M, Cortes A, van Heel DA, Brown M. Genetic insights into common pathways and complex relationships among immune-mediated diseases. Nat Rev Genet 2013;14:661–73. [7] Fernando MM, Stevens CR, Walsh EC, De Jager PL, Goyette P, Plenge RM, et al. Defining the role of the MHC in autoimmunity: a review and pooled analysis. PLoS Genet 2008;4:e1000024. [8] Sorrentino R, Böckmann RA, Fiorillo MT. HLA-B27 and antigen presentation: at the crossroads between immune defense and autoimmunity. Mol Immunol 2014;57:22–7. [9] Evans DM, Spencer CC, Pointon JJ, Su Z, Harvey D, Kochan G, et al. Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility. Nat Genet 2011;43:761–7. [10] Kirino Y, Bertsias G, Ishigatsubo Y, Mizuki N, Tugal-Tutkun I, Seyahi E, et al. Genome-wide association analysis identifies new susceptibility loci for Behc¸et’s disease and epistasis between HLA-B*51 and ERAP1. Nat Genet 2013;45:202–7. [11] Genetic Analysis of Psoriasis Consortium & the Wellcome Trust Case Control Consortium 2, Strange A, Capon F, Spencer CC, Knight J, Weale ME, et al. A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1. Nat Genet 2010;42: 985–90. [12] Hirschfield GM, Liu X, Han Y, Gorlov IP, Lu Y, Xu C, et al. Variants at IRF5-TNPO3, 17q12-21 and MMEL1 are associated with primary biliary cirrhosis. Nat Genet 2010;42:655–7. [13] Liu X, Invernizzi P, Lu Y, Kosoy R, Lu Y, Bianchi I, et al. Genome-wide metaanalyses identify three loci associated with primary biliary cirrhosis. Nat Genet 2010;42:658–60. [14] Miceli-Richard C, Gestermann N, Ittah M, Comets E, Loiseau P, Puechal X, et al. The CGGGG insertion/deletion polymorphism of the IRF5 promoter is a strong risk factor for primary Sjögren’s syndrome. Arthritis Rheum 2009;60(6):1991–7. [15] Kozyrev SV, Lewén S, Reddy PM, Pons-Estel B, Argentine Collaborative Group, Witte T, et al. Structural insertion/deletion variation in IRF5 is associated with a risk haplotype and defines the precise IRF5 isoforms expressed in systemic lupus erythematosus. Arthritis Rheum 2007;56:1234–41. [16] Graham RR, Kozyrev SV, Baechler EC, Reddy MV, Plenge RM, Bauer JW, et al. A common haplotype of interferon regulatory factor 5 (IRF5) regulates splicing and expression and is associated with increased risk of systemic lupus erythematosus. Nat Genet 2006;38:550–5. [17] Carmona FD, Martin JE, Beretta L, Simeón CP, Carreira PE. The systemic lupus erythematosus IRF5 risk haplotype is associated with systemic sclerosis. PLoS ONE 2013;8:e54419. [18] Stone RC, Du P, Feng D, Dhawan K, Rönnblom L. RNA-Seq for enrichment and analysis of IRF5 transcript expression in SLE. PLoS ONE 2013;8: e54487. [19] Dieudé P, Guedj M, Wipff J, Avouac J, Fajardy I. Association between the IRF5 rs2004640 functional polymorphism and systemic sclerosis: a new perspective for pulmonary fibrosis. Arthritis Rheum 2009;60:225–33. [20] Fossati-Jimack L, Ling GS, Cortini A, Szajna M, Malik TH. Phagocytosis is the main CR3-mediated function affected by the lupus-associated variant of CD11b in human myeloid cells. PLoS ONE 2013;8:e57082. [21] International Consortium for Systemic Lupus Erythematosus Genetics (SLEGEN), Harley JB, Alarcón-Riquelme ME, Criswell LA, Jacob CO, Kimberly RP, et al. Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet 2008;40:204–10. [22] Wills QF, Livak KJ, Tipping AJ, Enver T, Goldson AJ, Sexton DV. Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments. Nat Biotechnol 2013;31:748–52. [23] Okuma A, Hoshino K, Ohba T, Fukushi S, AibaS., Akira S, et al. Enhanced apoptosis by disruption of the STAT3-IB- signaling pathway in epithelial cells induces Sjögren’s syndrome-like autoimmune disease. Immunity 2013;38: 450–60. [24] Brendecke SM, Prinz M. IB- deficiency leaves epithelial cells high and dry. Immunity 2013;38:404–6. ˜ A, et al. [25] Paster W, Brockmeyer C, Fu G, Simister PC, de Wet B, Martinez-Riano GRB2-mediated recruitment of THEMIS to LAT is essential for thymocyte development. J Immunol 2013;190:3749–56. [26] Chabod M, Pedros C, Lamouroux L, Colacios C, Bernard I, Lagrange D, et al. A spontaneous mutation of the rat Themis gene leads to impaired
R. Sorrentino / Immunology Letters 158 (2014) 116–119 function of regulatory T cells linked to inflammatory bowel disease. PLoS Genet 2012;8:e1002461. [27] Lees CW, Barrett JC, Parkes M, Satsangi J. New IBD genetics: common pathways with other diseases. Gut 2011;60:1739–53. [28] Burn GL, Svensson L, Sanchez-Blanco C, Saini M, Cope AP. Why is PTPN22 a good candidate susceptibility gene for autoimmune disease? FEBS Lett 2011;585:3689–98.
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[29] Song GG, Kim JH, Kim YH, Lee YH. Association between CTLA-4 polymorphisms and susceptibility to celiac disease: a meta analysis. Hum Immunol 2013;74:1214–8. [30] Ueda H, Howson JM, Esposito L, Heward J, Snook X, Chamberlain G, et al. Association of the T regulatory gene CTLA4 with susceptibility to autoimmune disease. Nature 2003;423:506–11.
