Progress 04/15/17 to 04/14/21
Outputs
Target Audience:For years healthcare professionals,and allergic consumers and the diagnostic industryhave wanted to have an unambiguous testthat would obviate any type of Oral Food Challenge (OFC). While skin prick test, allergen-specific IgE measurement such as(i.e.ImmunoCap) and component resolved-diagnosis measure sensitivity (presence of IgE in the absence of clinical reactivity)and can assist in diagnosis, none are independently or completely reliable. The findings of this study are reported and disseminatedin scientific and non-scientific publications, reports and presentations atconsumer advocacy group and professional societies. The findings are also used for educational purposes. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project has allowed us to recruit a postdoctoral fellow to the field of food allergy. The recruit has participated in learning new skills and expertise and has participated in and presented papers in two internationally attended allergy conferences. She has also participated in more than one conference with companies and collaborators as well as the bioinformatics team (Rho). Two students have worked on the project for their summer projects. Also, the PIs have learned more about bioinformatics and statistics by interacting with the professional bioinformaticians at Rho. How have the results been disseminated to communities of interest?We have presented our work orally at multiple invited seminars locally and nationally at universities, conferences and commodity groups. We have also published abstracts and presented posters at conferences on this work. Our research progress and team's work has been advertised by our institution, which enhances the visibility of our many projects. What do you plan to do during the next reporting period to accomplish the goals?This is the final report. However, we will continue to analyze the large amounts of data collected and publish any results. We plan to 1) integrating IgE and IgG4 peptides into the same model to achieve higher diagnostic accuracy; 2) building a new model to include all chip lots, 3) Evaluate models on independent test data. Incorporating more non-allergic data; 4) incorporating additional ISAC (intact protein) data; 5) integrating the clinical data in order to determine how much the selected peptides add to the common biomarkers such as total and specific IgE/IgG4. To test improved microarray analysis for diagnostic capability for peanut and walnut allergy and future commercialization.
Impacts
What was accomplished under these goals?
Goal 1) Objective: To probe microarrays containing synthetic overlapping peptides to identify IgE and IgG4 binding sites. 1) Major activities completed / experiments conducted: Four hundred microarrays were screened with non-allergic and allergic serum from peanut and tree nut allergic individuals from around the US. 2) Data collected: Peptide IgE and IgG4 epitopes were identified for approximately 560 peanut and tree nut allergic individuals in the US, 84 from the UK and 73 from Spain. Preliminary data shows that the epitope recognition pattern for peanut allergic patients in different regions of the US and Spain are similar for most allergens with some variations in IgE and IgG4 epitopes. 3) Summary statistics and discussion of results: Algorithms to eliminate bad spots were developed. For the US pre and post Oral Immunotherapy data: Paired t-tests were run for each peptide within each treatment (e.g. Active Pre-OIT vs Active Post-OIT) to assess the significance of the mean difference between them. P-values were adjusted for multiple comparisons and our criteria for a significant finding was an adjusted p-value <0.10, which allowed us to determine which peptides were significantly altered by OIT in the active treatment group. Similar comparative analysis of peanut allergic vs non allergics show statistically significant differences in serum IgE and IgG4 binding. The comparison of the IgE/IgG ratio's for the OIT group identified the most significantly changed peptides to be within very few allergens. 4) Key outcomes or other accomplishments realized: a) Diagnostic peptides were identified and validated for improving diagnosis of peanut allergic individuals in the UK and published; b) Statistical algorithms were developed and tested to facilitate further analysis of US patient data sets. c) IgE and IgG4 epitope maps were developed for all 39 peanut and tree nut allergens on the array. Goal 2) Objective: To probe microarrays containing intact allergic proteins (or components) in order to identify IgE binding proteins. 1) Major activities completed / experiments conducted: Renewal of agreements with Thermo-Fisher for continued use of the laser scannerto screen ISAC arrays (http://www.phadia.com/en/Products/Allergy-testing-products/ImmunoCAP-ISAC/)with patient sera. 2) Data collected: Data showing IgE binding of 560 peanut and tree nut allergic sera (400 from the US) to 110 allergic proteins that are on the ISAC arrays. 3) Summary statistics and discussion of results: The data was collated into an Excel spreadsheet and incorporated into the peptide microarray analysis from Goal 1. 4) Key outcomes or other accomplishments realized: The key outcome is the collection of data and performing of screens for over 400 US patient sera. Also, uniform tables were created and coded to connect to the peptide microarray data and patient meta data to facilitate the integration of the peptide and protein data for each sera and for population comparisons. Interestingly, the intact allergen recognition pattern was somewhat different for sera collected from different regions around the United states but varied more significantly among different countries, particularly for the inhaled allergens on the ISAC array. Goal 3) Objective: Collaborate with professional statisticians to dentify the most promising diagnostic peptides/proteins. 1) Major activities completed / experiments conducted: Rho was given the IgE and IgG4 binding data for 400 peptide microarrays and 400 ISAC arrays and tables containing the patient meta data. 2) Data collected: Peptide microarray and intact protein microarray data the patient tables containing clinical information was collected and incorporated into one file along with microarray and ISAC patient codes. IgE and IgG4 binding microarray data from multiple USA regions (N, S, E, W, Mid - includes baseline Aimmune OIT data) cohort of allergic & non-allergic subjects were analyzed with the goal of developing prediction models for allergic status using peptides, ISAC, and peptides + ISAC arrays. 3) Summary statistics and discussion of results: Statistical analysis were performed by Rho on micro-arrays using serum collected for the US nut allergic population. In Step 1. The raw data from various regions around the US were combined, cleaned and reshaped. A subset of the IgE & IgG4 peptide data performed on the same array lot (61 allergic, 22 non-allergic) were subject to background correction and log2 transformation and reduced to one observation then a paired loess method of normalization was applied to peanut allergen peptides in order to find subset of peptides that in combination with one another are predictive of allergic status. 4) Key outcomes or other accomplishments realized. A preliminary publication (Santos et al 2020)clearly shows that a combination of peptides and proteins can improve the serum-based diagnostic ability over existing methods.At least 2 more manuscripts describing our results with the Aimmune Therapeutics clinical trial sera and the NIFA data containing multiple US regions are in preparation. Goal 4) Objective: To probe microarrays, containing only the best diagnosticin order to test and validate the diagnostic value. 1) Major activities completed / experiments conducted: Data obtained from screening peptide and protein microarrays with peanut and walnut allergics, non allergics and sera from peanut oral immunotherapy patients has been uploaded to Rho's high security portal for statistical comparisons. 2) Data collected: All of the microarray data proposed here was collected and uploaded to the bioinformatics/statistical company. Our group also collected and uploaded the patient clinical information. 3) Summary statistics and discussion of results: Upon comparison lot to lot variations in array batches were detected. For expediency, the arrays from a single lot, probed with US patient sera, were used to test the diagnostic accuracy of univariate and multivariate analyses. A small population (61 peanut allergic and 22 non peanut allergics), all on the same chip lot, were background corrected and log 2 transformed. The data was then normalized with "paired loess method" and the analysis was limited to the 11 peanut allergens. All data are being normalized for lot to lot variation and the number of sera for identification of combinations of peptides and proteins will be much higher than the primary analysis. 4) Key outcomes or other accomplishments realized: A database of IgE and IgG4-binding patterns to over 1550 peanut and tree nut was created.A multivariate classification model were used to find a subset of peptides, that in combination with one another, are predictive of the allergic status. In the "lasso" modeling technique, a subset of the most important peptides are selected, and iterates over different subsets of the data ensure results generalize to new populations and allow estimates of predictive accuracy. The preliminary data with a combination of 22 peanut allergen peptides, with the limited patients on one lot of arrays, has shown an 89.6% accuracy with the IgE model results. In this IgE model, 57/61 allergic patients were accurately diagnosed, 4/22 non-allergics were diagnosed as positive 5/22 non-allergics were diagnosed as peanut allergic. Using the IgG4 model, the analysis showed an 86.75% accuracy with the IgG4 model results. In this IgE model, 56/61 allergic patients were accurately diagnosed, 5/22 non-allergics were diagnosed as positive 6/22 non-allergics were diagnosed falsely as peanut allergic. Diagnostic peptides were identified and statistically validated for improving diagnosis of peanut allergic individuals US, manuscript, patent and collaborative efforts with commercial partners are in progress.
Publications
- Type:
Journal Articles
Status:
Under Review
Year Published:
2021
Citation:
Nesbit J.B., Foo, A.C.Y., Braun, B.A., Gipson, S.A.Y., Buschel P., DeRose, E.F., Cheng, H., Schein, C.H., Teuber S.S., Hurlburt, B.K., Mueller G.A., Maleki S.J. Structure and IgE cross-reactivity among walnut and peanut vicilin leader sequences. Allergy, Submitted June 2021.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2021
Citation:
Sani MZ, Bargahi A, Momenzadeh N, Dehghani P, Moghadam MV, Maleki SJ, Nabipour I, Shirkani A, Akhtari J, Hesamizadeh K, Heidari S, Omrani F, Akbarzadeh S, Mohammadi M. Genetically engineered fusion of allergen and viral-like particle induces a more effective allergen-specific immune response than a combination of them. Appl Microbiol Biotechnol. 2021; 105(1):77-91. doi: 10.1007/s00253-020-11012-0.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Ruiter B., Smith NP, Fleming E, Patil SU, Hurlburt BK, Maleki SJ, Shreffler WG. Peanut protein acts as a TH2 adjuvant by inducing RALDH2 in human antigen-presenting cells. J Allergy Clin Immunol. 2020; S0091-6749(20)32423-4. doi: 10.1016/j.jaci.2020.11.047.
- Type:
Journal Articles
Status:
Other
Year Published:
2021
Citation:
Kronfel, CM, Cheng, H, McBride JK, Krouse, R, Burns, P, Cabanillas, B, Crespo, JF, Simon, RJ, Maleki SJ, Hurlburt B.K. IgE binding epitopes of the peanut non-specific lipid transfer protein Ara h 9. In Preparation for PLoS1
- Type:
Other
Status:
Accepted
Year Published:
2021
Citation:
Maleki SJ, Teuber SS, Mustafa SS. Adult peanut allergy: What we know and what we need to learn. (Review)J Allergy Clin Immunol. 2021, 147(6):2069-2072. doi: 10.1016/j.jaci.2021.03.031
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Barashow SM, Hurlburt BK, McBride, JK, Maleki SJ,Ye, P, LI, Q, Burks AW, Kulis, MD, Kim EH. Biomarkers for Desensitization in Patients Undergoing Sublingual Immunotherapy for Peanut Allergy. Poster Presentation at the American Academy of Ashtma, Allergy and Immunology (AAAAI) 2021
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Nesbit J.B., Cheng, H., , Hurlburt, B.K., Maleki S.J. Peanut and walnut leader sequence epitopes and their relevance to cross-reactivity in allergy. Poster Presentation. Gordon Research Conference on Food Allergy 2020
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Gipson, S.A.Y., Nesbit J.B., Hurlburt, B.K., Cheng, H., Maleki S.J.�
Identification of IgE epitopes and purification of Jug r 4, a major walnut allergen. Poster Presentation. Gordon Research Conference on Food Allergy 2020�
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Hurlburt, BK, Cheng, H, Maleki, SJ, McBride, JK. Purification and Characterization of Pathogenesis Related Class 10 Panallergens. Poster Presentation. Gordon Research Conference on Food Allergy 2020�
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Kronfel, CM, Cheng, H, McBride JK, Krouse, R, Burns, P, Cabanillas, B, Crespo, JF, Simon, RJ, Maleki SJ, Hurlburt B.K. IgE binding epitopes of the peanut non-specific lipid transfer protein Ara h 9. Gordon Research Conference on Food Allergy 2020�
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2021
Citation:
Nesbit J.B., Foo, A.C.Y., Braun, B.A., Gipson, S.A.Y., Buschel P., DeRose, E.F., Cheng, H., Schein, C.H., Teuber S.S., Hurlburt, B.K., Mueller G.A., Maleki S.J.The ?-hairpin scaffold and variable amino acid sequences of Ara h 1 and Jug r 2 leader sequences collectively determine cross-reactivity between peanut and walnut. Poster Presentation at the European Academy of Allergy and Clinical Immunology (EAACI) 2020
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2021
Citation:
Gipson, S.A.Y., Nesbit J.B., Cheng, H., Teuber, S.S., Dreskin S.C., Mustafa, S.S. Hurlburt, B.K., Maleki S.J. Microarray Analysis of Major Epitopes Among Tree Nut-Allergic Individuals May Explain Patterns of Cross-Desensitization. Poster Presentation at the European Academy of Allergy and Clinical Immunology (EAACI) 2020
|
Progress 04/15/19 to 04/14/20
Outputs
Target Audience:The audience for this resarch is other scientists, regulatory agencies, peanut and tree nut industry, professionals dealing with food allergies, food allergic consumers, food industry/processing companies and pharmaceutical industry interested in food allergy product development and marketing. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project has allowed us to recruit a postdoctoral fellow to the field of food allergy. The recruit has participated in learning new skills and expertise and has participated in and presented papers in two internationally attended allergy conferences. She has also participated in more than one conference with companies and collaborators as well as the bioinformatics team (Rho). Two students have worked on the project for their summer projects.Also, the PIs have learned more about bioinformatics and statistics by interacting with the professional bioinformaticians at Rho. How have the results been disseminated to communities of interest?We have presented our work orally at multiple invited seminars locally and nationally at universities, conferences and for conusmer advocacy and commodity groups. We have also published manuscripts and abstracts and presented posters at conferences on this work. Our research progress and team's work has been advertised by our institution, which enhances the visibility of our many projects. What do you plan to do during the next reporting period to accomplish the goals?We plan to continue to analyze the large amounts of data collected. We plan to 1) integrating IgE and IgG4 peptides into the same model to achieve higher diagnostic accuracy; 2) building a new model to include all chip lots, 3) Evaluate models on independent test data. Incorporating more non-allergic data; 4) incorporating ISAC (intact protein) data; 5) integrating the clinical data in order to determine how much the selected peptides add to the common biomarkers such as total and specific IgE/IgG4. To test improved microarray analysis for diagnostic capability for peanut and walnut allergy and future commercialization.
Impacts
What was accomplished under these goals?
Goal 1) Objective: To probe microarrays containing synthetic overlapping peptides, from known peanut and tree nut (i.e. walnuts, cashew, pistachio, etc) allergens, with clinically well-characterized sera from allergic individuals in order to identify IgE and IgG4 binding sites. 1) Major activities completed / experiments conducted: Four hundred microarrays were screened with non-allergic and allergic serum from peanut and tree nut allergic individuals from around the US. The data from the UK peanut allergic vs non allergic patients allowed the identification of IgE and IgG4 bound peptides that were statistically different between allergic and sensitized individuals. 2) Data collected: Peptide IgE and IgG4 epitopes were identified for approximately 400 peanut and tree nut allergic individuals in the US and 84 from the UK. . Preliminary visual inspections shows that the epitope recognition pattern for peanut allergic patients in the US and UK may be different. 3) Summary statistics and discussion of results: Algorithms to eliminate bad spots were developed. For the US pre and post Oral Immunotherapy data: Paired t-tests were run for each peptide within each treatment (e.g. Active Pre-OIT vs Active Post-OIT) to assess the significance of the mean difference between them. P-values were adjusted for multiple comparisons and our criteria for a significant finding was an adjusted p-value <0.10, which allowed us to determine which peptides were significantly altered by OIT in the active treatment group. Similar comparative analysis of peanut allergic vs non allergics show statistically significant differences in serum IgE and IgG4 binding. 4) Key outcomes or other accomplishments realized: a) Diagnostic peptides were identified and validated for improving diagnosis of peanut allergic individuals in the UK and published; b) Statistical algorithms were developed and tested to facilitate further analysis of US patient data sets. Goal 2) Objective: To probe microarrays containing intact allergic proteins (or components), from peanut and tree nut (i.e. walnuts, cashew pistachio, etc), with clinically well-characterized sera from allergic individuals in order to identify IgE binding proteins. 1) Major activities completed / experiments conducted: Renewal of agreements with Thermo-Fisher for continued use of the laser scanner and discounted immune solid phase analysis for allergic components (ISAC) microarrays, offered as a diagnostic resource for physicians http://www.phadia.com/en/Products/Allergy-testing-products/ImmunoCAP-ISAC/). The ISAC arrays were screened with patient sera. 2) Data collected: Data showing IgE binding of 400 peanut and tree nut allergic sera to 110 allergic proteins that are on the ISAC arrays. 3) Summary statistics and discussion of results: The data has been collated into an Excel spreadsheet and sent to Rho to incorporate into the peptide microarray analysis from Goal 1. 4) Key outcomes or other accomplishments realized: The key outcome is the collection of data and performing of screens for over 400 US patient sera. Also, uniform tables were created and coded to connect to the peptide microarray data and patient meta data to facilitate the integration of the peptide and protein data for each sera and for population comparisons. Goal 3) Objective: Collaborate with professional statisticians to support us in evaluating our methods, consult on design, prepare analysis data sets, and perform in-depth statistical analysis to identify the most promising diagnostic peptides/proteins. 1) Major activities completed / experiments conducted: Rho has been given the IgE and IgG4 binding data for 400 peptide microarrays and 400 ISAC arrays and tables containing the patient meta data. 2) Data collected: Peptide microarray and intact protein microarray data the patient tables containing clinical information have been collected and incorporated into one file along with microarray and ISAC patient codes. 3) Summary statistics and discussion of results: Statistical analysis is being performed by Rho on micro-arrays using serum collected for the US nut allergic population. In Step 1. The raw data from various regions around the US were combined, cleaned and reshaped. A subset of the IgE & IgG4 peptide data performed on the same array lot (61 allergic, 22 non-allergic) were subject to background correction and log2 transformation and reduced to one observation then a paired loess method of normalization was applied to peanut allergen peptides in order to find subset of peptides that in combination with one another are predictive of allergic status. 4) Key outcomes or other accomplishments realized. The peptide microarray data originally used as preliminary data from the UK peanut allergic patient sera was analyzed and peptides were identified that when added to Ara h 2, a major peanut allergen (or component), enhanced the diagnosis of peanut allergy for the UK population (now published). This publication clearly shows that a combination of peptides and proteins can improve the serum-based diagnostic ability over existing methods. Another manuscript describing our results with the Aimmune Therapeutics clinical trial sera is planned for submission in 2020. Goal 4) Objective: To probe microarrays, containing only the best diagnostic peptides and intact nut allergen proteins, with clinically well-diagnosed patient sera in order to test and validate the diagnostic value. 1) Major activities completed / experiments conducted: Data obtained from screening peptide and protein microarrays with peanut and walnut allergics, non allergics and sera from peanut oral immunotherapy patients has been uploaded to Rho's high security portal for statistical comparisons. 2) Data collected: All of the microarray data proposed here was collected and uploaded to the bioinformatics/statistical company. Our group also collected and uploaded the patient clinical information. 3) Summary statistics and discussion of results: Upon comparison lot to lot variations in array batches were detected. For expediency, the arrays from a single lot, probed with US patient sera, were used to test the diagnostic accuracy of univariate and multivariate analyses. A small population (61 peanut allergic and 22 non peanut allergics), all on the same chip lot, were background corrected and log 2 transformed. Replicates were reduced to 1 observation by using median, which also handles outliers. The data was then normalized with "paired loess method" and the analysis was limited to the 11 peanut allergens. All data are being normalized for lot to lot variation and the number of sera for identification of combinations of peptides and proteins will be much higher than the primary analysis. 4) Key outcomes or other accomplishments realized: A multivariate classification model was used to find a subset of peptides, that in combination with one another, are predictive of the allergic status. In the "lasso" modeling technique, a subset of the most important peptides are selected, and iterates over different subsets of the data ensure results generalize to new populations and allow estimates of predictive accuracy. The preliminary data with a combination of 22 peanut allergen peptides, with the limited patients on one lot of arrays, has shown an 89.6% accuracy with the IgE model results. In this IgE model, 57/61 allergic patients were accurately diagnosed, 4/22 non-allergics were diagnosed as positive 5/22 non-allergics were diagnosed as peanut allergic. Using the IgG model, the analysis showed an 86.75% accuracy with the IgG4 model results. In this IgE model, 56/61 allergic patients were accurately diagnosed, 5/22 non-allergics were diagnosed as positive 6/22 non-allergics were diagnosed falsely as peanut allergic.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Nesbit J.B., Schein, C.H., Maleki, S.J. Cheng, H., Hurlburt, B.K. The N-terminal Leader Sequence of Walnut Jug r 2 is a cross-reactive allergen. J Allergy Clin Immunol. Vol. 143, Issue 2, AB237
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Hardy, L., Orgel, K., Duan, S., Maleki, S., Burks, A., Paulson, J., Macauley, M., Kulis Jr, M. Using Siglec-engaging Tolerance-inducing Antigenic Liposomes (STALs) to reduce memory B cell responses to the major peanut allergen Ara h 2. Journal of Allergy and Clinical Immunology, Volume 141, Issue 2, AB200
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Hurlburt, B., Cheng, H., Santos, A., Lack, G., Maleki S. Epitope Mapping Walnut Allergens Jug r 1 and Jug r 2. Journal of Allergy and Clinical Immunology, Volume 141, Issue 2, AB179,
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Finley, A., Maleki, S. Wild, L., Hurlburt, B. Characterizing the IgE Reactivity in Oral Allergy Syndrome to Celery and Carrots. Journal of Allergy and Clinical Immunology, Volume 141, Issue 2, AB244
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Kronfel, C., Cheng, H., Hurlburt, B., Simon, R., Maleki, S. Epitope Mapping for the Non-Specific Lipid Transfer Proteins (nsLTP) Among Peanut Allergic Patients. Journal of Allergy and Clinical Immunology, Volume 141, Issue 2, AB239
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Mohammadi, M., Falak, R., Emameh, R.Z., Maleki, S.J. Kardar G.A. Computational Analysis of Specific IgE Epitopes Responsible for Allergy to Fish. Current Immunology Reviews, 14 (2):130-136.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2019
Citation:
Maleki, S.J., Hurlburt, B. K. Understanding allergic cross-reactivity among peanut and tree nuts. Proceedings of 46th United States Japan National Resource Panel. 15-17.
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2020
Citation:
Santos, A.F., Barbosa-Morais, N.L., Hurlburt, B.K., Ramaswamy, S., Kwok, M., Cheng, H., James, L., Gould, H., Sutton, B., Maleki, S.J., Lack, G. IgE to Epitopes of Ara h 2 Enhance the Diagnostic Accuracy of Ara h 2-specific IgE. Allergy (00) 1-10. 2020. doi: 10.1111/all.14301
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Nesbit J.B., Schein, C.H., Braun, B.A., Gipson, S.A.Y., Cheng, H., Hurlburt, B.K., Maleki S.J. Epitopes with similar physicochemical properties contribute to cross reactivity between peanut and tree nuts. Molecular Immunology. 2020. doi.org/10.1016/j.molimm.2020.03.017
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
Soheila Maleki, Peanut and Tree Nut Allergy, Invited Speaker at Western Regional Research Center, Albany, CA
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
Soheila Maleki, Peanut and Tree Nut Allergy, Invited Speaker at Food Allergy and Anaphylaxis Network Annual Meeting, Hamburger University, Chicago, IL
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
Soheila Maleki, Cross-reactivity between peanuts and tree nuts, Invited Speaker at Jimei Univeristy, Nov 2019.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
Soheila Maleki, The relationship between structure and allergenicity of food allergens. The First International Symposium on Food Components, Structural Change and Quality Function Regulation (1st ISFSQ 2019) Dongguan University of Technology, Dongguan, Guangdong, China, 11.8-11.10, 2019. Organized Institute of Food Science and Technology of Chinese Academy of Agricultural Sciences (CAAS).
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
Soheila Maleki, Progress in Peanut and Tree Nut Allergy Research, Invited Key Note talk, National Food Research Institute (NFRI), Tsukuba Japan, Dec 2019.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Soheila Maleki, Structural Biology of Food Allergens and Cross Reactivity, Planned for London, UK, June 6-8, 2020 but presented in virtual meeting online.
|
Progress 04/15/18 to 04/14/19
Outputs
Target Audience:The only reliable diagnostic tool for food allergy is to feed the allergic food to the patient (oral food challenge or OFC) in a clinical setting and watch their reaction, which is lengthy, highly unpleasant and potentially dangerous, particularly if you have multiple nut allergies. With the development of immunotherapeutics, Oral Food Challenge (OFC) is the only way to determine if allergic individuals have become desensitized to individual nuts. Doctors, food allergic consumers and their families are in great need of a tool that will definitively diagnose food allergy. The development of a reliable diagnostic microarray assay will have a significant impact on food allergic consumers, physicians as well as the related pharmaceutical industries that develop diagnostic and therapeutic tools for food allergy. In addition, food allergy, particularly nut allergy poses a significant market barrier for the nut industry by burdening food manufacturers, restaurants, airplanes, schools, etc. with difficult-to- adhere-to cleaning and or labelling regulations. As a result, in order to reduce cost, ease the necessity for compliance, and fear of liability, companies may choose not to use nuts in their products or serve them in their facilities, as seen with schools and the airline industry. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project has allowed us to recruit a postdoctoral fellow to the field of food allergy. The recruit has participated in learning new skills and expertise and has participated in and presented papers in two internationally attended allergy conferences. She has also participated in more than one conference with companies and collaborators as well as the bioinformatics team (Rho). How have the results been disseminated to communities of interest?We have presented our work orally at multiple invited seminars locally and nationally at universities, conferences and commodity groups. We have also published abstracts and presented posters at conferences on this work. What do you plan to do during the next reporting period to accomplish the goals?Continue to screen peptide and protein microarrays with serum from patients around the US and present this data to Rho for bioinformatic analysis. To use the results from Rho and have the most predictive peptides synthesized for a new micro-array. To test this micro-array for diagnostic capability and commercialization.
Impacts
What was accomplished under these goals?
Nut allergies have tripled in the last 20 years. People with peanut and tree nut allergy are often allergic to other nuts and seeds. The only reliable diagnostic tool is to feed the allergic food to the patient (oral food challenge or OFC) in a clinical setting and watch their reaction, which is lengthy, highly unpleasant and potentially dangerous, particularly if you have multiple nut allergies. Therefore, allergists often advise a peanut or tree nut allergic patient to avoid all nuts instead of performing OFCs with each individual nut or relying on inaccurate diagnostics that measure blood Immunoglobulin E (IgE) antibody levels against nut extracts, which contain a mixture of proteins. Not only does this impose a significant hardship on the allergic consumer, their families, schools and physicians, but also poses a significant market barrier for the nut industry by burdening food manufacturers, restaurants, airplanes, schools, etc. with difficult cleaning and or labelling regulations to adhere to. As a result, in order to reduce cost or ease the necessity for regulatory compliance, companies may choose not to use nuts in their products or serve them in their facilities, as seen with the airline industry. We proposed to identify the exact amino acid sequences (or peptides) of each allergen to which the IgE and IgG4 antibodies from the blood of peanut or tree nut allergic individuals react. To accomplish this, a nut allergen-peptide library has been synthesized on the surface of microscope slides (peptide microarray) and incubated with the serum antibodies from allergic individuals, which are expected to bind to specific peptides. We hypothesize that identification of the segments of the allergens that are recognized by the antibodies (or epitopes) from the blood of conclusively diagnosed, nut allergic individuals, will provide biomarkers for more accurate or even definitive diagnosis of peanut and tree nut allergy. This would ultimately replace OFC with multiple nuts in order to have an accurate diagnosis and obviate the need for unsubstantiated nut elimination diets. Goal 1) To identify IgE and IgG4 binding peptides with sera from clinically-characterized nut-allergic individuals. Objective: To probe microarrays containing synthetic overlapping peptides, from known peanut and tree nut (i.e. walnuts, cashew, pistachio, etc) allergens, with clinically well-characterized sera from allergic individuals in order to identify IgE and IgG4 binding sites. 1) Major activities completed / experiments conducted: The microarrays were produced and serum from the blood of peanut and tree nut allergic individuals from Davis, CA, Denver, CO; New Orleans, LA, Rochester, NY, Chapel Hill, NC, Little Rock, AR and Aimmune Therapeutics (from clinical trials held all over the US were used to screen approximately 400 peptide microarrays. The conditions for optimal detection were worked out with approximately 85 patients from the UK (preliminary results in the proposal). 2) Data collected: peptide IgE and IgG4 epitopes were identified for approximately 400 peanut and tree nut allergic individuals. Visual inspection of the data (as opposed to statistically analyzed) for specific allergens under study were performed. Based on visual inspections, we were able to determine that the epitope recognition pattern for peanut allergic patients in the US and UK are different. 3) Summary statistics and discussion of results: The PIs have contracted a professional bioinformatics company (Rho) to analyze the massive amount of data that will be generated. A plan of work was agreed upon by the PIs and Rho. Using the previously generated data set from the UK patients Rho developed algorithms to help assess the microarrays and to eliminate bad spots on the microarray. The microarray data, previously screened with peanut allergic and non-allergic sera from the UK, have resulted in potentially diagnostic peptides for peanut allergic individuals in the UK. The data sets from our US patients is now being analyzed by Rho using these algorithms. We have bi-weekly conference calls with the Rho statistics team. 4) Key outcomes or other accomplishments realized. a) Based on visual inspections, we were able to determine that the epitope recognition pattern for peanut allergic patients in the US and UK are different; b) potentially diagnostic peptides were identified for peanut allergic individuals with the UK sera; c) Statistical algorithms were developed to facilitate further analysis of US patient data sets. Goal 2) Identify clinically important allergens and the relative contribution of conformational IgE and IgG4 epitopes. Objective: To probe microarrays containing intact allergic proteins (or components), from peanut and tree nut (i.e. walnuts, cashew pistachio, etc), with clinically well-characterized sera from allergic individuals in order to identify IgE and IgG4 binding proteins. 1) Major activities completed / experiments conducted: Negotiations with Thermo-Fisher were completed and an agreement was reached to provide the PIs with a laser scanner and discounted microarrays or slides that contain purified whole or intact allergen proteins, also referred to as components (as opposed to peptide arrays in goal 1). The arrays are called ISAC (http://www.phadia.com/en/Products/Allergy-testing-products/ImmunoCAP-ISAC/) and Thermo-Fisher/Phadia offers them as a diagnostic resource for physicians. 2) Data collected: 400 sera have been screened on ISAC chips. 3) Summary statistics and discussion of results: The data has been collated into an Excel spreadsheet and sent to Rho for analysis. 4) Key outcomes or other accomplishments realized. None. We are waiting on the Rho team analysis. Goal 3) To have professional bioinformatics and statistical analysis of the data from Goals 1 and 2. Objective: Collaborate with professional statisticians to support us in evaluating our methods, consult on design, prepare analysis data sets, and perform in-depth statistical analysis to identify the most promising diagnostic peptides/proteins. 1) Major activities completed / experiments conducted: An excellent bioinformatics/ statistical team at Rho has been contracted for the project and has helped us optimize and select the conditions for running and analysing our peptide microarray data. 2) Data collected; peptide microarray data originally used as preliminary data from the UK peanut allergic patient sera was analysed by their statisticians. They were able to identify potentially diagnostic peptides for peanut allergy for UK population. The manuscript has been submitted for publication. 3) Summary statistics and discussion of results: Statistical analysis is being performed by Rho on micro-arrays using serum collected for the US nut allergic population in this project. 4) Key outcomes or other accomplishments realized. Recruited an excellent group (Rho) to help with final statistical analysis of the data. The UK patient population microarray data and analysis is submitted for publication in the top journal in the field of allergy: Journal of Allergy and Clinical Immunology (JACI). Another manuscript describing our results with the Aimmune Therapeutics clinical trial sera is planned for submission in 2019. Goal 4) Design new peptide/protein combination microarrays and test with allergic patient sera to confirm diagnostic value. Objective: To probe microarrays, containing only the best diagnostic peptides and intact nut allergic proteins, with clinically well-diagnosed patient sera in order to test and validate the diagnostic value. 1) Major activities completed / experiments conducted: Identification of potentially diagnostic peptides for peanut allergy for UK population as proof of concept. 2) Data collected: None 3) Summary statistics and discussion of results: None 4) Key outcomes or other accomplishments realized: None. This goal is contingent on the results that Rho will provide.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Nesbit, Jacqueline B, Cheng, Hsiaopo, Hurlburt, Barry K., Maleki, Soheila J. Identification and assessment of the IgE epitopes of Ara h 1 and Jug r 2 leader sequences
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Hurlburt, Barry K.,Cheng, Hsiaopo, Maleki, Soheila J. Epitope Mapping of 2S albumins and Comparison of Ara h 2, Ara h 6 and Ara h 7 from Peanut. Journal of Allergy and Clinical Immunology, Vol. 143, Issue 2, AB68
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Kronfel, Christina M., Cheng, Hsiaopo, Hurlburt, Barry K., Simone, Reyna J., Maleki, Soheila J.IgE and IgG4 Epitope Profiles for the Major Peanut Allergens from Peanut Allergic Patients Undergoing Oral Immunotherapy. Journal of Allergy and Clinical Immunology, Vol. 143, Issue 2, AB241
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Maleki, Soheila J., Nesbit, Jacqueline B., Hurlburt, Barry K.,Foo, Alexander C., Cheng, Hsiaopo, Mueller, Geoffrey A. The NMR structure and IgE Epitopes of Ara h 1 Leader Sequence.Journal of Allergy and Clinical Immunology, Vol. 143, Issue 2, AB240
- Type:
Other
Status:
Published
Year Published:
2018
Citation:
Maleki, S.J., Hurlburt, B. K. Allergic cross-reactivity among peanut and tree nut allergens Proceedings of 45th United States Japan National Resource Panel. 2018. (Proceedings)
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Dyer, S., Nesbit J.B., Cabanillas, B., Cheng, H., Hurlburt B.K., Maleki, S.J., Contribution of Chemical Modifications and Conformational Epitopes to IgE binding by Ara h 3. Foods 7(11), 1-9. 2018
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Progress 04/15/17 to 04/14/18
Outputs
Target Audience:The only reliable diagnostic tool for food allergy is to feed the allergic food to the patient (oral food challenge or OFC) in a clinical setting and watch their reaction, which is lengthy, highly unpleasant and potentially dangerous, particularly if you have multiple nut allergies. With the development of immunotherapeutics, Oral Food Challenge (OFC) is the only way to determine if allergic individuals have become desensitized to individual nuts. Doctors, food allergic consumers and their families are in great need of a tool that will definitively diagnose food allergy. The development of a reliable diagnostic microarray assay will have a significant impact on food allergic consumers, physicians as well as the related pharmaceutical industries that develop diagnostic and therapeutic tools for food allergy. In addition, food allergy, particularly nut allergy poses a significant market barrier for the nut industry by burdening food manufacturers, restaurants, airplanes, schools, etc. with difficult-to- adhere-to cleaning and or labelling regulations. As a result, in order to reduce cost, ease the necessity for compliance, and fear of liability, companies may choose not to use nuts in their products or serve them in their facilities, as seen with schools and the airline industry. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project has allowed us to recruit a postdoctoral fellow to the field of food allergy. The recruit has participated in learning new skills and expertise and has participated in and presented papers in two internationally attended allergy conferences. She has also participated in more than one conference with companies and collaborators as well as the bioinformatics team (Rho). How have the results been disseminated to communities of interest?We have presented our work orally at multiple invitedseminars locally and nationally at universities, conferences andcommodity groups. We have also published abstracts and presented posters at conferences on this work. What do you plan to do during the next reporting period to accomplish the goals?Continue to screen peptide and proteinmicroarrays with serum from patients around the united states and present this dat to Rho for bioincomatic analysis.
Impacts
What was accomplished under these goals?
Nut allergies have tripled in the last 20 years. Up to 2% of children (> 0.6 million) in the United States have reactions to peanuts, and 1% to tree nuts, with symptoms ranging from skin irritation to life-threatening anaphylaxis. More than 50% of tree nut and peanut-allergic children suffer from severe reactions. One complicating factor is that people with peanut and tree nut allergy are also often allergic to other nuts and seeds. The only reliable diagnostic tool is to feed the allergic food to the patient (oral food challenge or OFC) in a clinical setting and watch their reaction, which is lengthy, highly unpleasant and potentially dangerous, particularly if you have multiple nut allergies. Therefore, allergists often advise a peanut or tree nut allergic patient to avoid all nuts instead of performing OFCs with each individual nut or relying on inaccurate diagnostics that measure blood Immunoglobulin E (IgE) antibody levels against nut extracts, which contain a mixture of proteins. Not only does this impose a significant hardship on the allergic consumer, their families, schools and physicians, but also poses a significant market barrier for the nut industry by burdening food manufacturers, restaurants, airplanes, schools, etc. with difficult cleaning and or labelling regulations to adhere to. As a result, in order to reduce cost or ease the necessity for regulatory compliance, companies may choose not to use nuts in their products or serve them in their facilities, as seen with the airline industry. We proposed to identify the exact amino acid sequences (or peptides) of each allergen to which the IgE and IgG4 antibodies from the blood of peanut or tree nut allergic individuals react. To accomplish this, a nut allergen-peptide library has been synthesized on the surface of microscope slides (peptide microarray) and incubated with the serum antibodies from allergic individuals, which are expected to bind to specific peptides. We hypothesize that identification of the segments of the allergens that are recognized by the antibodies (or epitopes) from the blood of conclusively diagnosed, nut allergic individuals, will provide biomarkers for more accurate or even definitive diagnosis of peanut and tree nut allergy. This would ultimately replace OFC with multiple nuts in order to have an accurate diagnosis and obviate the need for unsubstantiated nut elimination diets. The specific goals and objectives for the project are: Goal 1) To identify IgE and IgG4 binding peptides with sera from clinically-characterized nut-allergic individuals. Objective: To probe microarrays containing synthetic overlapping peptides, from known peanut and tree nut (i.e. walnuts, cashew, pistachio, etc) allergens, with clinically well-characterized sera from allergic individuals in order to identify IgE and IgG4 binding sites. 1) Major activities completed / experiments conducted: The microarrays were produced and serum from the blood of peanut and tree nut allergic individuals from Davis, CA, Denver, CO; New Orleans, LA and Little Rock, AR were used to screen approximately 100 peptide microarrays. The conditions for optimal detection were worked out with approximately 85 patients from the UK (preliminary results in the proposal). 2) Data collected: peptide IgE and IgG4 epitopes were identified for approximately 100 peanut and tree nut allergic individuals. Visual inspection of the data (as opposed to statistically analyzed) for specific allergens under study were performed. Based on visual inspections, we were able to determine that the epitope recognition pattern for peanut allergic patients in the US and UK are different. 3) Summary statistics and discussion of results: The PIs have contracted a professional bioinformatics company (Rho) to analyze the massive amount of data that will be generated. A plan of work was agreed upon by the PIs and Rho. Using the previously generated data set from the UK patients Rho developed algorithms to help assess the microarrays and to eliminate bad spots on the microarray. The microarray data, previously screened with peanut allergic and non-allergic sera from the UK, have resulted in potentially diagnostic peptides for peanut allergic individuals in the UK. The data sets from our US patients will now be easily analyzed by Rho using these algorithms. 4) Key outcomes or other accomplishments realized. a) Based on visual inspections, we were able to determine that the epitope recognition pattern for peanut allergic patients in the US and UK are different; b) potentially diagnostic peptides were identified for peanut allergic individuals in the UK; c) Statistical algorithms were developed to facilitate further analysis of US patient data sets. Goal 2) Identify clinically important allergens and the relative contribution of conformational IgE and IgG4 epitopes. Objective: To probe microarrays containing intact allergic proteins (or components), from peanut and tree nut (i.e. walnuts, cashew pistachio, etc), with clinically well-characterized sera from allergic individuals in order to identify IgE and IgG4 binding proteins. 1) Major activities completed / experiments conducted: Negotiations with Thermo-Fisher were completed and an agreement was reached to provide the PIs with a laser scanner and discounted microarrays or slides that contain purified whole or intact allergen proteins , also referred to as components (as opposed to peptide arrays in goal 1). The arrays are called ISAC (http://www.phadia.com/en/Products/Allergy-testing-products/ImmunoCAP-ISAC/) and Thermo-Fisher/Phadia offer them as a diagnostic resource for physicians. 2) Data collected: None 3) Summary statistics and discussion of results: None. 4) Key outcomes or other accomplishments realized. We have obtained the equipment, reagents and expertise necessary to accomplish this objective. Goal 3) To have professional bioinformatics and statistical analysis of the data from Goals 1 and 2. Objective: Collaborate with professional statisticians to support us in evaluating our methods, consult on design, prepare analysis data sets, and perform in-depth statistical analysis to identify the most promising diagnostic peptides/proteins. 1) Major activities completed / experiments conducted: An excellent bioinformatics/ statistical team at Rho has been contracted for the project and has helped us optimize and select the conditions for running and analysing our peptide microarray data. 2) Data collected; peptide microarray data originally used as preliminary data from the UK peanut allergic patient sera was analysed by their statisticians. They were able to identify potentially diagnostic peptides for peanut allergy for UK population. The manuscript is under revision for publication. 3) Summary statistics and discussion of results: No statistical analysis has been performed on serum collected for the US nut allergic population in this project. 4) Key outcomes or other accomplishments realized. Recruited an excellent group (Rho) to help with final statistical analysis of the data. The UK patient population microarray data and analysis is in revision for publication in the top journal in the field of allergy: Journal of Allergy and Clinical Immunology (JACI). Goal 4) Design new peptide/protein combination microarrays and test with allergic patient sera to confirm diagnostic value. Objective: To probe microarrays, containing only the best diagnostic peptides and intact nut allergic proteins, with clinically well-diagnosed patient sera in order to test and validate the diagnostic value. 1) Major activities completed / experiments conducted: None 2) Data collected: None 3) Summary statistics and discussion of results: None 4) Key outcomes or other accomplishments realized: None
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2017
Citation:
Santos A.F., Barbosa-Morais, N., Hurlburt, B.K., Ramaswamy, S., Kwok, M., Cheng, H., James L.K., Gould, H.J., Sutton, B.J., Maleki S.J., Lack, G. Identification of IgE epitopes important for mast cell activation in peanut allergy. World Immune Regulation Meeting (WIRM), Davos Switzerland. 2017.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Kronfel, Christina M; Cheng, Hsiaopo; Hurlburt, Barry K; Simon, Reyna J; Maleki, Soheila J. Epitope Mapping for the Non-Specific Lipid Transfer Proteins (nsLTP) Among Peanut Allergic Patients. Journal of Allergy and Clinical Immunology, Vol.141, Issue 2, Supplement, Page: AB239. 2018.Academy of Allergy Asthma and Immunology (AAAAI), Orlando, Fl. 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Finley, Abigail N; Maleki, Soheila J; Wild, Laurianne G; Hurlburt, Barry K. Characterizing the IgE Reactivity in Oral Allergy Syndrome to Celery and Carrots. Journal of Allergy and Clinical Immunology, Vol.141, Issue 2, Supplement, Page: AB244. 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Nesbit, Jacqueline B; Cheng, Hsiaopo; Hurlburt, Barry K; Maleki, Soheila J. Identification and assessment of the IgE epitopes of Ara h 1 and Jug r 2 leader sequences. Journal of Allergy and Clinical Immunology, Vol.141, Issue 2, Supplement, Page, AB179. 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Maleki, Soheila J.; Nesbit, Jacqueline B; Cheng, Hsiaopo; Hurlburt, Barry K. Epitope Mapping of 2S albumins and Comparison of Ara h 2, Ara h 6 and Ara h 7 from Peanut. Journal of Allergy and Clinical Immunology, Vol.141, Issue 2, Supplement, Page AB238. 2018
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Hurlburt, Barry K; Cheng, Hsiaopo; Alexandra Figueira Santos; Lack, Gideon; Maleki, Soheila J. Epitope Mapping Walnut Allergens Jug r 1 and Jug r 2. Journal of Allergy and Clinical Immunology, Vol.141, Issue 2, Supplement, Page: AB179. 2018.
- Type:
Other
Status:
Other
Year Published:
2018
Citation:
Barry K. Hurlburt. Structure, function and epitope mapping of peanut allergens, Distinguished Lecturer Series, Invited talk: Tulane Biochemistry Department, New Orleans, LA. April 2018.
- Type:
Other
Status:
Other
Year Published:
2018
Citation:
Soheila J. Maleki. Cross-reactivity between peanuts and tree nuts. Distinguished Lecturer Series, Invited talk: Biochemistry Department, Medical School, Indianapolis, IN (April 2018) & Tulane Univ., New Orleans, LA. (Nov. 2017).
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Maleki, S.J., Schein, S.H. Hurlburt. Allergic cross-reactivity among peanut and tree nut allergens Proceedings of 45th United States Japan National Resource Panel 2017. (Proceedings)
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Hurlburt B.K., Santos, A.F., Cheng, H., Barbosa-Morais, N., Lack, G., Maleki, S.J. IgE Epitopes Critical for Eliciting Mast Cell Activation and Allegic Symptoms in Peanut Allergy. Proceedings of 45th United States Japan National Resource Panel. Hirishima, Japan 2017. (Proceedings)
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