Quantitative Analysis of the Human Milk Whey Proteome Reveals Developing Milk and Mammary-Gland Functions across the First Year of Lactation

Insight into differences in whey proteome from human and eight dairy animal species for formula humanization

Human breastmilk fulfills the nutritional needs of infants and therefore is the best template for formula. In this study, whey proteins were investigated among human and eight dairy animal species using label-free proteomics approach. Totally, 965 proteins from milk whey were identified and large variations were observed between human and animals. Several proteins, including β-galactosidase, fatty acid synthase, osteopontin, lactoferrin, mannose receptor, and complement C4-A, which are associated with digestion and immune response, exhibited significantly higher levels in human milk whey. Conversely, specific animal milk whey demonstrated elevated abundance of lipocalin 2, lysozyme, and glycosylation-dependent cell adhesion molecule 1. These differential proteins are enriched in complement and coagulation cascades, lysosome, and phagosome pathways. The findings shed light on the variations in the whey proteome composition between human and animal milk, which can contribute to optimizing formula humanization.

Characterization of the internal working-life exposome using minimally and non-invasive sampling methods - a narrative review

During recent years, we are moving away from the 'one exposure, one disease'-approach in occupational settings and towards a more comprehensive approach, taking into account the totality of exposures during a life course by using an exposome approach. Taking an exposome approach however is accompanied by many challenges, one of which, for example, relates to the collection of biological samples. Methods used for sample collection in occupational exposome studies should ideally be minimally invasive, while at the same time sensitive, and enable meaningful repeated sampling in a large population and over a longer time period. This might be hampered in specific situations e.g., people working in remote areas, during pandemics or with flexible work hours. In these situations, using self-sampling techniques might offer a solution. Therefore, our aim was to identify existing self-sampling techniques and to evaluate the applicability of these techniques in an occupational exposome context by conducting a literature review. We here present an overview of current self-sampling methodologies used to characterize the internal exposome. In addition, the use of different biological matrices was evaluated and subdivided based on their level of invasiveness and applicability in an occupational exposome context. In conclusion, this review and the overview of self-sampling techniques presented herein can serve as a guide in the design of future (occupational) exposome studies while circumventing sample collection challenges associated with exposome studies.

Comparative analysis of whey proteins in yak milk from different breeds in China using a data-independent acquisition proteomics method

Yak milk is rich in essential milk proteins of nutritional and therapeutic value. In this study, whey proteins of milk from 3 yak breeds (Gannan, GN; Huanhu, HH; Maiwa, MW) in China were comprehensively identified and compared using a data-independent acquisition quantitative proteomics approach. A total of 632 proteins were identified in yak milk whey samples, in which immune-related proteins were abundant. Compared with other milks, more proteins were involved in oxidation-reduction process and with ATP binding. In addition, we identified 96, 155, and 164 differentially expressed proteins (DEP) for GN versus HH, GN versus MW, and HH versus MW, respectively. "Phagosome" and "complement and coagulation cascades" were the most significant pathways for DEP of GN versus HH and GN or HH versus MW yak milk based on the Kyoto Encyclopedia of Genes and Genomes pathway analysis. Protein-protein interaction network analysis showed that DEP for the 3 comparisons had significant biological interactions but were associated with different functions. The results provide useful information on yak milk from different breeds in China, and elucidate the biological functions of yak milk proteins.

Comparative proteomics analyses of whey proteins from breastmilk collected from two ethnic groups in northeast China

The current study aims to investigate differences in whey protein of breastmilk of volunteered mother collected from two ethnic groups (Korean and Han) in China using data-independent acquisition (DIA) based proteomics technique. The total detected 624 proteins were principally allocated to cellular process of biological process (BP), cell and cell part of cell component (CC) and binding of molecular function (MF) according to Gene Ontology (GO) annotation; and carbohydrate metabolism of Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Among the 54 differently expressed proteins, 8 were related with immunity. Enrichment data showed that intracellular of GO functions and viral myocarditis of KEGG pathways were most significantly enriched (p < 0.05). Protein-protein interaction (PPI) network suggested that 40S ribosomal protein S27a and 60S ribosomal protein L10a which interacted most with other proteins ranked the top two hub proteins by MCC (Maximal Clique Centrality) method. This study may have guiding role for development of infant formula powder for specific infants of Han or Korean groups according to responding breastmilk composition.

Are active efflux transporters contributing to infant drug exposure via breastmilk? A longitudinal study

Although most drugs are considered safe and compatible with breastfeeding, cases of toxic drug exposure have been reported. Active efflux transporters have been implicated as a mechanism in the transfer of drugs from mother to baby via breastmilk. Using breastmilk as a source of human mammary epithelial cells, this novel longitudinal study investigated the expression of four active transporters, namely, MDR1, MRP1, MRP2 and BCRP in the lactating human breast. BCRP gene was found to be strongly overexpressed with levels peaking at 5 months postpartum, potentially indicating a time where a breastfed infant may be at risk of inadvertent exposure to BCRP substrates. Serum albumin, a major component of human breastmilk was increasingly downregulated as lactation progresses. Xanthine oxidase/dehydrogenase, an enzyme in breastmilk attributed to a reduced risk of gastroenteritis caused by Escherichia coli and Salmonella enteritides, was downregulated. Lysozyme and fatty acid synthase are progressively upregulated. This study also shows that breastmilk-derived epithelial cells, when propagated in culture, exhibit characteristics significantly different to those derived directly from breastmilk. This serves to warn that in vitro studies are not a true representation of in vivo processes in the lactating breast; hence, application of in vitro data should be conducted with caution.

Analysis of Minor Proteins Present in Breast Milk by Using WGA Lectin

Breast milk is a complex and dynamic biological fluid and considered an essential source of nutrition in early life. In its composition, the proteins have a relevant biological activity and are related to the multiple benefits demonstrated when compared with artificial milks derived from cow’s milk. Understanding human milk composition provides an important tool for health care providers toward the management of infant feeding and the establishment of breastfeeding. In this work, a new technique was developed to increase the knowledge of human milk, because many of the components remain unknown. To isolate minor proteins present in breast milk by using WGA lectin, breast milk was centrifuged to remove cells and separate the fat phase from the serum phase. The serum obtained was separated into two groups: control (n = 3; whole serum sample from mature milk) and WGA lectin (n = 3; sample processed with WGA lectin to isolate glycosylated proteins). The samples were analyzed by high-performance liquid chromatography coupled to mass spectrometry (HPLC/MS). A total of 84 different proteins were identified from all of the samples. In the WGA lectin group, 55 different proteins were isolated, 77% of which had biological functions related to the immune response. Of these proteins, there were eight WGA lectin group exclusives, and two had not previously been described in breast milk (polyubiquitin-B and POTE ankyrin domain family member F). Isolation by WGA lectin is a useful technique to detect minor proteins in breast milk and to identify proteins that could not be observed in whole serum.

Comparative Whey Proteome Profiling of Donkey Milk With Human and Cow Milk

Donkey milk (DM), similar to human milk (HM) in chemical composition, has been suggested as the best potential hypoallergenic replacement diet for babies suffering from Cow milk (CM) protein allergy. In order to better understand DM protein, many studies based on proteomic have been performed. In this study, the label-free quantitative proteomic approach was conducted to quantitatively identify the differentially expressed whey proteins (DEPs) in DM vs. HM group and DM vs. CM group. In total, 241 and 365 DEPs were found in these two groups, respectively. Bioinformatics analysis of DEPs showed that the majority of DEPs participated in the lipoprotein metabolic process, regulation of cytokine production, chemical homeostasis, and catabolic process. The Kyoto Encyclopedia of Gene and Genomes (KEGG) pathways analysis found that these DEPs mainly participated in an antigen processing, complement, and coagulation cascades. These results may provide valuable information in the composition of milk whey proteins in DM, HM, and CM, especially for low abundant components, and expand our knowledge of different biological functions between DM and HM or CM.

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.

Quantification of FAM20A in human milk and identification of calcium metabolism proteins

BACKGROUND

FAM20A, a recently discovered protein, is thought to have a fundamental role in inhibiting ectopic calcification. Several studies have demonstrated that variants of FAM20A are causative for the rare autosomal recessive disorder, enamel-renal syndrome (ERS). ERS is characterized by defective mineralization of dental enamel and nephrocalcinosis suggesting that FAM20A is an extracellular matrix protein, dysfunction of which causes calcification of the secretory epithelial tissues. FAM20A is a low-abundant protein that is difficult to detect in biofluids such as blood, saliva, and urine. Thus, we speculated the abundance of FAM20A to be high in human milk, since the secretory epithelium of lactating mammary tissue is involved in the secretion of highly concentrated calcium. Therefore, the primary aim of this research is to describe the processes/methodology taken to quantify FAM20A in human milk and identify other proteins involved in calcium metabolism.

METHOD

This study used mass spectrometry-driven quantitative proteomics: (1) to quantify FAM20A in human milk of three women and (2) to identify proteins associated with calcium regulation by bioinformatic analyses on whole and milk fat globule membrane fractions.

RESULTS

Shotgun MS/MS driven proteomics identified FAM20A in whole milk, and subsequent analysis using targeted proteomics also successfully quantified FAM20A in all samples. Combination of sample preparation, fractionation, and LC-MS/MS proteomics analysis generated 136 proteins previously undiscovered in human milk; 21 of these appear to be associated with calcium metabolism.

CONCLUSION

Using mass spectrometry-driven proteomics, we successfully quantified FAM20A from transitional to mature milk and obtained a list of proteins involved in calcium metabolism. Furthermore, we show the value of using a combination of both shotgun and targeted driven proteomics for the identification of this low abundant protein in human milk.

HBFP: a new repository for human body fluid proteome

Body fluid proteome has been intensively studied as a primary source for disease biomarker discovery. Using advanced proteomics technologies, early research success has resulted in increasingly accumulated proteins detected in different body fluids, among which many are promising biomarkers. However, despite a handful of small-scale and specific data resources, current research is clearly lacking effort compiling published body fluid proteins into a centralized and sustainable repository that can provide users with systematic analytic tools. In this study, we developed a new database of human body fluid proteome (HBFP) that focuses on experimentally validated proteome in 17 types of human body fluids. The current database archives 11 827 unique proteins reported by 164 scientific publications, with a maximal false discovery rate of 0.01 on both the peptide and protein levels since 2001, and enables users to query, analyze and download protein entries with respect to each body fluid. Three unique features of this new system include the following: (i) the protein annotation page includes detailed abundance information based on relative qualitative measures of peptides reported in the original references, (ii) a new score is calculated on each reported protein to indicate the discovery confidence and (iii) HBFP catalogs 7354 proteins with at least two non-nested uniquely mapping peptides of nine amino acids according to the Human Proteome Project Data Interpretation Guidelines, while the remaining 4473 proteins have more than two unique peptides without given sequence information. As an important resource for human protein secretome, we anticipate that this new HBFP database can be a powerful tool that facilitates research in clinical proteomics and biomarker discovery.

Database URL:https://bmbl.bmi.osumc.edu/HBFP/

Shotgun proteomics of homogenate milk reveals dynamic changes in protein abundances between colostrum, transitional and mature milk of swine

Milk is an easily digestible source of nutrients and bioactive factors, its composition reflects the neonate's needs, and changes from colostrum to transitional and mature milk. Our objective was to measure milk fat, lactose, total carbohydrate, and protein content in parallel with global proteome of homogenate milk samples to characterize changes across the three phases of swine lactation. Milk samples were collected from multiparous sows (n=9) on postnatal day 0 (D0; colostrum), 3 (D3; early transitional), 7 (D7; late transitional) and 14 (D14; mature). On D3, percent fat (16 ± 2.1) and lactose (3.8 ± 0.3) were higher (P<0.05) than on D0 (10 ± 3.9, and 1.5 ± 0.3; respectively). Levels of fat and lactose were not different between D3 and D14. Percent total protein decreased (P<0.05) between D0 (11 ± 2.1) and D3 (5 ± 0.7), but there was no significant change in percent protein between D3 and D14. Total carbohydrates increased (P<0.05) between D3 (944 ± 353 µg/ml) and D14 (1150 ± 462 µg/ml). Quantitative proteomic analysis using liquid chromatography tandem mass spectrometry (LC-MS/MS) of homogenate D0, D3, and D14 milk samples (n=6) identified 772 protein groups which corresponded to 501 individual protein-coding genes. A total of 207 high confidence proteins were detected in n=3 sows/day. Of the high confidence proteins, 81 proteins were common amongst all three days of lactation. Among the proteins that decreased between the days (FDR < 0.05) were multiple apolipoproteins and XDH which decreased between D0 to D3. Proteins that increased across the days (FDR < 0.05) were complement factors and14-3-3 proteins (YWHAQ, YWHAE). Our data provide a good characterization of milk proteome changes that likely reflect mammary function as well as the neonate's phase-specific developmental needs. This data may be useful in developing approaches to enhance the health and welfare of swine.

ADIPOR1 regulates genes involved in milk fat metabolism in goat mammary epithelial cells

BACKGROUND

Fat metabolism is a complex process regulated by a number of factors. Adiponectin receptor 1 (ADIPOR1) gene takes active part in lipid metabolism. Although, there have been some researches indicating that ADIPOR1 could influence the milk fat metabolism through targeting some factors, little is known about the effect of ADIPOR1 on goat milk fat metabolism. To investigate the regulatory role of ADIPOR1 on milk fat metabolism in GMECs, we analysed overexpression in the presence and absence of AdipoRon (50 μM) and examined knockdown using siRNA. Using RT-qPCR, we assessed ADIPOR1 mRNA expressions among different lactation stages in goat mammary gland and the expression of six genes that regulate milk fat metabolism in GMECs.

RESULTS

ADIPOR1 mRNA expression level was higher during the various lactation stages, except dry-off period. Knockdown and overexpression results revealed a significant decrease and increase in mRNA expression of ADIPOR1 and genes considered: SREBF1, ACACA, FASN, SCD, ATGL, and HSL, respectively. Treatment of GMECs with AdipoRon 50 μM resulted in a significant (p < 0.05) increase in the mRNA expression of all measured genes, except SREBF1.

CONCLUSION

Overall, ADIPOR1 plays a central role in regulating the transcription of several genes involved in milk fat metabolism.

Comparative Analysis of Whey Proteins in Human Milk Using a Data-Independent Acquisition Proteomics Approach during the Lactation Period

Human milk (HM) is the primary source of nutrients and bioactive components that supports the growth and development of infants. However, the proteins present in human milk may change depending on the period of lactation. In this light, the objective of the present study was to evaluate the effect of lactation period on HM utilizing a data-independent acquisition (DIA) approach to identify the differences in HM whey protein proteomes. As part of the study, whey proteins of January, February, and June in human milk were studied. The results identified a total of 1563 proteins in HM whey proteins of which 114 groups were subunits of differentially expressed proteins as revealed by cluster analysis. Protein expression was observed to be affected by the period of lactation with expression levels of plasminogen, thrombospondin-1, and tenascin higher during January, keratin, type I cytoskeletal 9 highest in February, and transcobalamin-1 highest in June. The results of this study contribute to expand our understanding of the human whey proteome but also provide strong evidence for the nutritional difference of HM during different lactation periods.

Personalized Profiling Reveals Donor- and Lactation-Specific Trends in the Human Milk Proteome and Peptidome

BACKGROUND

Human milk is the most genuine form of personalized nutrition, whereby its nutritional and bioactive constituents support the changing needs of the growing infant. Personalized proteome profiling strategies may provide insights into maternal-infant relationships. Proteins and endogenous peptides in human milk play an important role as nutrients for growth and have distinct functionality such as immune defense. Comprehensive monitoring of all of the human milk proteinaceous components, including endogenous peptides, is required to fully understand the changing role of the human milk proteome throughout lactation.

OBJECTIVE

We aimed to investigate the personalized nature of the human milk proteome and peptidome for individual mother-infant dyads.

METHODS

Two individual healthy milk donors, aged 29 and 32 y and both of a normal BMI, were longitudinally observed over weeks 1, 2, 3, 4, 6, 8, 10, 12, and 16 postpartum. Milk collection was standardized. Comprehensive variations in the human milk proteinaceous components were assessed using quantitative LC-MS/MS methods.

RESULTS

We longitudinally profiled the concentrations of >1300 milk proteins and 2000 endogenous milk peptides spanning 16 wk of lactation for 2 individual donors. We observed many gradual and alike changes in both donors related to temporal effects, for instance early lactation was marked by high concentrations of proteins and peptides involved in lactose synthesis and immune development. Uniquely, in 1 of the 2 donors, we observed a substantial anomaly in the milk composition, exclusively at week 6, likely indicating a response to inflammation and/or infection.

CONCLUSIONS

Here, we provide a resource for characterizing the lactational changes in the human milk proteome, encompassing thousands of proteins and endogenous peptides. Further, we demonstrate the feasibility and benefit of personalized profiling to monitor the influence of milk on the development of the newborn, as well as the health status of each individual mother-infant pair.

Changes in bioactive proteins and serum proteome of human milk under different frozen storage

This study aimed to investigate changes in macronutrients, total bacterial count, and serum proteome of human milk (HM) under different frozen storage (-18°C and -60°C, 60 d and 180 d) by using IBT Labeling proteomics techniques and ELISA kit. The results indicated that total protein concentrations and total aerobic bacterial counts were significantly decreased at -18°C, while no difference at -60°C. A total of 1617 proteins were identified and quantified, and 173 proteins were significantly different. The -18°C storage had much higher influence on HM serum protein profiles than that of -60°C. Increased milk fat globule membrane (MFGM) proteins at -18°C are highly related to the damage of MFGM and transfer of MFGM proteins. The reduction of bioactive proteins is probably related to the ice-induced denaturation. In conclusion, fast cooling and ultra-low constant temperature are more suitable for the cryopreservation of human milk.

Human body-fluid proteome: quantitative profiling and computational prediction

Empowered by the advancement of high-throughput bio technologies, recent research on body-fluid proteomes has led to the discoveries of numerous novel disease biomarkers and therapeutic drugs. In the meantime, a tremendous progress in disclosing the body-fluid proteomes was made, resulting in a collection of over 15 000 different proteins detected in major human body fluids. However, common challenges remain with current proteomics technologies about how to effectively handle the large variety of protein modifications in those fluids. To this end, computational effort utilizing statistical and machine-learning approaches has shown early successes in identifying biomarker proteins in specific human diseases. In this article, we first summarized the experimental progresses using a combination of conventional and high-throughput technologies, along with the major discoveries, and focused on current research status of 16 types of body-fluid proteins. Next, the emerging computational work on protein prediction based on support vector machine, ranking algorithm, and protein-protein interaction network were also surveyed, followed by algorithm and application discussion. At last, we discuss additional critical concerns about these topics and close the review by providing future perspectives especially toward the realization of clinical disease biomarker discovery.

The "weanling's dilemma" revisited: Evolving bodies of evidence and the problem of infant paleodietary interpretation

Breastfeeding is known to be a powerful mediator of maternal and childhood health, with impacts throughout the life course. Paleodietary studies of the past 30 years have accordingly taken an enduring interest in the health and diet of young children as a potential indicator of population fertility, subsistence, and mortality patterns. While progress has been made in recent decades toward acknowledging the agency of children, many paleodietary reconstructions have failed to incorporate developments in cognate disciplines revealing synergistic dynamics between maternal and offspring biology. Paleodietary interpretation has relied heavily on the "weanling's dilemma," in which infants are thought to face a bleak choice between loss of immunity or malnutrition. Using a review of immunological and epidemiological evidence for the dynamic and supportive role that breastfeeding plays throughout the complementary feeding period, this article offers context and nuance for understanding past feeding transitions. We suggest that future interpretative frameworks for infant paleodietary and bioarchaeological research should include a broad knowledge base that keeps pace with relevant developments outside of those disciplines.

Changes in whey proteome with lactation stage and parity in dairy cows using a label-free proteomics approach

Milk yield and several components of milk that are affected by physiological factors have been widely investigated. However, the effects of lactation stage and parity on bovine milk whey proteins have not been well elucidated. To aid in unraveling the proteome profile and exploring the protein biosynthesis of mammary glands, a label-free proteomic approach was used to characterize whey proteomes depending on the lactation stage and parity of dairy cows. The results of this study show that the abundances of several proteins, such as early lactation protein, syntenin, and heparanase, were associated with specific stages of the lactation cycle; this was evidenced by a principal component analysis. In addition, several proteins, such as hemoglobin subunits beta and alpha, β-lactoglobulin, CD320, and apolipoprotein E, corresponded to the parity of the dairy cows and were herein considered as useful biomarkers to distinguish different parities. Most of the differentially expressed proteins from specific lactation stages and parity milk groups were annotated in the response to stimulus and protein metabolic processes. The findings reveal that developmental changes in whey proteomes correspond to lactation stages and parities, which in turn provides new insight into the underlying implications of the production of specific proteins to meet the health benefits of offspring and host, and allow us to explore the mechanisms of protein biosynthesis in mammary glands associated with physiological changes in dairy cows.

The Functional Power of the Human Milk Proteome

Human milk is the most complete and ideal form of nutrition for the developing infant. The composition of human milk consistently changes throughout lactation to meet the changing functional needs of the infant. The human milk proteome is an essential milk component consisting of proteins, including enzymes/proteases, glycoproteins, and endogenous peptides. These compounds may contribute to the healthy development in a synergistic way by affecting growth, maturation of the immune system, from innate to adaptive immunity, and the gut. A comprehensive overview of the human milk proteome, covering all of its components, is lacking, even though numerous analyses of human milk proteins have been reported. Such data could substantially aid in our understanding of the functionality of each constituent of the proteome. This review will highlight each of the aforementioned components of human milk and emphasize the functionality of the proteome throughout lactation, including nutrient delivery and enhanced bioavailability of nutrients for growth, cognitive development, immune defense, and gut maturation.

Comparative Analysis of Whey N-Glycoproteins in Human Colostrum and Mature Milk Using Quantitative Glycoproteomics

Glycosylation is a ubiquitous post-translational protein modification that plays a substantial role in various processes. However, whey glycoproteins in human milk have not been completely profiled. Herein, we used quantitative glycoproteomics to quantify whey N-glycosylation sites and their alteration in human milk during lactation; 110 N-glycosylation sites on 63 proteins and 91 N-glycosylation sites on 53 proteins were quantified in colostrum and mature milk whey, respectively. Among these, 68 glycosylation sites on 38 proteins were differentially expressed in human colostrum and mature milk whey. These differentially expressed N-glycoproteins were highly enriched in "localization", "extracellular region part", and "modified amino acid binding" according to gene ontology annotation and mainly involved in complement and coagulation cascades pathway. These results shed light on the glycosylation sites, composition and biological functions of whey N-glycoproteins in human colostrum and mature milk, and provide substantial insight into the role of protein glycosylation during infant development.

An interactomics overview of the human and bovine milk proteome over lactation

Background

Milk is the most important food for growth and development of the neonate, because of its nutrient composition and presence of many bioactive proteins. Differences between human and bovine milk in low abundant proteins have not been extensively studied. To better understand the differences between human and bovine milk, the qualitative and quantitative differences in the milk proteome as well as their changes over lactation were compared using both label-free and labelled proteomics techniques. These datasets were analysed and compared, to better understand the role of milk proteins in development of the newborn.

Methods

Human and bovine milk samples were prepared by using filter-aided sample preparation (FASP) combined with dimethyl labelling and analysed by nano LC LTQ-Orbitrap XL mass spectrometry.

Results

The human and bovine milk proteome show similarities with regard to the distribution over biological functions, especially the dominant presence of enzymes, transport and immune-related proteins. At a quantitative level, the human and bovine milk proteome differed not only between species but also over lactation within species. Dominant enzymes that differed between species were those assisting in nutrient digestion, with bile salt-activated lipase being abundant in human milk and pancreatic ribonuclease being abundant in bovine milk. As lactation advances, immune-related proteins decreased slower in human milk compared to bovine milk. Notwithstanding these quantitative differences, analysis of human and bovine co-expression networks and protein-protein interaction networks indicated that a subset of milk proteins displayed highly similar interactions in each of the different networks, which may be related to the general importance of milk in nutrition and healthy development of the newborn.

Conclusions

Our findings promote a better understanding of the differences and similarities in dynamics of human and bovine milk proteins, thereby also providing guidance for further improvement of infant formula.

Electronic supplementary material

The online version of this article (doi:10.1186/s12953-016-0110-0) contains supplementary material, which is available to authorized users.

Comprehensive Proteomic Analysis of Human Milk-derived Extracellular Vesicles Unveils a Novel Functional Proteome Distinct from Other Milk Components

Breast milk contains several macromolecular components with distinctive functions, whereby milk fat globules and casein micelles mainly provide nutrition to the newborn, and whey contains molecules that can stimulate the newborn's developing immune system and gastrointestinal tract. Although extracellular vesicles (EV) have been identified in breast milk, their physiological function and composition has not been addressed in detail. EV are submicron sized vehicles released by cells for intercellular communication via selectively incorporated lipids, nucleic acids, and proteins. Because of the difficulty in separating EV from other milk components, an in-depth analysis of the proteome of human milk-derived EV is lacking. In this study, an extensive LC-MS/MS proteomic analysis was performed of EV that had been purified from breast milk of seven individual donors using a recently established, optimized density-gradient-based EV isolation protocol. A total of 1963 proteins were identified in milk-derived EV, including EV-associated proteins like CD9, Annexin A5, and Flotillin-1, with a remarkable overlap between the different donors. Interestingly, 198 of the identified proteins are not present in the human EV database Vesiclepedia, indicating that milk-derived EV harbor proteins not yet identified in EV of different origin. Similarly, the proteome of milk-derived EV was compared with that of other milk components. For this, data from 38 published milk proteomic studies were combined in order to construct the total milk proteome, which consists of 2698 unique proteins. Remarkably, 633 proteins identified in milk-derived EV have not yet been identified in human milk to date. Interestingly, these novel proteins include proteins involved in regulation of cell growth and controlling inflammatory signaling pathways, suggesting that milk-derived EVs could support the newborn's developing gastrointestinal tract and immune system. Overall, this study provides an expansion of the whole milk proteome and illustrates that milk-derived EV are macromolecular components with a unique functional proteome.

Changes over lactation in breast milk serum proteins involved in the maturation of immune and digestive system of the infant

To objective of this study was to better understand the biological functions of breast milk proteins in relation to the growth and development of infants over the first six months of life. Breast milk samples from four individual women collected at seven time points in the first six months after delivery were analyzed by filter aided sample preparation and dimethyl labeling combined with liquid chromatography tandem mass spectrometry. A total of 247 and 200 milk serum proteins were identified and quantified, respectively. The milk serum proteome showed a high similarity (80% overlap) on the qualitative level between women and over lactation. The quantitative changes in milk serum proteins were mainly caused by three groups of proteins, enzymes, and transport and immunity proteins. Of these 21 significantly changed proteins, 30% were transport proteins, such as serum albumin and fatty acid binding protein, which are both involved in transporting nutrients to the infant. The decrease of the enzyme bile salt-activated lipase as well as the immunity proteins immunoglobulins and lactoferrin coincide with the gradual maturation of the digestive and immune system of infants. The human milk serum proteome didn't differ qualitatively but it did quantitatively, both between mothers and as lactation advanced. The changes of the breast milk serum proteome over lactation corresponded with the development of the digestive and immune system of infants.

BIOLOGICAL SIGNIFICANCE

Breast milk proteins provide nutrition, but also contribute to healthy development of infants. Despite the previously reported large number of identified breast milk proteins and their changes over lactation, less is known on the changes of these proteins in individual mothers. This study is the first to determine the qualitative and quantitative changes of milk proteome over lactation between individual mothers. The results indicate that the differences in the milk proteome between individual mothers are more related to the quantitative level than qualitative level. The correlation between the changes of milk proteins and the gradual maturation of the gastrointestinal tract and immune system in infants, contributes to a better understanding of the biological functions of human milk proteins for the growth and development of infants.

Sensing Small Changes in Protein Abundance: Stimulation of Caco-2 Cells by Human Whey Proteins

Mass spectrometry (MS)-based proteomic approaches have largely facilitated our systemic understanding of cellular processes and biological functions. Cutoffs in protein expression fold changes (FCs) are often arbitrarily determined in MS-based quantification with no demonstrable determination of small magnitude changes in protein expression. Therefore, many biological insights may remain veiled due to high FC cutoffs. Herein, we employ the intestinal epithelial cell (IEC) line Caco-2 as a model system to demonstrate the dynamicity of tandem-mass-tag (TMT) labeling over a range of 5-40% changes in protein abundance, with the variance controls of ± 5% FC for around 95% of TMT ratios when sampling 9-12 biological replicates. We further applied this procedure to examine the temporal proteome of Caco-2 cells upon exposure to human whey proteins (WP). Pathway assessments predict subtle effects due to WP in moderating xenobiotic metabolism, promoting proliferation and various other cellular functions in differentiating enterocyte-like Caco-2 cells. This demonstration of a sensitive MS approach may open up new perspectives in the system-wide exploration of elusive or transient biological effects by facilitating scrutiny of narrow windows of proteome abundance changes. Furthermore, we anticipate this study will encourage more investigations of WP on infant gastrointestinal tract development.

Comparative Proteomics of Human and Macaque Milk Reveals Species-Specific Nutrition during Postnatal Development

Milk has been well established as the optimal nutrition source for infants, yet there is still much to be understood about its molecular composition. Therefore, our objective was to develop and compare comprehensive milk proteomes for human and rhesus macaques to highlight differences in neonatal nutrition. We developed a milk proteomics technique that overcomes previous technical barriers including pervasive post-translational modifications and limited sample volume. We identified 1606 and 518 proteins in human and macaque milk, respectively. During analysis of detected protein orthologs, we identified 88 differentially abundant proteins. Of these, 93% exhibited increased abundance in human milk relative to macaque and include lactoferrin, polymeric immunoglobulin receptor, alpha-1 antichymotrypsin, vitamin D-binding protein, and haptocorrin. Furthermore, proteins more abundant in human milk compared with macaque are associated with development of the gastrointestinal tract, the immune system, and the brain. Overall, our novel proteomics method reveals the first comprehensive macaque milk proteome and 524 newly identified human milk proteins. The differentially abundant proteins observed are consistent with the perspective that human infants, compared with nonhuman primates, are born at a slightly earlier stage of somatic development and require additional support through higher quantities of specific proteins to nurture human infant maturation.

Differential digestion of human milk proteins in a simulated stomach model

A key element in understanding how human milk proteins support the health and development of the neonate is to understand how individual proteins are affected during digestion. In the present study, a dynamic gastric model was used to simulate infant gastric digestion of human milk, and a subsequent proteomic approach was applied to study the behavior of individual proteins. A total of 413 human milk proteins were quantified in this study. This approach demonstrated a high degree of variability in the susceptibility of human milk proteins to gastric digestion. Specifically this study reports that lipoproteins are among the class of slowly digested proteins during gastric processes. The levels of integral lysozyme C and partial lactadherin in milk whey increase over digestion. Mucins, ribonuclease 4, and macrophage mannose receptor 1 are also resistant to gastric digestion. The retention or enhancement in whey protein abundance can be ascribed to the digestive release of milk-fat-globule-membrane or immune-cell enclosed proteins that are not initially accessible in milk. Immunoglobulins are more resistant to digestion compared to total milk proteins, and within the immunoglobulin class IgA and IgM are more resistant to digestion compared to IgG. The gastric digestion of milk proteins becomes more apparent from this study.