The MALT1 locus and peanut avoidance in the risk for peanut allergy
Authors: Alexandra Winters, Henry T. Bahnson, Ingo Ruczinski, Meher P. Boorgula, Claire Malley, Ali R. Keramati, Sameer Chavan, David Larson, Karen Cerosaletti, Peter H. Sayre, Marshall Plaut, George Du Toit, Gideon Lack, Kathleen C. Barnes, Gerald T. Nepom, Rasika A. Mathias
Journal: Journal of Allergy and Clinical Immunology (2019)

The Learning Early About Peanut allergy (LEAP) study1Du Toit G. Roberts G. Sayre P.H. Bahnson H.T. Radulovic S. Santos A.F. et al.Randomized trial of peanut consumption in infants at risk for peanut allergy.N Engl J Med. 2015; 372: 803-813Crossref PubMed Scopus (1321) Google Scholar, 2Togias A. Cooper S.F. Acebal M.L. Assa'ad A. Baker J.R. Beck L.A. et al.Addendum guidelines for the prevention of peanut allergy in the United States: report of the National Institute of Allergy and Infectious Diseases-sponsored expert panel.Ann Allergy Asthma Immunol. 2017; 118: 166-173.e7Abstract Full Text Full Text PDF PubMed Scopus (45) Google Scholar motivated a change in pediatric guidelines for the early introduction of dietary peanut as an effective strategy for the prevention of peanut allergy. LEAP study participants were presumed to be at increased risk for peanut allergy,3Du Toit G. Roberts G. Sayre P.H. Plaut M. Bahnson H.T. Mitchell H. et al.Identifying infants at high risk of peanut allergy: the Learning Early About Peanut Allergy (LEAP) screening study.J Allergy Clin Immunol. 2013; 131 (e1-12): 135-143Abstract Full Text Full Text PDF PubMed Scopus (199) Google Scholar and dietary introduction of peanut protein beginning in the first 4 to 11 months of life significantly decreased the frequency of peanut allergy later in childhood and modulated the immune response to peanuts in this at-risk group.1Du Toit G. Roberts G. Sayre P.H. Bahnson H.T. Radulovic S. Santos A.F. et al.Randomized trial of peanut consumption in infants at risk for peanut allergy.N Engl J Med. 2015; 372: 803-813Crossref PubMed Scopus (1321) Google Scholar Whole-genome sequencing (WGS) was performed to identify the genetic determinants of peanut allergy in the LEAP study participants (see the Methods section and Table E1 in this article's Online Repository at www.jacionline.org). Following published standards for WGS data (see the Methods section in this article's Online Repository),4Mathias R.A. Taub M.A. Gignoux C.R. Fu W. Musharoff S. O'Connor T.D. et al.A continuum of admixture in the Western Hemisphere revealed by the African diaspora genome.Nat Commun. 2016; 7: 12522Crossref PubMed Scopus (88) Google Scholar there were 542 per-protocol LEAP study participants available for genome-wide genetic association tests, including 49 with peanut allergy, which was defined as a positive result on a double-blind, placebo-controlled oral food challenge at 60 months of age (see the Methods section in this article's Online Repository). The deconvolution of genetic ancestry aligns well with self-reported race/ethnicity (see the Method section and Fig E1 in this article's Online Repository at www.jacionline.org). Given the high success of early introduction of dietary peanut in the LEAP study, 48 participants with peanut allergy were from the peanut avoidance arm, and only 1 was from the consumption arm (see Table E1). Therefore genome-wide association was assessed for peanut allergy in the 275 participants from the avoidance arm (n = 48 for participants with peanut allergy and n = 227 for participants without peanut allergy) on a total of 4,444,069 single nucleotide variants (SNVs; Fig 1 and see the Methods section and Fig E2 in this article's Online Repository at www.jacionline.org) in a discovery analysis. Subsequent follow-up of the peak genetic signal was extended to include the participants from the consumption arm (n = 267), with immunologic quantitative traits of importance (Fig 2) to facilitate examination of the identified genetic loci in the context of the intervention.Fig 2A, Proportion of allergic and nonallergic LEAP study participants at 60 months of age by treatment group and MALT1 carrier status in all LEAP study participants (left) and the sensitized group (right; defined as those with peanut-specific IgE levels of 0.1 kU/L or greater at 60 months). B, IgE response to Ara h 1, Ara h 2, and Ara h 3 over the course of the LEAP study in all participants (n = 542). Arachis hypogaea status was imputed to 0 for all participants with peanut-specific IgE levels of less than 0.1 kU/L. C, Proportion of density plots showing relative distribution of peanut-specific IgE and IgE to Ara h 1, Ara h 2, and Ara h 3 between the MALT1 carrier and noncarrier groups at 60 months of age. The horizontal reference line at 12% indicates the proportion of the population with at least 1 MALT1 risk allele, which shows a null distribution with equal proportions of participants at all titer levels between the carriers and noncarriers. A hypogaea status was imputed to −2 (log10) for all participants with peanut-specific IgE levels of less than 0.1 kU/L. For all panels, imputed genotypes were used for 7 participants missing allele calls at rs57265082, and noncarriers were defined as having at least 1 copy of the T allele (because of the low MAF; see Table E2 in this article's Online Repository at www.jacionline.org).View Large Image Figure ViewerDownload Hi-res image Download (PPT) The peak association for peanut allergy in the avoidance group was observed on chromosome 18 (Fig 1, A), mapping to the mucosa-associated lymphoid tissue lymphoma translocation (MALT1) gene (Fig 1, C, and see Table E3 in this article's Online Repository at www.jacionline.org). The region (Chr18:56337602..56456191) includes strong regulatory signatures for MALT1 expression, as well as expression of the intergenic noncoding RNA RP11-108P20.1 in Genotype-Tissue Expression data (see Figs E3 and E4 in this article's Online Repository at www.jacionline.org). However, the specific set of SNVs with P values of less than 10−5 for peanut allergy only have expression quantitative trait locus signatures for MALT1 (see Table E4 in this article's Online Repository at www.jacionline.org). The peak associated SNV was rs57265082, with an estimated odds ratio (OR) of 10.99, minor allele frequency (MAF) of 5.6%, and P value of 6.49 × 10−8. Gene-based analysis was performed across rare exonic SNVs (MAF ≤ 5%) by using the Sequence Kernel Association Test (see Tables E5 and E6 in this article's Online Repository at www.jacionline.org). There was nominal association with either all rare exonic SNVs (P = .0830) or all rare damaging exonic SNVs (P = .0828); however, with the inclusion of the peak WGS variant rs57265082, the gene-based evidence was very strong (P = 1.89 × 10−10). Conditioning on the peak SNV rs57265082 shows that the observed common variant signal is a single genetic locus within the region (see Fig E5 in this article's Online Repository at www.jacionline.org). There are overall strong differences in the clinical profiles of the MALT1 risk allele carriers compared with noncarriers within the participants in the peanut avoidance group (see Table E7 in this article's Online Repository at www.jacionline.org). MALT1 is not associated with baseline selection criteria of egg allergy or eczema (P = .3241 and P = .1626, respectively, in the avoidance group), and the association between peanut allergy and MALT1 is independent of these baseline selections (see Table E8 in this article's Online Repository at www.jacionline.org). We observe no association between the key filaggrin variant R501X, which is documented to play a role in eczema and peanut allergy (P = .4014 and MAF of 3.6% in the avoidance group), but recognize that our sample size of 275 might be underpowered for this. We observed a weaker association with rs57265082 to sensitization (at 60 months, sensitization is defined as those with peanut-specific IgE levels of 0.1 kU/L or greater) in the peanut avoidance group (OR, 4.55; P = .0011). Additionally, the MALT1 locus remains significantly associated with peanut allergy (P = .0003), even within the subset of sensitized participants in the peanut avoidance group (Fig 2, A), supporting its role as a genetic risk factor for allergy and not only sensitization. With the inclusion of the LEAP study participants from the consumption arm (n = 267), MALT1 was found to be significantly associated with an IgE response to multiple specific peanut allergenic protein components (ie, Ara h 1, Ara h 2, and Ara h 3) at 60 months (P = 1.11 × 10−5, Fig 2, B, and see the Methods section in this article's Online Repository) in the full set of LEAP study participants adjusting for intervention. When examining specific IgE to peanut, as well as the 3 major allergenic components of peanut, we observed a progressive divergence in the upper end of the IgE distributions in MALT1 carriers (Fig 2, C), with 2 key observations to note. First, the intervention with peanut exposure effectively reduced peanut-specific IgE, irrespective of carrier status (truncated distributions in Fig 2, C, bottom panel). Second, within the avoidance group, levels of peanut-specific IgE between the carriers and noncarriers are markedly different; rs57265082 carriers within the peanut avoidance group had the highest peanut-specific IgE levels compared with noncarriers (Fig 2, C, upper panel). Mean titers of peanut-specific IgE were significantly different between carriers and noncarriers and by treatment group (interaction P = 1.86 × 10−5), even after adjusting for the baseline differences in peanut-specific IgE levels (see Fig E6, A, in this article's Online Repository at www.jacionline.org). Importantly, this effect of MALT1 on peanut-specific IgE levels in the peanut avoidance group is independent of total IgE (P = 2.03 × 10−5 for peanut-specific IgE and P = .366 for total IgE; see Fig E6, B). Finally, the additional value of knowing rs57265082 carrier status in predicting a participant's likelihood of allergy was evaluated, and rs57265082 was found to be an independent predictor of allergy in the avoidance group (see Fig E7 in this article's Online Repository at www.jacionline.org). In this first report of the genetics of peanut allergy within the LEAP study, a key biological candidate, the MALT1 gene, is implicated as an independent risk factor for peanut allergy in the context of peanut avoidance. These associations are irrespective of sensitization status (in Fig E7, sensitization at baseline is defined by using skin prick positivity, and in Fig 2, A, sensitization at 60 months is defined as peanut-specific IgE levels of 0.1 kU/L or greater), supporting a relationship with progression to symptomatic allergy after peanut sensitization, a disease pattern that is inhibited by early and continuous consumption of peanuts. MALT1 encodes a paracaspase that functions as a critical part of the CARMA1-BCL10-MALT1 complex, causing nuclear factor κB activation in B and T cells in response to an antigen binding to the B- or T-cell receptor.5Thome M. CARMA1, BCL-10 and MALT1 in lymphocyte development and activation.Nat Rev Immunol. 2004; 4: 348-359Crossref PubMed Scopus (332) Google Scholar In T cells this forms part of the signaling cascade leading to T-cell activation6Vickery B.P. Chin S. Burks A.W. Pathophysiology of food allergy.Pediatr Clin North Am. 2011; 58 (ix-x): 363-376Abstract Full Text Full Text PDF PubMed Scopus (70) Google Scholar and involves the 2 MALT1 isoforms MALT1A and MALT1B.7Meininger I. Griesbach R.A. Hu D. Gehring T. Seeholzer T. Bertossi A. et al.Alternative splicing of MALT1 controls signalling and activation of CD4(+) T cells.Nat Commun. 2016; 7: 11292Crossref PubMed Scopus (72) Google Scholar Given that our top SNVs affect MALT1 expression, it is possible that these variants might predispose a subject to greater allergic disease by altering MALT1 expression or affecting the ratio of MALT1A to MALT1B, thus increasing TH2 differentiation after antigen presentation. Additional genes encoding other members of the CARMA1-BCL10-MALT1 complex do not show evidence for association within our discovery data (see Fig E8 in this article's Online Repository at www.jacionline.org). MALT1 has not been implicated in prior genetic studies, and we are also unable to replicate prior published associations (see Table E9 in this article's Online Repository at www.jacionline.org).8Asai Y. Eslami A. van Ginkel C.D. Akhabir L. Wan M. Yin D. et al.A Canadian genome-wide association study and meta-analysis confirm HLA as a risk factor for peanut allergy independent of asthma.J Allergy Clin Immunol. 2018; 141: 1513-1516Abstract Full Text Full Text PDF PubMed Scopus (17) Google Scholar, 9Asai Y. Eslami A. van Ginkel C.D. Akhabir L. Wan M. Ellis G. et al.Genome-wide association study and meta-analysis in multiple populations identifies new loci for peanut allergy and establishes C11orf30/EMSY as a genetic risk factor for food allergy.J Allergy Clin Immunol. 2018; 141: 991-1001Abstract Full Text Full Text PDF PubMed Scopus (47) Google Scholar It is important to note that the prior studies compare nonallergic control subjects with individuals with peanut allergy,8Asai Y. Eslami A. van Ginkel C.D. Akhabir L. Wan M. Yin D. et al.A Canadian genome-wide association study and meta-analysis confirm HLA as a risk factor for peanut allergy independent of asthma.J Allergy Clin Immunol. 2018; 141: 1513-1516Abstract Full Text Full Text PDF PubMed Scopus (17) Google Scholar, 9Asai Y. Eslami A. van Ginkel C.D. Akhabir L. Wan M. Ellis G. et al.Genome-wide association study and meta-analysis in multiple populations identifies new loci for peanut allergy and establishes C11orf30/EMSY as a genetic risk factor for food allergy.J Allergy Clin Immunol. 2018; 141: 991-1001Abstract Full Text Full Text PDF PubMed Scopus (47) Google Scholar and the genetic associations identified in these likely represent the risk of allergic sensitization and not specifically peanut allergy. In contrast, the LEAP study included only participants who were at high risk for peanut allergy, many of whom were sensitized at baseline, and this unique ascertainment of the LEAP study facilitates our ability to test specifically for the risk of peanut allergy. Yet another singular advantage of the LEAP study is that we are able to interrogate the avoidance group (high incidence of peanut allergy) and contrast this with the consumption group (low incidence of peanut allergy) by using quantitative immunologic markers to identify the genetic determinants of peanut allergy that are relevant in the absence of peanut exposure. This homogeneity of exposure (ie, avoidance) and ascertainment (ie, baseline risk factors) within the LEAP study account for the ability to detect a strong association with MALT1 despite the limited sample size of 275 in the discovery analysis; in fact, the P value of 6.49 × 10−8 for single-variant tests is near the Bonferroni threshold for genome-wide association study significance (5 × 10−8), and our gene-based analysis results in a P value of 1.89 × 10−10. Targeted genotyping of rs57265082 on additional LEAP study participants, including the non–per-protocol participants, does not change the results from the discovery sample (see the Methods section and Table E10 in this article's Online Repository at www.jacionline.org). Furthermore, of the 7 participants within the consumption arm who had peanut allergy at baseline, 3 were MALT1 carriers (unadjusted OR for peanut allergy at baseline in the LEAP study consumption group, 5.3; P = .0188, Pearson χ2 test). However, the lack of a suitable population to use as a replication group is a major limitation of this study, and additional replication will be important to follow-up on these associations observed within the LEAP study. One striking observation is the differing effect of MALT1 carrier status on peanut-specific IgE patterns between the 2 intervention arms in the LEAP study. The introduction of dietary peanut as a strategy for the prevention of peanut allergy is equally effective within carriers and noncarriers. However, our results indicate that within the LEAP study participants, MALT1 carriers from the peanut avoidance group have the highest risk for peanut allergy (58.6% of carriers of the MALT1 variant in the avoidance group go on to have peanut allergy in contrast to only 12.7% of the noncarriers, see Table E7). Coupled with the observations that (1) acquisition of additional peanut antigen target specificities in the IgE response is markedly increased in MALT1 carriers and (2) this peanut-specific IgE response is independent of total IgE, our findings support a genotype-phenotype relationship that implicates the MALT1 pathway in the allergic immune pathogenesis of peanut allergy. We thank Drs Daniel Rotrosen and Alkis Togias from the National Institute of Allergy and Infectious Diseases for their review of the manuscript, Ms Monica Campbell from the University of Colorado for her help preparing samples for genotyping, and all the LEAP study participants who took part in the study. 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