Network analysis of the proteome and peptidome sheds light on human milk as a biological system.

Proteins and peptides found in human milk have bioactive potential to benefit the newborn and support healthy development. Research has been carried out on the health benefits of proteins and peptides, but many questions still need to be answered about the nature of these components, how they are formed, and how they end up in the milk. This study explored and elucidated the complexity of the human milk proteome and peptidome. Proteins and peptides were analyzed with non-targeted nanoLC-Orbitrap-MS/MS in a selection of 297 milk samples from the CHILD Cohort Study. Protein and peptide abundances were determined, and a network was inferred using Gaussian graphical modeling (GGM), allowing an investigation of direct associations. This study showed that signatures of (1) specific mechanisms of transport of different groups of proteins, (2) proteolytic degradation by proteases and aminopeptidases, and (3) coagulation and complement activation are present in human milk. These results show the value of an integrated approach in evaluating large-scale omics data sets and provide valuable information for studies that aim to associate protein or peptide profiles from biofluids such as milk with specific physiological characteristics.

Corrigendum: The human milk proteome and allergy of mother and child: exploring associations with protein abundances and protein network connectivity.

[This corrects the article DOI: 10.3389/fimmu.2022.977470.].

Raw milk kefir: microbiota, bioactive peptides, and immune modulation.

This study aims to characterize the microbiota and peptidomic composition of raw milk kefir, and to address the potential anti-allergic effects of raw milk kefir using validated research models for food allergy. Raw milk kefir was produced after incubation with a defined freeze-dried starter culture. Kefir was sampled during fermentation at seven time intervals. For comparison, kefir was also prepared from heat-treated milk. Peptide compositions were determined for the raw and heated milk, and kefir end products made from these milks. In a murine food allergy model, the two kefir end products were investigated for their allergy modulating effects. In both kefirs, we identified amplicon sequence variants identical to those in the starter culture, matching the bacteria Lactococcus lactis, Streptococcus thermophilus, Leuconostoc and the yeast Debaryomyces. In raw milk kefir, additional sequence variants of Lactococcus lactis and the yeasts Pichia and Galactomyces could be identified, which were absent in heated milk kefir. Analysis of peptide compositions in both kefirs indicated that the number and intensity of peptides drastically increased after fermentation. Heating of the milk negatively affected the diversity of the peptide composition in kefir. Only raw milk kefir suppressed the acute allergic skin response to the food allergen ovalbumin in sensitised mice. These effects coincided with differences in the T-cell compartment, with lower percentages of activated Th1 cells and IFNg production after treatment with kefir made from heated milk. The results of this study indicate specific properties of raw milk kefir that may contribute to its additional health benefits.

The human milk proteome and allergy of mother and child: Exploring associations with protein abundances and protein network connectivity.

Background: The human milk proteome comprises a vast number of proteins with immunomodulatory functions, but it is not clear how this relates to allergy of the mother or allergy development in the breastfed infant. This study aimed to explore the relation between the human milk proteome and allergy of both mother and child. Methods: Proteins were analyzed in milk samples from a subset of 300 mother-child dyads from the Canadian CHILD Cohort Study, selected based on maternal and child allergy phenotypes. For this selection, the definition of "allergy" included food allergy, eczema, allergic rhinitis, and asthma. Proteins were analyzed with non-targeted shotgun proteomics using filter-aided sample preparation (FASP) and nanoLC-Orbitrap-MS/MS. Protein abundances, based on label-free quantification, were compared using multiple statistical approaches, including univariate, multivariate, and network analyses. Results: Using univariate analysis, we observed a trend that milk for infants who develop an allergy by 3 years of age contains higher abundances of immunoglobulin chains, irrespective of the allergy status of the mother. This observation suggests a difference in the milk's immunological potential, which might be related to the development of the infant's immune system. Furthermore, network analysis showed overall increased connectivity of proteins in the milk of allergic mothers and milk for infants who ultimately develop an allergy. This difference in connectivity was especially noted for proteins involved in the protein translation machinery and may be due to the physiological status of the mother, which is reflected in the interconnectedness of proteins in her milk. In addition, it was shown that network analysis complements the other methods for data analysis by revealing complex associations between the milk proteome and mother-child allergy status. Conclusion: Together, these findings give new insights into how the human milk proteome, through differences in the abundance of individual proteins and protein-protein associations, relates to the allergy status of mother and child. In addition, these results inspire new research directions into the complex interplay of the mother-milk-infant triad and allergy.

Exploring Human Milk Dynamics: Interindividual Variation in Milk Proteome, Peptidome, and Metabolome.

Human milk is a dynamic biofluid, and its detailed composition receives increasing attention. While most studies focus on changes over time or differences between maternal characteristics, interindividual variation receives little attention. Nevertheless, a comprehensive insight into this can help interpret human milk studies and help human milk banks provide targeted milk for recipients. This study aimed to map interindividual variation in the human milk proteome, peptidome, and metabolome and to investigate possible explanations for this variation. A set of 286 milk samples was collected from 29 mothers in the third month postpartum. Samples were pooled per mother, and proteins, peptides, and metabolites were analyzed. A substantial coefficient of variation (>100%) was observed for 4.6% and 36.2% of the proteins and peptides, respectively. In addition, using weighted correlation network analysis (WGCNA), 5 protein and 11 peptide clusters were obtained, showing distinct characteristics. With this, several associations were found between the different data sets and with specific sample characteristics. This study provides insight into the dynamics of human milk protein, peptide, and metabolite composition. In addition, it will support future studies that evaluate the effect size of a parameter of interest by enabling a comparison with natural variability.

Feeding fiction: Fraud vulnerability in the food service industry.

This study examines fraud vulnerability in the food service industry; identifies underlying fraud vulnerability factors; and studies the differences in fraud vulnerability between casual dining restaurants, fine dining restaurants and mass caterers for four product groups. Vulnerability was assessed by an adapted SSAFE food fraud vulnerability assessment, tailored to the food service sector situation. The 15 food service operators rated high vulnerability for 40% of the fraud indicators. This is considerably more than food manufacturers, wholesalers and retailers did previously. In particular, more opportunities and fewer controls were noted. Overall fraud vulnerability was more determined by the type of food service operator than by the type of food product. Casual dining restaurants appeared most vulnerable, followed by fine dining restaurants. Mass caterers seemed the least vulnerable operators, because they had more adequate food fraud controls in place. Considering its high vulnerability, reinforcement of mitigation measures in the food service industry is urgently recommended.

Maternal Allergy and the Presence of Nonhuman Proteinaceous Molecules in Human Milk.

Human milk contains proteins and/or protein fragments that originate from nonhuman organisms. These proteinaceous molecules, of which the secretion might be related to the mother's allergy status, could be involved in the development of the immune system of the infant. This may lead, for example, to sensitization or the induction of allergen-specific tolerance. The aim of this study was to investigate the relation between maternal allergy and the levels of nonhuman proteinaceous molecules in their milk. In this study, we analysed trypsin-digested human milk serum proteins of 10 allergic mothers and 10 nonallergic mothers. A search was carried out to identify peptide sequences originating from bovine or other allergenic proteins. Several methods were applied to confirm the identification of these sequences, and the differences between both groups were investigated. Out of the 78 identified nonhuman peptide sequences, 62 sequences matched Bos taurus proteins. Eight peptide sequences of bovine ß -lactoglobulin had significantly higher levels in milk from allergic mothers than in milk from nonallergic mothers. Dietary bovine ß -lactoglobulin may be absorbed through the intestinal barrier and secreted into human milk. This seems to be significantly higher in allergic mothers and might have consequences for the development of the immune system of their breastfed infant.

Linking growing conditions to stable isotope ratios and elemental compositions of Costa Rican bananas (Musa spp.).

Traceability of agricultural produce is getting increasingly important for numerous reasons including marketing, certification, and food safety. Globally, banana (Musa spp.) with its high nutritional value and easy accessibility, is a popular fruit among consumers. Bananas are produced throughout the (sub-)tropics under a wide range of environmental conditions. Environmental conditions could influence the composition of bananas. Understanding the effect of these conditions on fruit composition provides a way of increasing the fruit's traceability and linking it to its origin - a crucial aspect for the increasing global supply chain. In this study, we examined the influence of growing conditions on the isotopic and elemental composition of bananas produced in 15 Costa Rican farms. A total of 88 bananas (peel and pulp) were collected from the farms and analysed for isotopic signatures (δ13C, δ15N, and δ18O) and elemental compositions. The growing conditions were characterized in terms of climate, topography and soil conditions. The isotopic ratios differed significantly between groups of farms. The δ13C and δ15N values were mainly influenced by soil types, while rainfall and temperatures related more to the δ18O values. The elemental compositions of the bananas were primarily influenced by the local rainfall and soil types, while the geographical origin could be distinguished using principal component analysis. The overall results link the growing conditions to the isotopic and elemental compositions of bananas, thereby also providing a way to trace its origin.

Modulation of Glucosinolate Composition in Brassicaceae Seeds by Germination and Fungal Elicitation.

Glucosinolates (GSLs) are of interest for potential antimicrobial activity of their degradation products and exclusive presence in Brassicaceae. Compositional changes of aliphatic, benzenic, and indolic GSLs of Sinapis alba, Brassica napus, and B. juncea seeds by germination and fungal elicitation were studied. Rhizopus oryzae (nonpathogenic), Fusarium graminearum (nonpathogenic), and F. oxysporum (pathogenic) were employed. Thirty-one GSLs were detected by reversed-phase ultrahigh-performance liquid chromatography photodiode array with in-line electrospray ionization mass spectrometry (RP-UHPLC-PDA-ESI-MSn). Aromatic-acylated derivatives of 3-butenyl GSL, p-hydroxybenzyl GSL, and indol-3-ylmethyl GSL were for the first time tentatively annotated and confirmed to be not artifacts. For S. alba, germination, Rhizopus elicitation, and F. graminearum elicitation increased total GSL content, mainly consisting of p-hydroxybenzyl GSL, by 2-3 fold. For B. napus and B. juncea, total GSL content was unaffected by germination or elicitation. In all treatments, aliphatic GSL content was decreased (≥50%) in B. napus and remained unchanged in B. juncea. Indolic GSLs were induced in all species by germination and nonpathogenic elicitation.

The sound of salts by Broadband Acoustic Resonance Dissolution Spectroscopy.

Salts are available in different grades and in a wide price range. Some contain more impurities than others, while some have special culinary traits that determine their identity. Acoustic profiling, which is based on the 'hot chocolate effect', may provide an interesting strategy to characterise salts of various origins to underpin their identity. In this study, the link between the identity of 60 food grade and technical salts and their acoustic properties was examined by Broad Acoustic Resonance Dissolution Spectroscopy. In particular, the influence of the composition of the salts and the impact of the salts' particle size distributions on their acoustic profiles were examined. Sodium and potassium contents were measured by flame photometry and the salts' particle size distributions by laser light diffraction. Reference salts (NaCl, KCl, MgCl2) and mixtures thereof were analysed for comparison, as well as intact and ground versions of the salt samples. The results show that both the composition and morphology of the salt crystals determine the down-slope of the resonance frequency, which is caused by the rate of release of entrained and dissolved gas. Coarse salts with high levels of non-NaCl constituents showed a rapid decline in sound frequency, which corresponds to a high gas release rate. On the other hand fine salts composed of pure NaCl revealed a slower change in sound frequency and thus lower gas release rates. The frequency minimums were however not affected by the salts' compositions nor particle size distributions. It is primarily the particle size distribution that affects the rate at which gas is released, and thus the change in sound frequency. Only when the particles are more similar in size, the composition also starts playing a role. Since both particle size distribution and composition is unique for each salt, the various salts show distinct acoustic profiles. Evidently, the current study shows that 'listening' to the sound of salts reveals interesting information about their identity and origin.

Basic fibroblast growth factor and fibroblastic growth factor receptor-1 may contribute to head and neck paraganglioma development by an autocrine or paracrine mechanism.

Paragangliomas are hypervascular tumors arising from neural crest-derived paraganglia that are associated with the autonomic nerve system. Mutations in genes coding for subunits of mitochondrial complex II are associated with hereditary paragangliomas, and it has been suggested that these mutations result in a pseudohypoxic signal triggering tumorigenesis. Fibroblastic growth factors are hypoxia-inducible angiogenic stimuli that are involved in the angiogenesis and tumorigenesis of several neoplasms. It has been demonstrated that basic fibroblastic growth factor (bFGF) is a survival factor for cultured chief cells of the carotid body, capable of inducing proliferation. To examine the role of this growth factor in paragangliomas, we studied the immunohistochemical expression of bFGF and its high affinity receptor fibroblastic growth factor receptor 1 (FGFR1) in 7 normal carotid bodies and in 33 head and neck paragangliomas, including 2 malignant cases and their metastases. Immunohistochemical expression of bFGF and FGFR1 in tumors was confirmed by real-time polymerase chain reaction. FGFR1 was moderately present in carotid bodies, and there was strong and significantly enhanced cytoplasmatic staining of FGFR1 in all paragangliomas. Chief cells in carotid bodies and tumors showed strong cytoplasmatic staining for bFGF. The results indicate that FGFR1 and bFGF may contribute to the development of head and neck paragangliomas.

Multicolor fluorescence in situ hybridization analysis of a synovial sarcoma of the larynx with a t(X;18)(p11.2;q11.2) and trisomies 2 and 8.

Approximately 10% of all mesenchymal malignancies are classified as synovial sarcomas, which show a balanced translocation t(X;18)(p11.2;q11.2) at the cytogenetic level. The occurrence of this neoplasm in the head and neck region is rare, and its lowest frequency is found in the larynx. When synovial sarcomas are present in such unusual locations, diagnosis based solely on histologic features might be problematic, and to our knowledge, cytogenetic data have been reported so far in only one case of synovial sarcoma of the larynx. Because of the rarity and shortage of consistent prognostic markers, there is no clear consensus for the treatment of these patients. Cytogenetic analysis of a primary case of synovial sarcoma of the larynx was performed by using a 48-color fluorescence in situ hybridization technique that allows differential staining of short and long chromosome arms to establish the karyotype. We report here the molecular cytogenetic analyses of a synovial sarcoma of the larynx harboring the diagnostic t(X;18), as well as trisomies 2 and 8. The karyotypic information on synovial sarcomas of the larynx is scarce, and our data might add to the diagnosis and prognosis of this tumor.

Multiparameter DNA flow-sorting demonstrates diploidy and SDHD wild-type gene retention in the sustentacular cell compartment of head and neck paragangliomas: chief cells are the only neoplastic component.

Head and neck paragangliomas are considered to be biphasic tumours, composed of two distinct cell types: chief cells and sustentacular cells. A substantial number of these tumours show mutations in the SDHD gene located at chromosome 11q23. Although there is general agreement that paragangliomas are a neoplastic proliferation of chief cells, the nature of sustentacular cells is still a matter of debate. To clarify the nature of sustentacular cells further, multiparameter DNA flow cytometry was performed utilizing S-100 labelling as a selective marker of the sustentacular fraction simultaneously with DNA content measurement in six head and neck paragangliomas. S-100-positive fractions and other tumour-cell populations were flow-sorted and restriction digestion analysis of SDHD mutations was performed on each fraction. Flow cytometry demonstrated that the S-100 labelled cells were diploid. Restriction digestion analysis in informative cases revealed retention of the wild-type SDHD allele in S-100-positive fractions and loss of the wild-type allele in S-100-negative fractions. These data strongly suggest that sustentacular cells should be regarded as a non-neoplastic cell population that may be induced as a tumour-specific stromal component by chief cells.

G2M arrest, blocked apoptosis, and low growth fraction may explain indolent behavior of head and neck paragangliomas.

Head and neck paragangliomas are characterized by unusually slow growth and a strong hereditary component, which is associated with inactivating mutations in subunits of complex II of the mitochondrial respiratory chain. It is unclear how mutations induce tumorigenesis and lead to the indolent clinical behavior that often plays a prominent role in treatment strategies. To better understand the natural course of the tumors, we studied a number of growth-related parameters in 42 hereditary and sporadic paragangliomas. Computerized image analysis showed that the fraction of Ki-67-positive cells was generally below 1%, in accordance with the slow growth. Weak or negative immunohistochemical staining indicated wild-type TP53 status, whereas p-21(waf) expression was heterogeneous. Most tumors showed strong expression of Bcl-x(L), and no apoptotic cells could be detected with the terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick-end labeling assay. Flow cytometry showed abnormal DNA content profiles in 52% of the tumors, including overt aneuploidy as well as G(2)/M arrest or tetraploidization. These results fit into a model in which a stress-activated cell cycle checkpoint at the G(2) to M transition and inhibition of apoptosis permit the expansion of only a minor fraction of cycling cells with high likelihood of polyploidization.