Predicting the allergenicity of legume proteins using a PBMC gene expression assay_Pilot experiment
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE168698 | GEO | 2021/03/17
REPOSITORIES: GEO
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Project description:Food proteins differ in their allergenic potential. Currently, there is no predictive and validated bio-assay to evaluate the allergenicity of novel food proteins. The objective of this study was to investigate the potential of a human peripheral blood mononuclear cell (PBMC) gene expression assay to identify biomarkers to predict the allergenicity of legume proteins. PBMCs from healthy donors were exposed to weakly and strongly allergenic legume proteins. Inclusion of multiple protein pairs from 2S albumins (lupine and peanut) and 7S globulins (white bean and soybean) in a larger study, led to the selection of CCL2, CCL7, and RASD2 as biomarkers to distinguish weakly from strongly allergenic proteins.
2021-03-17 | GSE169030 | GEO
Project description:Germination offers advantages to improve legume protein digestibility as it disintegrates seed structure and hydrolyzes proteins and anti-nutrients. Seed permeability (related to polyphenol content of seed coats) is an important factor affecting the duration of seed germination and its impact in protein digestibility and bioactivity. The objective was to compare the effect of seed germination on protease activity, structure and proteolysis of four selected legumes with contrasting seed coat polyphenol profiles (gray zero tannin [GZL], beluga [BL] and dehulled red [DL] lentils; and zero tannin/low vicine-convicine fava bean [ZF]). Protein hydrolysis was characterized during germination and digestion with respect to proteins, peptides and free amino acids (FAA). In vitro antihypertensive and antioxidant activities of digests were investigated, and peptidomic characterization (HPLC-MS/MS) and identification of bioactive fragments in intestinal digests were performed. Regardless of seed type, germination increased protease activity and reduced levels of phytic acid, trypsin inhibitors and tannins (only in BL). Significant proteolysis of the 7S and 11S globulins and concomitant increase peptides and FAA was observed in all sprouted legumes. Digestion kinetics in sprouts revealed a faster generation of FAA and peptides than in dry seeds, with changes more evident for DL associated to faster imbibition, germination and sprout growth. In contrast, BL sprouts showed the lowest protein digestibility, likely due to lower protease activity levels, seed structure disintegration and higher anti-nutrient levels in comparison to GZL, DL and ZF. Moreover, digestion of sprouts resulted in a higher number of resistant peptides in DL and ZF that matched with previously reported bioactive sequences, suggesting a promising health potential of legume sprouts that was confirmed in vitro. Results suggested that the germination process improved protein digestibility and health promoting potential of lentil and fava bean proteins although these changes were more evident in DL due to its rapid imbibition, faster germination and sprout development. This study will provide important information for either plant breeders to develop legume varieties with permeable seed coats or food producers that could use dehulled seeds for efficient production of sprouts as sustainable food sources of plant proteins with improved nutritional and healthy properties.
2021-11-02 | PXD027847 | Pride
Project description:Soybean (Glycine max) and mung bean (Vigna radiata) are key legumes with global importance, but their mechanisms for coping with cold stress—a major challenge in agriculture—have not been thoroughly investigated, especially in a comparative study. This research aimed to fill this gap by examining how these two major legumes respond differently to cold stress and exploring the role of uniconazole, a potential stress mitigator. Our comprehensive approach involved transcriptomic and metabolomic analyses, revealing distinct responses between soybean and mung bean under cold stress conditions. Notably, uniconazole was found to significantly enhance cold tolerance in mung bean by upregulating genes associated with photosynthesis, while its impact on soybean was either negligible or adverse. To further understand the molecular interactions, we utilized advanced machine learning algorithms for protein structure prediction, focusing on photosynthetic pathways. This enabled us to identify LOC106780309 as a direct binding target for uniconazole, confirmed through isothermal titration calorimetry. This research establishes a new comparative approach to explore how soybean and mung bean adapt to cold stress, offers key insights to improve the hardiness of legumes against environmental challenges, and contributes to sustainable agricultural practices and food security.
2024-07-19 | GSE193328 | GEO
Project description:We report the changes in transcriptome that results from RNAi suppression of 7S and 11S storage protein synthesis in soybean seeds, Proteomic results show that other proteins compensate for the storage protein shortfall. The transcriptome analysis show numerous changes result from suppressing storage proteins but compensating proteins are accumulated without parallel changes in the protein's transcription.
2010-05-01 | GSE21116 | GEO
Project description:Common bean (Phaseolus vulgaris) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and specificity in common bean cross-species hybridization (CSH) GeneChip data compared to that of soybean. We employed a method that masked putative probes targeting inter-species variable (ISV) regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and specificity. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by about 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR analysis of a total of 20 randomly selected genes and purine-ureides pathway genes demonstrated an increased specificity after masking for ISV regions. We also evaluated masked probe frequency per probe set to gain insight into the sequence divergence pattern between common bean and soybean. The results from this study suggested that transcript profiling in common bean can be done using the soybean GeneChip. However, a significant decrease in sensitivity and specificity can be expected. Problems associated with CSH GeneChip data can be mitigated by masking probes targeting ISV regions. In addition to transcript profiling CSH of the GeneChip in combination with masking probes in the ISV regions can be used for comparative ecological and/or evolutionary genomics studies.
2010-03-01 | GSE18822 | GEO
Project description:Common bean (Phaseolus vulgaris) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and specificity in common bean cross-species hybridization (CSH) GeneChip data compared to that of soybean. We employed a method that masked putative probes targeting inter-species variable (ISV) regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and specificity. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by about 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR analysis of a total of 20 randomly selected genes and purine-ureides pathway genes demonstrated an increased specificity after masking for ISV regions. We also evaluated masked probe frequency per probe set to gain insight into the sequence divergence pattern between common bean and soybean. The results from this study suggested that transcript profiling in common bean can be done using the soybean GeneChip. However, a significant decrease in sensitivity and specificity can be expected. Problems associated with CSH GeneChip data can be mitigated by masking probes targeting ISV regions. In addition to transcript profiling CSH of the GeneChip in combination with masking probes in the ISV regions can be used for comparative ecological and/or evolutionary genomics studies. We hybridized cRNA purified from nodule, leaf, and root of common bean and soybean in, triplicate, to the soybean GeneChip (18 GeneChip hybridizations = 2 species x 3 organs x 3 replicates).
2010-03-07 | E-GEOD-18822 | biostudies-arrayexpress
Project description:We report the changes in transcriptome that results from RNAi suppression of 7S and 11S storage protein synthesis in soybean seeds, Proteomic results show that other proteins compensate for the storage protein shortfall. The transcriptome analysis show numerous changes result from suppressing storage proteins but compensating proteins are accumulated without parallel changes in the protein's transcription. Total RNA samples prepared from midmaturation wildtype and storage protein RNAi (SP-) soybeans were used to produce cDNA that was subjected to Illumina sequencing. The resulting sequences were assembled and analyzed to characterize the changes in transcriptome that results from suppressing storage protein synthesis/accumulation.
2010-05-01 | E-GEOD-21116 | biostudies-arrayexpress
Project description:Seeds, including soybean (Glycine max), contain bioactive proteins with anti-nutritional and immunological properties that affect metabolism and assimilation of seed derived nutrients and as allergens that can induce escalating adverse immune responses. The presence of anti-nutritional proteins requires soybean protein to be processed by heat that results in energy costs and alteration of soybean protein’s physiochemical properties. Nulls for bioactive seed proteins have been isolated from the USDA soybean collection including Kunitz trypsin inhibitor (TI) and soybean agglutinin (LE) and immunodominant soybean allergen P34 proteins. Each of these nulls has the potential to partially address concerns of soybean feed/food consumption and stacked together these traits can form a basis for engineering improved soybean cultivars. A stack of cultivars of recessive nulls of TI, LE, and P34 was created in a cv Williams 82 background termed “Triple Null”. The reduction of these proteins slightly diminishes the overall protein content of the seed that was analyzed by 2D IEF/SDS gels and proteomics. P34 and Kunitz Trypsin Inhibitor nulls are frame shift mutants shown by mass spectroscopy to accumulate small amounts of authentic protein. Triple Null’s capacity for biolistic transformation was assessed showing that Triple Null can be transformed permitting stacking of transgene traits. Triple Null has possible application as a conventional feed/food source and for immunotherapy to mitigate soybean allergenic response and be leveraged as a transformation platform to stack other production or consumer traits.
2022-02-23 | PXD000967 | Pride
Project description:This pilot study is designed to test the effects of a high legume (dried bean) diet on hunger and other indicators of health over the course of eight weeks, compared to a more conventional healthy diet.
| 2176646 | ecrin-mdr-crc
Project description:Thermal processing of allergenic foods has the potential to induce a number of changes in the constituent allergens, but many of the effects of heat treatment are poorly defined. Like numerous other commonly allergenic tree nuts, walnuts often undergo heat treatment, such as roasting, prior to consumption. This study evaluated the changes in solubility and detectability of allergens from roasted walnuts using tandem mass spectrometry methods. Walnuts were roasted at 132 °C or 180 °C for 5, 10, or 20 minutes prior to preparation for LC-MS/MS using sequential or simultaneous protocols for extraction and trypsin digestion. LC-MS/MS data analysis incorporated label-free quantification and Maillard adduct screening. Relatively minor changes in detection were demonstrated following roasting in some allergenic proteins (2S albumin, LTP, and the 7S vicilin N-terminal region) with the LC-MS/MS method. The mature 7S vicilin and 11S legumin, however, showed significantly increased detection in the highest heat treatment sample when using the simultaneous extraction/digestion protocol, an effect likely due to increased digestibility of the proteins following heating. The results of this study indicate that individual walnut allergens respond differently to thermal processing, and the detection of these proteins by LC-MS/MS is dependent on the protein in question, its susceptibility to proteolytic digestion, the degree of thermal processing, and the sample preparation methodology.
2016-05-18 | PXD000907 | Pride