Vitamin D and Atopy

Recently, our research team found a strong and significant association between loss-of-function (LOF) mutations in filaggrin (FLG), a gene that encodes a skin barrier protein, in European and Canadian individuals with peanut allergy (PA).1Brown S.J. Asai Y. Cordell H.J. Campbell L.E. Zhao Y. Liao H. et al.Loss-of-function variants in the filaggrin gene are a significant risk factor for peanut allergy.J Allergy Clin Immunol. 2011; 127: 661-667Abstract Full Text Full Text PDF PubMed Scopus (326) Google Scholar These mutations result in a barrier defect and have been associated with atopic dermatitis, asthma, and allergic rhinitis.2Irvine A.D. McLean W.H. Leung D.Y. Filaggrin mutations associated with skin and allergic diseases.N Engl J Med. 2011; 365: 1315-1327Crossref PubMed Scopus (812) Google Scholar This finding represents the strongest genetic risk factor found to date for PA, a highly heritable disease,3Sicherer S.H. Furlong T.J. Maes H.H. Desnick R.J. Sampson H.A. Gelb B.D. Genetics of peanut allergy: a twin study.J Allergy Clin Immunol. 2000; 106: 53-56Abstract Full Text Full Text PDF PubMed Scopus (229) Google Scholar with an estimated odds ratio (OR) between 1.9 (Canadian) and 5.3 (English, Dutch, and Irish combined).1Brown S.J. Asai Y. Cordell H.J. Campbell L.E. Zhao Y. Liao H. et al.Loss-of-function variants in the filaggrin gene are a significant risk factor for peanut allergy.J Allergy Clin Immunol. 2011; 127: 661-667Abstract Full Text Full Text PDF PubMed Scopus (326) Google Scholar Because there is no uniformly accepted definition of PA short of oral food challenge, it is worthwhile to examine whether the association between the FLG LOF mutations and PA varies with the diagnostic criteria for PA. Furthermore, the frequent coexistence of PA with other atopic conditions may mean that the association between PA and FLG LOF mutations is confounded. Although we controlled for eczema in the European populations in our previous work, data on eczema were not available for the Canadian control group; however, data on asthma were available. Asthma is a potential confounder, as it has known relationships with both PA4Liu A.H. Jaramillo R. Sicherer S.H. Wood R.A. Bock S.A. Burks A.W. et al.National prevalence and risk factors for food allergy and relationship to asthma: results from the National Health and Nutrition Examination Survey 2005-2006.J Allergy Clin Immunol. 2010; 126: 798-806.e13Abstract Full Text Full Text PDF PubMed Scopus (379) Google Scholar and FLG mutations.5Palmer C.N. Ismail T. Lee S.P. Terron-Kwiatkowski A. Zhao Y. Liao H. et al.Filaggrin null mutations are associated with increased asthma severity in children and young adults.J Allergy Clin Immunol. 2007; 120: 64-68Abstract Full Text Full Text PDF PubMed Scopus (174) Google Scholar By using statistical sensitivity analyses, we examined the effect of PA diagnostic criteria and asthma on the relationship between PA and FLG LOF mutations in a Canadian PA case group. Because the PA case group was composed of both English- and French-speaking individuals, we also investigated whether the difference in OR between the Canadian and European populations could be due to some common French-Canadian mutations not yet identified in FLG.Caucasian subjects from a well-described Canadian pediatric PA case group were recruited (n = 679), and DNA was isolated from salivary samples.1Brown S.J. Asai Y. Cordell H.J. Campbell L.E. Zhao Y. Liao H. et al.Loss-of-function variants in the filaggrin gene are a significant risk factor for peanut allergy.J Allergy Clin Immunol. 2011; 127: 661-667Abstract Full Text Full Text PDF PubMed Scopus (326) Google Scholar One control group consisted of adult Caucasians recruited from the general population of Ontario, Canada; DNA was provided by the Ontario Population Genomics Platform at The Centre for Applied Genomics (Toronto) (n = 894). A second control group of newborn babies from Quebec City was sampled on the basis of French-Canadian surname (stored blood; n = 268).6Girouard J. Giguere Y. Delage R. Rousseau F. Prevalence of HFE gene C282Y and H63D mutations in a French-Canadian population of neonates and in referred patients.Hum Mol Genet. 2002; 11: 185-189Crossref PubMed Scopus (18) Google Scholar All samples were genotyped in Dundee, Scotland, for the 4 most common FLG LOF mutations found in Caucasians (R501X, 2282del4, R2447X, and S3247X). rs and accession numbers for mutations are available in the Online Repository at www.jacionline.org (see Table E1)."Mutation carriers" were defined as those with heterozygous, homozygous, or compound heterozygous mutations. Those individuals with none of the 4 FLG mutations were classified as "nonmutation carriers." The association between mutation status and PA was compared with the Ontario control group, the Quebec control group, and the combined control group. To evaluate whether the association between PA and mutation status changed with case definition, a continuum of PA case definitions was constructed and the resulting OR trends with case definition were examined by using the combined control groups. The methodology and rationale for these definitions are given in the Online Repository available at www.jacionline.org (see Tables E2 and E3). To increase power, case definitions were transformed into an ordered variable and the association between PA and FLG mutations was examined by using regression modeling through increasingly stringent definitions of PA to see whether the OR changed significantly.We also examined the effect of asthma on FLG mutation status and PA. Logistic regression using the Ontario control group was conducted with PA status, age, sex, asthma, and interaction terms for PA and age, PA and sex, and PA and asthma. Because there may be interaction between mutation status, asthma, and smoking,7Berg N.D. Husemoen L.L. Thuesen B.H. Hersoug L.G. Elberling J. Thyssen J.P. et al.Interaction between filaggrin null mutations and tobacco smoking in relation to asthma.J Allergy Clin Immunol. 2012; 129 (e1-2): 374-380Abstract Full Text Full Text PDF PubMed Scopus (30) Google Scholar and self-identified asthmatic patients may have significant misclassification, analyses controlled for smoking history in the controls and misclassification in the asthma variable in both controls and cases. A constructed atopic asthma variable was used to control for the effect of smoking with 4 assumptions: (1) Those individuals who have atopic asthma in childhood are less likely to smoke as adults. (2) Those adults who have asthma and have never smoked are more likely to have atopic asthma. (3) If a patient reports bronchial emphysema, he or she does not have atopic asthma. (4) Asthma reported in the case group is atopic. To examine the possibility of error due to self-report of asthma, we completed a sensitivity analysis taking into account data from the PA registry that found that 6% had "forgotten" previously noted atopic history, while 12% more reported atopic history on the current questionnaire than at baseline registry recruitment. Random sampling and subsequent logistic regression modeling was completed 100 times to see the overall effect of error in asthma reporting on the relationship of PA and FLG LOF mutations using these parameters.Finally, a similar sensitivity analysis of PA status was conducted, as PA status could be affected by the age disparity between the Ontario control group and the cases, because it is estimated that up to 20% of individuals with PA may have resolution of their allergy.8Skolnick H.S. Conover-Walker M.K. Koerner C.B. Sampson H.A. Burks W. Wood R.A. The natural history of peanut allergy.J Allergy Clin Immunol. 2001; 107: 367-374Abstract Full Text Full Text PDF PubMed Scopus (467) Google Scholar This sensitivity analysis also took into account the 1% prevalence of PA in the general population.9Ben-Shoshan M. Harrington D.W. Soller L. Fragapane J. Joseph L. St Pierre Y. et al.A population-based study on peanut, tree nut, fish, shellfish, and sesame allergy prevalence in Canada.J Allergy Clin Immunol. 2010; 125: 1327-1335Abstract Full Text Full Text PDF PubMed Scopus (174) Google ScholarOf the 679 cases eligible to participate, 99.3% had good quality DNA. Demographic information is presented in Table I. The 674 cases had approximately twice as many mutations as the controls (20% vs 11%), and the OR for PA and FLG mutation status was similar in the Ontario and Quebec control groups (Table II). The genotype frequencies in cases and controls are shown in the Online Repository available at www.jacionline.org (see Table E4). Among the 13 case definitions, there was no significant difference in the OR for the relationship between PA and FLG mutation status. Seven representative case definitions are shown in Table III. Logistic regression of the ordered case definition criteria variable produced similar results.Table IDemographics: PA cases and controlsCharacteristicPA casesOntario controlsQuebec controlsNo. of subjects674894268Age (y)∗Age on January 1, 2009. Mean ± SD9.3 ± 4.065.5 ± 10.29.7 ± 0.5 Range0-2133-847-10 No. with missing data020Sex No. of males416281157 Proportion of males (CI)0.617 (0.580-0.654)0.315 (0.284-0.346)0.586 (0.526-0.645)∗ Age on January 1, 2009. Open table in a new tab Table IIFLG genotypes and statistical tests of PA cases compared with control groupsPA casesOntario controlsQuebec controlsCombined controlsNo. of analyzed subjects∗Genotyping failures occurred in 11 PA cases, 5 of the Ontario controls, and 1 of the Quebec controls.6638892671156No. of FLG heterozygotes†One FLG mutation detected.1129429123No. of FLG homozygotes/compound heterozygotes‡Two of the same (FLG homozygote) or 2 different (compound heterozygote) FLG mutations detected.18415Total no. with 1 or 2 FLG mutations1309830128Proportion with 1 or 2 FLG mutations0.1960.1100.1120.110ORNA1.971.931.9695% CINA1.47-2.651.24-3.061.49-2.58χ2 test (P value)NA22.33 (2.30 × 10−6)9.37 (2.21 × 10−3)25.22 (5.12 × 10−7)NA, Not applicable.∗ Genotyping failures occurred in 11 PA cases, 5 of the Ontario controls, and 1 of the Quebec controls.† One FLG mutation detected.‡ Two of the same (FLG homozygote) or 2 different (compound heterozygote) FLG mutations detected. Open table in a new tab Table IIIPA case definition analysis (PA cases compared with the combined control group)No. of subjectsOR95% CIMinimum criteria to be considered for inclusion:a.Convincing history of PA∗A convincing history was defined as a minimum of 2 mild symptoms/signs or either 1 moderate or 1 severe symptom/sign occurring within 120 min after peanut contact or ingestion. (1) Mild: pruritus, urticaria, flushing, and/or rhinoconjunctivitis. (2) Moderate: angioedema, throat tightness, change in voice, coughing, difficulty breathing (other than wheeze), nausea and/or vomiting, and/or abdominal pain. (3) Severe: wheezing, stridor, cyanosis, and/or circulatory collapse. and (i) SPT ≥3 mm or (ii) psIgE ≥ 0.35 kU/L orb.No history of peanut ingestion/uncertain history of allergy and (i) SPT ≥3 mm and (ii) psIgE ≥15 kU/L orc.Any history suggestive of an IgE-mediated reaction not compatible with anaphylaxis and (i) SPT ≥8 mm or (ii) SPT ≥4 mm if <2 y old or (iii) psIgE ≥15 kU/L ord.Positive OFC6741.961.49-2.58psIgE ≥15 kU/L or SPT ≥8 mm, or positive OFC†The definition used in our previous work1 required a history of anaphylaxis or a history suggestive of type I hypersensitivity to peanut along with SPT ≥8 mm and psIgE ≥15 kU/L.5261.971.47-2.65psIgE ≥57 kU/L or SPT ≥8 mm, or positive OFC4862.071.53-2.78psIgE ≥57 kU/L or SPT ≥15 mm, or positive OFC2672.071.42-2.96psIgE ≥15 kU/L, or SPT ≥8 mm AND anaphylaxis, or positive OFC2662.091.44-3.00psIgE ≥57 kU/L, or SPT ≥8 mm AND anaphylaxis, or positive OFC2532.211.52-3.18psIgE ≥57 kU/L, or SPT ≥15 mm AND anaphylaxis, or positive OFC1222.281.38-3.69OFC, Oral food challenge; psIgE, peanut-specific immunoglobulin E; SPT, skin prick test.∗ A convincing history was defined as a minimum of 2 mild symptoms/signs or either 1 moderate or 1 severe symptom/sign occurring within 120 min after peanut contact or ingestion. (1) Mild: pruritus, urticaria, flushing, and/or rhinoconjunctivitis. (2) Moderate: angioedema, throat tightness, change in voice, coughing, difficulty breathing (other than wheeze), nausea and/or vomiting, and/or abdominal pain. (3) Severe: wheezing, stridor, cyanosis, and/or circulatory collapse.† The definition used in our previous work1 required a history of anaphylaxis or a history suggestive of type I hypersensitivity to peanut along with SPT ≥8 mm and psIgE ≥15 kU/L. Open table in a new tab The self-reported prevalence of asthma was 11% in the Ontario controls, compared with 65% in the PA cases (see Table E5 in this article's Online Repository at www.jacionline.org). Univariate analysis found PA status to be the strongest predictor of a mutation, followed by asthma. Neither age nor gender had an appreciable relationship with the presence of FLG mutations on univariate or multivariate analysis and were not included in the final model. Multivariate logistic regression found no evidence for an effect of asthma (OR, 1.12; 95% CI, 0.79-1.59) on the relationship between PA (OR, 1.81; 95% CI, 1.29-2.55) and FLG LOF mutations. The proportion of mutations was similar in those PA cases with and without asthma. Peanut-allergic individuals with asthma had at least 1 mutation in 19.8% of the cases (95% CI, 0.159-0.236), while 18.7% (95% CI, 0.136-0.238) of the PA cases without asthma had at least 1 mutation.An additional analysis using a constructed atopic asthma variable to control for the effect of smoking yielded similar results. PA status remained significant (OR, 1.88; 95% CI, 1.27-2.80), while history of atopic asthma was not (OR, 1.44; 95% CI, 0.59-3.53). Results were also unchanged after the sensitivity analysis of the self-reported asthma variable, with only PA status remaining significant in the multivariate analysis. The sensitivity analysis on PA status similarly had little effect on the findings. While 20% resolution in cases alone finds that both PA and asthma status are nonsignificant, modeling 20% resolution of cases with 1% prevalence in the general population finds that only PA status remains significant in the multivariate model.This study substantiates the relationship between PA and FLG LOF mutations, and moreover this relationship appears independent of diagnostic criteria of PA and history of asthma, although residual confounding is always possible. All sets of diagnostic criteria used in this study were intended to define individuals with clinical allergy, although it is possible that some individuals who were merely sensitized could have been included in the less stringent definitions of PA. Despite this possibility, the association between the FLG LOF mutations and PA does not appear to vary with the diagnostic criteria for PA. Although the point estimates for the OR increase as the PA definition becomes more stringent, the sample size decreases and the CIs overlap; thus, the differences are not statistically significant.The similarity of the OR in the 2 control groups provides indirect evidence that it is unlikely that there are common FLG mutations not yet identified in French-Canadians, under the assumption of similar prevalence of PA. If unidentified common French-Canadian FLG variants exist, one would expect the observed OR to be higher when the PA cases were compared with the Quebec controls, due to a lower detection of mutations in the control group. However, further evidence such as the sequencing of FLG in French-Canadians would be of interest.Limitations of this study include the inability to verify ethnicity by using genetic markers of ethnicity, which were not available for either the cases or controls. However, of the 47 identified FLG mutations, those examined here are shared in many European populations2Irvine A.D. McLean W.H. Leung D.Y. Filaggrin mutations associated with skin and allergic diseases.N Engl J Med. 2011; 365: 1315-1327Crossref PubMed Scopus (812) Google Scholar (see Table E6 in this article's Online Repository at www.jacionline.org), including the expected ancestries of our case and control groups, giving us confidence that population stratification is not the cause of the difference in mutation frequency in the cases and controls. The rate of mutations in the control groups is comparable to the number seen in other Caucasian general populations (Table E6), which also leads us to believe that we have not overestimated the association. This study was also impeded by the inability to confirm asthma status by diagnostic means and that the only control group for which we had asthma and smoking history was a group of adults. While genotype will not change with age, the age difference could have affected ethnicity (eg, through different times of immigration) and PA status because of generational lifestyle, dietary, or environmental differences. Asthma status could also be affected by this age difference, because of smoking history, failure to remember a history of childhood asthma, as well as the possibility that cases have not yet developed asthma, although there is already a large proportion of PA cases who report asthma. In an effort to address these issues, sensitivity analyses of both PA and smoking status were undertaken, which found no appreciable effects on the findings of this study.The results of this study lend credence to the hypothesis that sensitization in allergic in at least some patients may through the J. J. I. R. to peanut oral and allergic PubMed Scopus Google Scholar peanut is a risk factor for the of H. peanut as a risk factor for the of peanut allergy.J Allergy Clin Immunol. Full Text Full Text PDF PubMed Scopus Google Scholar and may be a for the of peanut for a young to peanut may be to to such as that with peanut R. M. The prevalence of peanut sensitization in childhood is due to to 2011; PubMed Scopus Google Scholar filaggrin is not the to these through the skin or could result in to If the to either barrier or may allergic research in barrier and environmental is to further of the of atopic Recently, our research team found a strong and significant association between loss-of-function (LOF) mutations in filaggrin (FLG), a gene that encodes a skin barrier protein, in European and Canadian individuals with peanut allergy (PA).1Brown S.J. Asai Y. Cordell H.J. Campbell L.E. Zhao Y. Liao H. et al.Loss-of-function variants in the filaggrin gene are a significant risk factor for peanut allergy.J Allergy Clin Immunol. 2011; 127: 661-667Abstract Full Text Full Text PDF PubMed Scopus (326) Google Scholar These mutations result in a barrier defect and have been associated with atopic dermatitis, asthma, and allergic rhinitis.2Irvine A.D. McLean W.H. Leung D.Y. Filaggrin mutations associated with skin and allergic diseases.N Engl J Med. 2011; 365: 1315-1327Crossref PubMed Scopus (812) Google Scholar This finding represents the strongest genetic risk factor found to date for PA, a highly heritable disease,3Sicherer S.H. Furlong T.J. Maes H.H. Desnick R.J. Sampson H.A. Gelb B.D. Genetics of peanut allergy: a twin study.J Allergy Clin Immunol. 2000; 106: 53-56Abstract Full Text Full Text PDF PubMed Scopus (229) Google Scholar with an estimated odds ratio (OR) between 1.9 (Canadian) and 5.3 (English, Dutch, and Irish combined).1Brown S.J. Asai Y. Cordell H.J. Campbell L.E. Zhao Y. Liao H. et al.Loss-of-function variants in the filaggrin gene are a significant risk factor for peanut allergy.J Allergy Clin Immunol. 2011; 127: 661-667Abstract Full Text Full Text PDF PubMed Scopus (326) Google Scholar Because there is no uniformly accepted definition of PA short of oral food challenge, it is worthwhile to examine whether the association between the FLG LOF mutations and PA varies with the diagnostic criteria for PA. Furthermore, the frequent coexistence of PA with other atopic conditions may mean that the association between PA and FLG LOF mutations is confounded. Although we controlled for eczema in the European populations in our previous work, data on eczema were not available for the Canadian control group; however, data on asthma were available. Asthma is a potential confounder, as it has known relationships with both PA4Liu A.H. Jaramillo R. Sicherer S.H. Wood R.A. Bock S.A. Burks A.W. et al.National prevalence and risk factors for food allergy and relationship to asthma: results from the National Health and Nutrition Examination Survey 2005-2006.J Allergy Clin Immunol. 2010; 126: 798-806.e13Abstract Full Text Full Text PDF PubMed Scopus (379) Google Scholar and FLG mutations.5Palmer C.N. Ismail T. Lee S.P. Terron-Kwiatkowski A. Zhao Y. Liao H. et al.Filaggrin null mutations are associated with increased asthma severity in children and young adults.J Allergy Clin Immunol. 2007; 120: 64-68Abstract Full Text Full Text PDF PubMed Scopus (174) Google Scholar By using statistical sensitivity analyses, we examined the effect of PA diagnostic criteria and asthma on the relationship between PA and FLG LOF mutations in a Canadian PA case group. Because the PA case group was composed of both English- and French-speaking individuals, we also investigated whether the difference in OR between the Canadian and European populations could be due to some common French-Canadian mutations not yet identified in Caucasian subjects from a well-described Canadian pediatric PA case group were recruited (n = 679), and DNA was isolated from salivary samples.1Brown S.J. Asai Y. Cordell H.J. Campbell L.E. Zhao Y. Liao H. et al.Loss-of-function variants in the filaggrin gene are a significant risk factor for peanut allergy.J Allergy Clin Immunol. 2011; 127: 661-667Abstract Full Text Full Text PDF PubMed Scopus (326) Google Scholar One control group consisted of adult Caucasians recruited from the general population of Ontario, Canada; DNA was provided by the Ontario Population Genomics Platform at The Centre for Applied Genomics (Toronto) (n = 894). A second control group of newborn babies from Quebec City was sampled on the basis of French-Canadian surname (stored blood; n = 268).6Girouard J. Giguere Y. Delage R. Rousseau F. Prevalence of HFE gene C282Y and H63D mutations in a French-Canadian population of neonates and in referred patients.Hum Mol Genet. 2002; 11: 185-189Crossref PubMed Scopus (18) Google Scholar All samples were genotyped in Dundee, Scotland, for the 4 most common FLG LOF mutations found in Caucasians (R501X, 2282del4, R2447X, and S3247X). rs and accession numbers for mutations are available in the Online Repository at www.jacionline.org (see Table carriers" were defined as those with heterozygous, homozygous, or compound heterozygous mutations. Those individuals with none of the 4 FLG mutations were classified as "nonmutation carriers." The association between mutation status and PA was compared with the Ontario control group, the Quebec control group, and the combined control group. To evaluate whether the association between PA and mutation status changed with case definition, a continuum of PA case definitions was constructed and the resulting OR trends with case definition were examined by using the combined control groups. The methodology and rationale for these definitions are given in the Online Repository available at www.jacionline.org (see Tables E2 and E3). To increase power, case definitions were transformed into an ordered variable and the association between PA and FLG mutations was examined by using regression modeling through increasingly stringent definitions of PA to see whether the OR changed also examined the effect of asthma on FLG mutation status and PA. Logistic regression using the Ontario control group was conducted with PA status, age, sex, asthma, and interaction terms for PA and age, PA and sex, and PA and asthma. Because there may be interaction between mutation status, asthma, and smoking,7Berg N.D. Husemoen L.L. Thuesen B.H. Hersoug L.G. Elberling J. Thyssen J.P. et al.Interaction between filaggrin null mutations and tobacco smoking in relation to asthma.J Allergy Clin Immunol. 2012; 129 (e1-2): 374-380Abstract Full Text Full Text PDF PubMed Scopus (30) Google Scholar and self-identified asthmatic patients may have significant misclassification, analyses controlled for smoking history in the controls and misclassification in the asthma variable in both controls and cases. A constructed atopic asthma variable was used to control for the effect of smoking with 4 assumptions: (1) Those individuals who have atopic asthma in childhood are less likely to smoke as adults. (2) Those adults who have asthma and have never smoked are more likely to have atopic asthma. (3) If a patient reports bronchial emphysema, he or she does not have atopic asthma. (4) Asthma reported in the case group is atopic. To examine the possibility of error due to self-report of asthma, we completed a sensitivity analysis taking into account data from the PA registry that found that 6% had "forgotten" previously noted atopic history, while 12% more reported atopic history on the current questionnaire than at baseline registry recruitment. Random sampling and subsequent logistic regression modeling was completed 100 times to see the overall effect of error in asthma reporting on the relationship of PA and FLG LOF mutations using these a similar sensitivity analysis of PA status was conducted, as PA status could be affected by the age disparity between the Ontario control group and the cases, because it is estimated that up to 20% of individuals with PA may have resolution of their allergy.8Skolnick H.S. Conover-Walker M.K. Koerner C.B. Sampson H.A. Burks W. Wood R.A. The natural history of peanut allergy.J Allergy Clin Immunol. 2001; 107: 367-374Abstract Full Text Full Text PDF PubMed Scopus (467) Google Scholar This sensitivity analysis also took into account the 1% prevalence of PA in the general population.9Ben-Shoshan M. Harrington D.W. Soller L. Fragapane J. Joseph L. St Pierre Y. et al.A population-based study on peanut, tree nut, fish, shellfish, and sesame allergy prevalence in Canada.J Allergy Clin Immunol. 2010; 125: 1327-1335Abstract Full Text Full Text PDF PubMed Scopus (174) Google Scholar the 679 cases eligible to participate, 99.3% had good quality DNA. Demographic information is presented in Table I. The 674 cases had approximately twice as many mutations as the controls (20% vs 11%), and the OR for PA and FLG mutation status was similar in the Ontario and Quebec control groups (Table II). The genotype frequencies in cases and controls are shown in the Online Repository available at www.jacionline.org (see Table E4). Among the 13 case definitions, there was no significant difference in the OR for the relationship between PA and FLG mutation status. Seven representative case definitions are shown in Table III. Logistic regression of the ordered case definition criteria variable produced similar results. Not Oral food challenge; psIgE, peanut-specific immunoglobulin E; SPT, skin prick The self-reported prevalence of asthma was 11% in the Ontario controls, compared with 65% in the PA cases (see Table E5 in this article's Online Repository at www.jacionline.org). Univariate analysis found PA status to be the strongest predictor of a mutation, followed by asthma. Neither age nor gender had an appreciable relationship with the presence of FLG mutations on univariate or multivariate analysis and were not included in the final model. Multivariate logistic regression found no evidence for an effect of asthma (OR, 1.12; 95% CI, 0.79-1.59) on the relationship between PA (OR, 1.81; 95% CI, 1.29-2.55) and FLG LOF mutations. The proportion of mutations was similar in those PA cases with and without asthma. Peanut-allergic individuals with asthma had at least 1 mutation in 19.8% of the cases (95% CI, 0.159-0.236), while 18.7% (95% CI, 0.136-0.238) of the PA cases without asthma had at least 1 additional analysis using a constructed atopic asthma variable to control for the effect of smoking yielded similar results. PA status remained significant (OR, 1.88; 95% CI, 1.27-2.80), while history of atopic asthma was not (OR, 1.44; 95% CI, 0.59-3.53). Results were also unchanged after the sensitivity analysis of the self-reported asthma variable, with only PA status remaining significant in the multivariate analysis. The sensitivity analysis on PA status similarly had little effect on the findings. While 20% resolution in cases alone finds that both PA and asthma status are nonsignificant, modeling 20% resolution of cases with 1% prevalence in the general population finds that only PA status remains significant in the multivariate

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We have reconstituted human mitochondrial transcription in vitro on DNA oligonucleotide templates representing the light strand and heavy strand-1 promoters using protein components (RNA polymerase and transcription factors A and B2) isolated from Escherichia coli. We show that 1 eq of each transcription factor and polymerase relative to the promoter is required to assemble a functional initiation complex. The light strand promoter is at least 2-fold more efficient than the heavy strand-1 promoter, but this difference cannot be explained solely by the differences in the interaction of the transcription machinery with the different promoters. In both cases, the rate-limiting step for production of the first phosphodiester bond is open complex formation. Open complex formation requires both transcription factors; however, steps immediately thereafter only require transcription factor B2. The concentration of nucleotide required for production of the first dinucleotide product is substantially higher than that required for subsequent cycles of nucleotide addition. In vitro, promoter-specific differences in post-initiation control of transcription exist, as well as a second rate-limiting step that controls conversion of the transcription initiation complex into a transcription elongation complex. Rate-limiting steps of the biochemical pathways are often those that are targeted for regulation. Like the more complex multisubunit transcription systems, multiple steps may exist for control of transcription in human mitochondria. The tools and mechanistic framework presented here will facilitate not only the discovery of mechanisms regulating human mitochondrial transcription but also interrogation of the structure, function, and mechanism of the complexes that are regulated during human mitochondrial transcription.

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The innate immune system in humans consists of both cellular and humoral components that collaborate to eradicate invading bacteria from the body. Here, we discover that the gram-positive bacterium Bacillus anthracis, the causative agent of anthrax, does not grow in human serum. Fractionation of serum by gel filtration chromatography led to the identification of human transferrin as the inhibiting factor. Purified transferrin blocks growth of both the fully virulent encapsulated B. anthracis Ames and the non-encapsulated Sterne strain. Growth inhibition was also observed in serum of wild-type mice but not of hypotransferrinemic mice that only have approximately 1% circulating transferrin levels. We were able to definitely assign the bacteriostatic activity of transferrin to its iron-binding function: neither iron-saturated transferrin nor a recombinant transferrin mutant unable to bind iron could inhibit growth of B. anthracis. Additional iron could restore bacterial growth in human serum. The observation that other important gram-positive pathogens are not inhibited by transferrin suggests they have evolved effective mechanisms to circumvent serum iron deprivation. These findings provide a better understanding of human host defense mechanisms against anthrax and provide a mechanistic basis for the antimicrobial activity of human transferrin.

The multipotentiality and self-renewal ability of stem cells are controlled by intrinsic genetic pathways that are subject to regulation by extrinsic signals emanating from the stem cell niche. The stem cell niche provides a microenvironment composed of cellular structures or extracellular matrix in which stem cells are maintained as undifferentiated (1Li L. Xie T. Annu. Rev. Cell Dev. Biol. 2005; 21: 605-631Crossref PubMed Scopus (942) Google Scholar, 2Lin H. Nat. Rev. Genet. 2002; 3: 931-940Crossref PubMed Scopus (305) Google Scholar, 3Scadden D.T. Nature. 2006; 441: 1075-1079Crossref PubMed Scopus (1508) Google Scholar, 4Spradling A. Drummond-Barbosa D. Kai T. Nature. 2001; 414: 98-104Crossref PubMed Scopus (1215) Google Scholar, 5Watt F.M. Hogan B.L. Science. 2000; 287: 1427-1430Crossref PubMed Scopus (1474) Google Scholar, 6Fuchs E. Tumbar T. Guasch G. Cell. 2004; 116: 769-778Abstract Full Text Full Text PDF PubMed Scopus (1481) Google Scholar). The concept of "the stem cell niche" was first proposed in studies of the HSC 2The abbreviations used are:HSChematopoietic stem cellGSCgerm line stem cellBMbone marrowCARCXCL12-abundant reticularCBscystoblastsESCescort stem cellCPscyst progenitorsAng-1angiopoietin-1.2The abbreviations used are:HSChematopoietic stem cellGSCgerm line stem cellBMbone marrowCARCXCL12-abundant reticularCBscystoblastsESCescort stem cellCPscyst progenitorsAng-1angiopoietin-1. (7Schofield R. Blood Cells. 1978; 4: 7-25PubMed Google Scholar); however, in vivo evidence of its existence was first shown in the Drosophila GSC (8Cox D.N. Chao A. Baker J. Chang L. Qiao D. Lin H. Genes Dev. 1998; 12: 3715-3727Crossref PubMed Scopus (802) Google Scholar, 9King F.J. Lin H. Development (Camb.). 1999; 126: 1833-1844PubMed Google Scholar, 10Xie T. Spradling A.C. Science. 2000; 290: 328-330Crossref PubMed Scopus (620) Google Scholar). Over the past several years, there has been much progress made in identifying stem cell niches in different mammal tissues, including nerves, hair follicles, intestines, teeth, and BM (11Tumbar T. Guasch G. Greco V. Blanpain C. Lowry W.E. Rendl M. Fuchs E. Science. 2004; 303: 359-363Crossref PubMed Scopus (1631) Google Scholar, 12Yen T.H. Wright N.A. Stem Cell Rev. 2006; 2: 203-212Crossref PubMed Scopus (227) Google Scholar, 13Conover J.C. Notti R.Q. Cell Tissue Res. 2008; 331: 211-224Crossref PubMed Scopus (123) Google Scholar, 14Doetsch F. Curr. Opin. Genet. Dev. 2003; 13: 543-550Crossref PubMed Scopus (529) Google Scholar, 15Ohshima H. Nakasone N. Hashimoto E. Sakai H. Nakakura-Ohshima K. Harada H. Arch. Oral Biol. 2005; 50: 153-157Crossref PubMed Scopus (81) Google Scholar, 16Wilson A. Trumpp A. Nat. Rev. Immunol. 2006; 6: 93-106Crossref PubMed Scopus (1050) Google Scholar). In this review, our focus is on comparing Drosophila GSC niches and mouse HSC niches (two of the best characterized niches). By such comparison, we hope to provide some common principles of stem cell niches that will be useful in other tissue stem cell niche studies. hematopoietic stem cell germ line stem cell bone marrow CXCL12-abundant reticular cystoblasts escort stem cell cyst progenitors angiopoietin-1. hematopoietic stem cell germ line stem cell bone marrow CXCL12-abundant reticular cystoblasts escort stem cell cyst progenitors angiopoietin-1. In recent years, remarkable progress has been made in the identification and characterization of the stem cell niches in invertebrate systems (10Xie T. Spradling A.C. Science. 2000; 290: 328-330Crossref PubMed Scopus (620) Google Scholar, 17Tulina N. Matunis E. Science. 2001; 294: 2546-2549Crossref PubMed Scopus (506) Google Scholar, 18Kiger A.A. Jones D.L. Schulz C. Rogers M.B. Fuller M.T. 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These advantages facilitated identification of the cellular components of the stem cell niche and definition of the molecular basis of physical interaction between stem cells and their niches (23Song X. Xie T. Proc. Natl. Acad. Sci. U. S. A. 2002; 99: 14813-14818Crossref PubMed Scopus (184) Google Scholar, 24Yamashita Y.M. Jones D.L. Fuller M.T. Science. 2003; 301: 1547-1550Crossref PubMed Scopus (595) Google Scholar) and revealed key niche signals involved in stem cell regulation (18Kiger A.A. Jones D.L. Schulz C. Rogers M.B. Fuller M.T. Science. 2001; 294: 2542-2545Crossref PubMed Scopus (538) Google Scholar, 25LaFever L. Drummond-Barbosa D. Science. 2005; 309: 1071-1073Crossref PubMed Scopus (248) Google Scholar, 26Szakmary A. Cox D.N. Wang Z. Lin H. Curr. Biol. 2005; 15: 171-178Abstract Full Text Full Text PDF PubMed Scopus (124) Google Scholar, 27Xie T. Spradling A.C. Cell. 1998; 94: 251-260Abstract Full Text Full Text PDF PubMed Scopus (530) Google Scholar, 28Yamashita Y.M. Fuller M.T. Jones D.L. J. Cell Sci. 2005; 118: 665-672Crossref PubMed Scopus (166) Google Scholar, 29Parisi M.J. Lin H. Cell Res. 1998; 8: 15-21Crossref PubMed Scopus (38) Google Scholar, 30King F.J. Szakmary A. Cox D.N. Lin H. Mol. Cell. 2001; 7: 497-508Abstract Full Text Full Text PDF PubMed Scopus (126) Google Scholar, 31Wang Z. Lin H. Science. 2004; 303: 2016-2019Crossref PubMed Scopus (197) Google Scholar). In the murine hematopoietic system, HSCs have been well defined (32Spangrude G.J. Heimfeld S. Weissman I.L. Science. 1988; 241: 58-62Crossref PubMed Scopus (2226) Google Scholar, 33Weissman I.L. Science. 2000; 287: 1442-1446Crossref PubMed Scopus (713) Google Scholar), but identification of the HSC niches is just beginning. This search has been hampered by the complexity of the BM structure and cellular components and by the lack of unique HSC markers or distinctive characteristics of BM stromal cells. Two HSC niches have been proposed in murine BM, an osteoblastic niche and a vascular niche, in which osteoblasts and vascular endothelial cells have been demonstrated as major components, respectively (34Zhang J. Niu C. Ye L. Huang H. He X. Tong W.G. Ross J. Haug J. Johnson T. Feng J.Q. Harris S. Wiedemann L.M. Mishina Y. Li L. Nature. 2003; 425: 836-841Crossref PubMed Scopus (2385) Google Scholar, 35Calvi L.M. Adams G.B. Weibrecht K.W. Weber J.M. Olson D.P. Knight M.C. Martin R.P. Schipani E. Divieti P. Bringhurst F.R. Milner L.A. Kronenberg H.M. Scadden D.T. Nature. 2003; 425: 841-846Crossref PubMed Scopus (2799) Google Scholar, 36Arai F. Hirao A. Ohmura M. Sato H. Matsuoka S. Takubo K. Ito K. Koh G.Y. Suda T. Cell. 2004; 118: 149-161Abstract Full Text Full Text PDF PubMed Scopus (1540) Google Scholar, 37Nilsson S.K. Johnston H.M. Whitty G.A. Williams B. Webb R.J. Denhardt D.T. Bertoncello I. Bendall L.J. Simmons P.J. Haylock D.N. Blood. 2005; 106: 1232-1239Crossref PubMed Scopus (605) Google Scholar, 38Heissig B. Rafii S. Akiyama H. Ohki Y. Sato Y. Rafael T. Zhu Z. Hicklin D.J. Okumura K. Ogawa H. Werb Z. Hattori K. J. Exp. Med. 2005; 202: 739-750Crossref PubMed Scopus (195) Google Scholar, 39Moore K.A. Curr. Opin. Hematol. 2004; 11: 107-111Crossref PubMed Scopus (56) Google Scholar, 40Taichman R.S. Blood. 2005; 105: 2631-2639Crossref PubMed Scopus (469) Google Scholar, 41Kiel M.J. Yilmaz O.H. Iwashita T. Terhorst C. Morrison S.J. Cell. 2005; 121: 1109-1121Abstract Full Text Full Text PDF PubMed Scopus (2414) Google Scholar). A recent study suggested that a population of reticular cells named CAR cells, which express a high level of CXCL12 (also known as stromal cell-derived factor-1 or pre-B cell growth-stimulating factor), are in contact with HSCs in both osteoblastic and vascular niches (42Sugiyama T. Kohara H. Noda M. Nagasawa T. Immunity. 2006; 25: 977-988Abstract Full Text Full Text PDF PubMed Scopus (1693) Google Scholar). Drosophila ovary and testis provide attractive models for stem cell niche studies. In Drosophila ovary, cap cells, a specific type of somatic cell located at the tip of the germarium in the ovary, function as the niche for GSCs. An E-cadherin/β-catenin-formed cell-cell adhesion junction mediates the physical interaction between GSCs and their niche cells (23Song X. Xie T. Proc. Natl. Acad. Sci. U. S. A. 2002; 99: 14813-14818Crossref PubMed Scopus (184) Google Scholar, 46Song X. Zhu C.H. Doan C. Xie T. Science. 2002; 296: 1855-1857Crossref PubMed Scopus (389) Google Scholar), ensuring stem cell control by niche signals. Normally, asymmetric division of stem cells results in two daughter cells with different fates: one daughter cell attaches to the niche and is maintained as a stem cell (self-renewal), whereas the other daughter cell leaves the niche and develops into a cystoblast (1Li L. Xie T. Annu. Rev. Cell Dev. Biol. 2005; 21: 605-631Crossref PubMed Scopus (942) Google Scholar, 4Spradling A. Drummond-Barbosa D. Kai T. Nature. 2001; 414: 98-104Crossref PubMed Scopus (1215) Google Scholar). CBs undergo four incomplete cell divisions to form an interconnected 2–16-cell germ line cyst. In addition to the GSC, another type of cell called the ESC also attaches to cap cells interspersed between the GSCs. Together with cap cells, ESCs encapsulate GSCs to separate GSCs from their differentiated daughter cells. When the GSCs divide and detach from the niche to produce CBs and cyst cells, the ESCs also proliferate and differentiate to produce more escort cells. The escort cells expand and continue to encapsulate CBs and cysts during the process of cyst formation and are finally replaced by follicle cells after the 16-cell germ line cyst stage (Fig. 1a). Interestingly, the newly formed cysts (prior to the eight-cell cyst stage, while still encapsulated by the escort cell) can revert to the stem cell state under certain circumstances, suggesting that they may still retain (albeit limited) stem cell properties (47Kai T. Spradling A. Nature. 2004; 428: 564-569Crossref PubMed Scopus (267) Google Scholar). A similar niche is also found in Drosophila testis and is composed of hub cells located at the end of the testis (48Le Bras S. Van Doren M. Dev. Biol. 2006; 294: 92-103Crossref PubMed Scopus (96) Google Scholar). Male GSCs surrounding the hub cells are interspersed with CPs (which are counterparts of ESCs in the ovary). Both GSCs and CPs are attached to the hub cells through an adhesion junction. Similar to ESCs in the ovary, proliferation and differentiation of CPs always accompany proliferation and differentiation of GSCs. CPs in the testis produce cyst cells, which encapsulate the gonialblasts (the immediate daughters of male GSCs) during spermatogonium formation (Fig. 1b). The newly formed gonialblasts can also revert to stem cells under certain circumstances, resembling their counterpart cells (CBs and cysts) in the ovary (49Brawley C. Matunis E. Science. 2004; 304: 1331-1334Crossref PubMed Scopus (326) Google Scholar). The role of cap and hub cells in GSC regulation has been well studied, but the contribution of ESCs and their offspring in the ovary and CPs and their progeny in the testis to GSC self-renewal, proliferation, and differentiation is largely unknown. However, it is known that a dialogue between the two types of cells is required for the coordination during organogenesis (30King F.J. Szakmary A. Cox D.N. Lin H. Mol. Cell. 2001; 7: 497-508Abstract Full Text Full Text PDF PubMed Scopus (126) Google Scholar). Cap and hub cells provide an attachment point for anchoring GSCs to the niche; they also produce signals that inhibit differentiation but promote self-renewal of stem cells (17Tulina N. Matunis E. Science. 2001; 294: 2546-2549Crossref PubMed Scopus (506) Google Scholar). The stem cell niches in mammals are very complicated because of the complexity of cellular components of mammalian tissues, even though the mechanism for niche regulation is conserved from invertebrate to vertebrate. In mammals, BM tissue is composed of more than eight different hematopoietic cell lineages supported by a network of mesenchymal stromal cells and vascular endothelial cells. The two HSC niches, osteoblastic (34Zhang J. Niu C. Ye L. Huang H. He X. Tong W.G. Ross J. Haug J. Johnson T. Feng J.Q. Harris S. Wiedemann L.M. Mishina Y. Li L. Nature. 2003; 425: 836-841Crossref PubMed Scopus (2385) Google Scholar, 35Calvi L.M. Adams G.B. Weibrecht K.W. Weber J.M. Olson D.P. Knight M.C. Martin R.P. Schipani E. 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The vascular niche might also exist in fetal hematopoietic tissues such as yolk sac, aorta-gonad-mesonephros region, placenta, liver, and spleen (54Tavian M. Peault B. Exp. Hematol. 2005; 33: 1062-1069Abstract Full Text Full Text PDF PubMed Scopus (61) Google Scholar, 55Basto D. Trovisco V. Lopes J.M. Martins A. Pardal F. Soares P. Reis R.M. Acta Neuropathol. 2005; 109: 207-210Crossref PubMed Scopus (84) Google Scholar, 56Gekas C. Dieterlen-Lièvre F. Orkin S.H. Millola H.K.A. Dev. Cell. 2005; 8: 365-375Abstract Full Text Full Text PDF PubMed Scopus (504) Google Scholar) as well as in adult spleen and liver. Both niches may be critical for HSC self-renewal. Cooperation between these two niches might be required for maintaining normal hematopoietic homeostasis and re-establishing hematopoiesis after injury. Accumulated evidence supports the existence of an osteoblastic niche in BM. The concurrence of hematopoiesis and osteogenesis in BM suggests a close relationship between bone-forming cells and hematopoietic cells (57Patt H.M. Maloney M.A. Proc. Soc. Exp. Biol. Med. 1972; 140: 205-207Crossref PubMed Scopus (35) Google Scholar, 58Maloney M.A. Patt H.M. Proc. Soc. Exp. Biol. Med. 1975; 149: 94-97Crossref PubMed Scopus (12) Google Scholar). Early studies demonstrated that endosteal BM is more highly enriched with HSCs/progenitors compared with central BM (59Lord B.I. Testa N.G. Hendry J.H. Blood. 1975; 46: 65-72Crossref PubMed Google Scholar, 60Gong J.K. Science. 1978; 199: 1443-1445Crossref PubMed Scopus (195) Google Scholar). The facts that hematopoiesis recovery after myeloablative injury occurs on the endosteal bone surface (45Heissig B. Hattori K. Dias S. Friedrich M. Ferris B. Hackett N.R. Crystal R.G. Besmer P. Lyden D. Moore M.A. Werb Z. Rafii S. 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