Proteomic characterization of specific minor proteins in the human milk casein fraction

Peptidome profiling of human, bovine, and donkey colostrum through label-free quantitative analysis reveals proteolysis of milk proteins

Proteins and peptides play vital roles in different biological processes in vivo. As a dynamic hydrolysis system, milk is rich in proteins and proteases and provides a constant supply of endogenous bioactive peptides to newborn mammals. Previous studies have primarily focused on researching bioactive peptides by adding exogenous enzymes to milk samples. However, such an approach overlooks the significance of endogenous peptides and parent proteins that naturally exist in milk. Herein, we analyzed and compared parent proteins and their releasing peptides in human colostrum (HC), bovine colostrum (BC), and donkey colostrum (DC). The predominant proteins and hydrolyzed peptides in the three types of milk were identified. Among them, peptides were found to possess common bioactivities, including ACE inhibitory, antioxidant, antibacterial and immunomodulatory properties in HC, BC, and DC. Furthermore, the biological functions of these parent proteins were clarified using bioinformatics. These insights offer a novel perspective on natural bioactive peptides and the potential utilization of specific parent proteins and peptides to develop infant formulae derived from diverse milk sources.

Deciphering the difference of casein fraction in human milk associated with infant gender using quantitative proteomics

Human milk is an ideal natural food for infants, and the infant's gender may have impact on protein composition of breast milk. In this study, we used 4D label-free quantitative proteomics techniques to identify and quantitatively analyze casein fraction in breast milk secreted for male and female infants. The results showed that a total of 2064 proteins were identified in human milk, and 95 of them were differentially abundant proteins. Compared to breast milk secreted by mothers of female infants, 21 proteins were up-regulated, and 59 proteins were down-regulated in breast milk secreted by mothers of male infants. The most abundant domain among the differentially abundant proteins was the immunoglobulin V-set domain, which may be involved in immune regulation. Gene Ontology functional analysis revealed that, the main biological processes, molecular functions, and cellular components corresponded to cellular process, binding, and cell part, respectively. The Kyoto Encyclopedia of Genes and Genomes pathways were mainly associated with human diseases and metabolism, with biosynthesis of cofactors being the most involved pathway. The results contribute to our understanding of the composition of casein in breast milk, and may provide information about the nutritional differences in breast milk from mothers of newborns of different genders.

Analysis of milk with liquid chromatography–mass spectrometry: a review

As a widely consumed foodstuff, milk and dairy products are increasingly studied over the years. At the present time, milk profiling is used as a benchmark to assess the properties of milk. Modern biomolecular mass spectrometers have become invaluable to fully characterize the milk composition. This review reports the analysis of milk and its components using liquid chromatography coupled with mass spectrometry (LC–MS). LC–MS analysis as a whole will be discussed subdivided into the major constituents of milk, namely, lipids, proteins, sugars and the mineral fraction.

Developmental changes in proteins of casein micelles in goat milk using data-independent acquisition-based proteomics methods during the lactation cycle

Casein micelles (CM) play an important role in milk secretion, stability, and processing. The composition and content of milk proteins are affected by physiological factors, which have been widely investigated. However, the variation in CM proteins in goat milk throughout the lactation cycle has yet to be fully clarified. In the current study, milk samples were collected at d 1, 3, 30, 90, 150, and 240 of lactation from 15 dairy goats. The size of CM was determined using laser light scattering, and CM proteins were separated, digested, and identified using data-independent acquisition (DIA) and data-dependent acquisition (DDA)-based proteomics approaches. According to clustering and principal component analysis, protein profiles identified using DIA were similar to those identified using the DDA approach. Significant differences in the abundance of 115 proteins during the lactation cycle were identified using the DIA approach. Developmental changes in the CM proteome corresponding to lactation stages were revealed: levels of lecithin cholesterol acyltransferase, folate receptor α, and prominin 2 increased from 1 to 240 d, whereas levels of growth/differentiation factor 8, peptidoglycan-recognition protein, and 45 kDa calcium-binding protein decreased in the same period. In addition, lipoprotein lipase, glycoprotein IIIb, and α-lactalbumin levels increased from 1 to 90 d and then decreased to 240 d, which is consistent with the change in CM size. Protein-protein interaction analysis showed that fibronectin, albumin, and apolipoprotein E interacted more with other proteins at the central node. These findings indicate that changes in the CM proteome during lactation could be related to requirements of newborn development, as well as mammary gland development, and may thus contribute to elucidating the physical and chemical properties of CM.

Perspective: Human Milk Composition and Related Data for National Health and Nutrition Monitoring and Related Research

National health and nutrition monitoring is an important federal effort in the United States and Canada, and the basis for many of their nutrition and health policies. Understanding of child exposures through human milk (HM) remains out of reach due to lack of current and representative data on HM's composition and intake volume. This article provides an overview of the current national health and nutrition monitoring activities for HM-fed children, HM composition (HMC) and volume data used for exposure assessment, categories of potential measures in HM, and associated variability factors. In this Perspective, we advocate for a framework for collection and reporting of HMC data for national health and nutrition monitoring and programmatic needs, including a shared vision for a publicly available Human Milk Composition Data Repository (HMCD-R) to include essential metadata associated with HMC. HMCD-R can provide a central, integrated platform for researchers and public health officials for compiling, evaluating, and sharing HMC data. The compiled compositional and metadata in HMCD-R would provide pertinent measures of central tendency and variability and allow use of modeling techniques to approximate compositional profiles for subgroups, providing more accurate exposure assessments for purposes of monitoring and surveillance. HMC and related metadata could facilitate understanding the complexity and variability of HM composition, provide crucial data for assessment of infant and maternal nutritional needs, and inform public health policies, food and nutrition programs, and clinical practice guidelines.

Comparative Analysis of the Protein Composition of Goat Milk from French Alpine, Nubian, and Creole Breeds and Holstein Friesian Cow Milk: Implications for Early Infant Nutrition

Simple Summary

Goat’s milk is a food that contains proteins of value for nutrition. The protein profile in the milk of goat breeds is different from that of cow milk, with a lower relative abundance of allergenic proteins. In addition, regardless of the breed, goat milk has beta-casein of type A2 in a more significant proportion than cow milk, which impacts different bioactive peptides hydrolyzed in the milk of the species.

Abstract

Of the diversity of proteins and high digestibility, goat milk will be a food of significant value for infant nutrition. The genetic polymorphisms of milk proteins play an essential role in the different degrees of allergic reactions. This work aimed to identify the proteins and peptides in the composition of goat milk and compare them to those in cow’s milk. The work was performed with goats French Alpine, Nubian, and Creole breeds and Holstein Friesian milking cows at the Universidad Autónoma de Querétaro, Amazcala. We investigated the relative abundance of goat and cow milk protein fractions by SDS-PAGE resolution and the densitometric analysis of gels. The protein alfa-casein was (17.67 ± 0.46) for Creole, (19.18 ± 0.88) French Alpine, (17.35 ± 0.49) Nubian, and (35.92 ± 1.96) Holstein cows. The relative abundance obtained from alfa-casein was statistically different between goats and cows, and this protein was vital because it is a protein related to allergies. On the other hand, the amino acid in position 67 of the beta-casein from three goat breeds is a Proline, so it is assumed that the beta-casein variant of goat milk is an A2-type. The latter has excellent relevance for infant nutrition and differs from cow milk.

Structure And Biological Functions Of Milk Caseins

Caseins, which are contained in milk, play a significant role in the development of clinical symptoms of allergic reactions in adults and children. To date, the properties of caseins have been studied, their primary structure has been identified. However, despite available scientific reviews and original articles, an issue of the structural organization of milk casein micelles and their biological functions is still very controversial. In this regard, the proposed review is relevant, since it most fully reflects current information about various types of caseins, their physicochemical and immunobiological properties, and analyzes in detail the existing theories on the structural organization of casein micelles. Of particular interest in our review are the data on the comparative analysis of the structure and properties of caseins in both human breast milk and cow’s milk, as well as the section dealing with the allergenic activity of cow’s milk caseins and their cross-reactivity with milk proteins of other mammalian species. The objective of this review is to summarize current data on the structure and properties of casein proteins, and to determine their role in the formation of sensitization to dairy products.

Proteomics of Human Biological Fluids for Biomarker Discoveries: Technical Advances and Recent Applications

INTRODUCTION

Biological fluids are routine samples for diagnostic testing and monitoring. Blood samples are typically measured because of their moderate collection invasiveness and high information content on health and disease. Several body fluids, such as cerebrospinal fluid (CSF), are also studied and suited to specific pathologies. Over the last two decades proteomics has quested to identify protein biomarkers but with limited success. Recent technologies and refined pipelines have accelerated the profiling of human biological fluids.

AREAS COVERED

We review proteomic technologies for the identification of biomarkers. Those are based on antibodies/aptamers arrays or mass spectrometry (MS), but new ones are emerging. Advances in scalability and throughput have allowed to better design studies and cope with the limited sample size that had until now prevailed due to technological constraints. With these enablers, plasma/serum, CSF, saliva, tears, urine, and milk proteomes have been further profiled; we provide a non-exhaustive picture of some recent highlights (mainly covering literature from last five years in the Scopus database) using MS-based proteomics.

EXPERT OPINION

While proteomics has been in the shadow of genomics for years, proteomic tools and methodologies have reached a certain maturity. They are better suited to discover innovative and robust biofluid biomarkers.

Natural Association of Lysozyme and Casein Micelles in Human Milk

Using reversed phase high-performance liquid chromatography with ultraviolet (UV) detection and electrospray ionization (ESI)-quadrupole time-of-flight mass spectrometry (RP-HPLC-UV-ESI-Q-TOF), the lysozyme content in the milk of 10 volunteering mothers was quantified, ranging from 29 to 96 μg/mL. Following ultracentifugation, it was found that the lysozyme in human milk, unlike other whey proteins, is mainly bound to casein micelles (ca. 75%). The enzymatic activity of human lysozyme, measured as lytic activity against cell walls of Micrococcus lysodeikticus, was similar for the micelle-bound and free protein, indicating that the micellar structure should not affect the antibacterial activity of lysozyme. The results indicate that lysozyme is an integral component of casein micelles 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/

Distribution and variation in proteins of casein micellar fractions response to heat-treatment from five dairy species

Casein micelles (CMs) contribute to the physicochemical properties and stability of milk. However, how the proteome of CMs changes following heat treatment has not been elucidated. Here, changes in the proteins of CMs in samples of Holstein, buffalo, yak, goat, and camel milk following heat treatment were investigated using a LC-MS/MS approach. According to the hierarchical clustering results, Holstein, yak, and buffalo milk samples had similar CMs protein components, followed by goat and camel milk samples. Changes in lipoprotein lipase and α-lactalbumin in CMs were dependent on the intensity of heat treatment and were similar among the studied species, whereas changes in κ-casein, lactoferrin, and apolipoprotein A-I differed among different types of milk. These results provide information on the distribution and variations of the proteomes of CMs following heat treatment, which will assist in the identification of proteins that are dissociated and attached to CMs from different dairy species during heat treatment.

Proteomics of Human Milk: Definition of a Discovery Workflow for Clinical Research Studies

Milk is a complex biological fluid composed mainly of water, carbohydrates, lipids, proteins, and diverse bioactive factors. Human milk represents a unique tailored source of nutrients that adapts during lactation to the specific needs of the developing infant. Proteins in milk have been studied for decades, and proteomics, peptidomics, and glycoproteomics are the main approaches previously deployed to decipher the proteome of human milk. In the present work, we aimed at implementing a highly automated pipeline for the proteomic analysis of human milk with liquid chromatography mass spectrometry (MS). Commercial human milk samples were used to evaluate and optimize workflows. Centrifugation for defatting milk samples was assessed before and after reduction, alkylation, and enzymatic digestion of proteins, without and with presence of surfactants. Skimmed milk samples were analyzed using isobaric labeling-based quantitative MS on an Orbitrap Tribrid mass spectrometer. Sample fractionation using isoelectric focusing was also evaluated to more deeply profile the human milk proteome. Finally, the most appropriate workflow was transferred to a liquid handling workstation for automated sample preparation. In conclusion, we have defined and describe herein an efficient highly automated proteomic workflow for human milk sample analysis. It is compatible with clinical research, possibly allowing the analysis of sufficiently large cohorts of samples.

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 protein and peptide fractions of kashk, a traditional Middle East fermented dairy product

Kashk is a typical dairy product of Iran, made from sour milk. It is traditionally produced from buttermilk in a dry, round-shaped form. Today, it is also produced at industrial level in a liquid form starting from fermented milk. We aimed to characterise the kashk proteome and peptidome comparing a traditional product with the industrial using a combination of proteomic approaches including advanced chromatographic and electrophoretic separation technique coupled to tandem mass spectrometry. We identified also phosphorylated casein-derived peptides (CPP) and investigated kashk protein digestibility using a static model of food protein digestion. The molecular characterization, coupled with bioinformatic in silico analysis, allowed the identification of potential bioactive peptides.

Storage-Dependent Generation of Potent Anti-ZIKV Activity in Human Breast Milk

Zika virus (ZIKV) causes congenital neurologic birth defects, notably microcephaly, and has been associated with other serious complications in adults. The virus has been detected in human breast milk and possible transmissions via breastfeeding have been reported. Breast milk is rich in nutrients and bio-active substances that might directly affect viral infectivity. Thus, here, we analyzed the effect of human breast milk on ZIKV infection. We observed that fresh human breast milk had no effect on ZIKV, but found that upon storage, milk effectively suppressed infection. The antiviral activity is present in the fat-containing cream fraction of milk and results in the destruction of the structural integrity of viral particles, thereby abrogating infectivity. The release of the factor is time dependent but varies with donors and incubation temperatures. The viral titer of milk that was spiked with ZIKV decreased considerably upon storage at 37 °C for 8 h, was lost entirely after 2 days of 4 °C storage, but was not affected at -20 °C. This suggests that cold storage of milk inactivates ZIKV and that the antiviral factor in milk may also be generated upon breastfeeding and limit this transmission route of ZIKV.

Absolute Quantification of Human Milk Caseins and the Whey/Casein Ratio during the First Year of Lactation

Whey proteins and caseins in breast milk provide bioactivities and also have different amino acid composition. Accurate determination of these two major protein classes provides a better understanding of human milk composition and function, and further aids in developing improved infant formulas based on bovine whey proteins and caseins. In this study, we implemented a LC-MS/MS quantitative analysis based on iBAQ label-free quantitation, to estimate absolute concentrations of α-casein, β-casein, and κ-casein in human milk samples (n = 88) collected between day 1 and day 360 postpartum. Total protein concentration ranged from 2.03 to 17.52 with a mean of 9.37 ± 3.65 g/L. Casein subunits ranged from 0.04 to 1.68 g/L (α-), 0.04 to 4.42 g/L (β-), and 0.10 to 1.72 g/L (α-), with β-casein having the highest average concentration among the three subunits. Calculated whey/casein ratio ranged from 45:55 to 97:3. Linear regression analyses show significant decreases in total protein, β-casein, κ-casein, total casein, and a significant increase of whey/casein ratio during the course of lactation. Our study presents a novel and accurate quantitative analysis of human milk casein content, demonstrating a lower casein content than earlier believed, which has implications for improved infants formulas.

Proteomic analysis and cross species comparison of casein fractions from the milk of dairy animals

Casein micelles contribute to the physicochemical properties of milk and may also influence its functionality. At present, however, there is an incomplete understanding of the casein micelle associated proteins and its diversity among the milk obtained from different species. Therefore, milk samples were collected from seven dairy animals groups, casein fractions were prepared by ultracentrifugation and their constituent proteins were identified by liquid chromatography tandem mass spectrometry. A total of 193 distinct proteins were identified among all the casein micelle preparations. Protein interaction analysis indicated that caseins could interact with major whey proteins, including β-lactoglobulin, α-lactalbumin, lactoferrin, and serum albumin, and then whey proteins interacted with other proteins. Pathway analysis found that the peroxisome proliferator-activated receptor signaling pathway is shared among the studied animals. Additionally, galactose metabolism pathway is also found to be commonly involved for proteins derived from camel and horse milk. According to the similarity of casein micelle proteomes, two major sample clusters were classified into ruminant animals (Holstein and Jersey cows, buffaloes, yaks, and goats) and non-ruminants (camels and horses). Our results provide new insights into the protein profile associated with casein micelles and the functionality of the casein micelle from the studied animals.

A Quantitative Proteomics Approach to Clinical Research with Non-Traditional Samples

The proper handling of samples to be analyzed by mass spectrometry (MS) can guarantee excellent results and a greater depth of analysis when working in quantitative proteomics. This is critical when trying to assess non-traditional sources such as ear wax, saliva, vitreous humor, aqueous humor, tears, nipple aspirate fluid, breast milk/colostrum, cervical-vaginal fluid, nasal secretions, bronco-alveolar lavage fluid, and stools. We intend to provide the investigator with relevant aspects of quantitative proteomics and to recognize the most recent clinical research work conducted with atypical samples and analyzed by quantitative proteomics. Having as reference the most recent and different approaches used with non-traditional sources allows us to compare new strategies in the development of novel experimental models. On the other hand, these references help us to contribute significantly to the understanding of the proportions of proteins in different proteomes of clinical interest and may lead to potential advances in the emerging field of precision medicine.

Characterization of the bovine milk proteome in early-lactation Holstein and Jersey breeds of dairy cows

Milk is a highly nutritious natural product that provides not only a rich source of amino acids to the consumer but also hundreds of bioactive peptides and proteins known to elicit health-benefitting activities. We investigated the milk protein profile produced by Holstein and Jersey dairy cows maintained under the same diet, management and environmental conditions using proteomic approaches that optimize protein extraction and characterization of the low abundance proteins within the skim milk fraction of bovine milk. In total, 935 low abundance proteins were identified. Gene ontology classified all proteins identified into various cellular localization and function categories. A total of 43 low abundance proteins were differentially expressed between the two dairy breeds. Bioactive proteins involved in host-defense, including lactotransferrin (P=0.0026) and complement C2 protein (P=0.0001), were differentially expressed by the two breeds, whereas others such as osteopontin (P=0.1788) and lactoperoxidase (P=0.2973) were not. This work is the first to outline the protein profile produced by two important breeds of dairy cattle maintained under the same diet, environment and management conditions in order to observe likely true breed differences. This research now allows us to better understand and contrast further research examining the bovine proteome that includes these different breeds.

BIOLOGICAL SIGNIFICANCE

Within the last decade, the amount of research characterizing the bovine milk proteome has increased due to growing interest in the bioactive proteins that are present in milk. Proteomic analysis of low abundance whey proteins has mainly focused on human breast milk; however, previous research has highlighted the presence of bioactive proteins in bovine milk. Recent publications outlining the cross-reactivity of bovine bioactive proteins on human biological function highlight the need for further investigation into the bovine milk proteome. The rationale behind this study is to characterize and compare the low abundance protein profile in the skim milk fraction produced from Holstein and Jersey breeds of dairy cattle, which are two major dairy cattle breeds in the USA. A combination of fractionation strategies was used to efficiently enrich the low abundance proteins from bovine skim milk for proteomic profiling. A total of 935 low abundance proteins were identified and compared between the two bovine breeds. The results from this study provide insight into breed differences and similarities in the milk proteome profile produced by two breeds of dairy cattle.

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.

Infant formula and infant nutrition: bioactive proteins of human milk and implications for composition of infant formulas

Human milk contains an abundance of biologically active components that are highly likely to contribute to the short- and long-term benefits of breastfeeding. Many of these components are proteins; this article describes some of these proteins, such as α-lactalbumin, lactoferrin, osteopontin, and milk fat globule membrane proteins. The possibility of adding their bovine counterparts to infant formula is discussed as well as the implications for infant health and development. An important consideration when adding bioactive proteins to infant formula is that the total protein content of formula needs to be reduced, because formula-fed infants have significantly higher concentrations of serum amino acids, insulin, and blood urea nitrogen than do breastfed infants. When reducing the protein content of formula, the amino acid composition of the formula protein becomes important because serum concentrations of the essential amino acids should not be lower than those in breastfed infants. Both the supply of essential amino acids and the bioactivities of milk proteins are dependent on their digestibility: some proteins act only in intact form, others act in the form of larger or small peptides formed during digestion, and some are completely digested and serve as a source of amino acids. The purity of the proteins or protein fractions, potential contaminants of the proteins (such as lipopolysaccharide), as well as the degree of heat processing used during their isolation also need to be considered. It is likely that there will be more bioactive components added to infant formulas in the near future, but guidelines on how to assess their bioactivities in vitro, in animal models, and in clinical studies need to be established. The extent of testing needed is likely going to depend on the degree of complexity of the components and their bioequivalence with the human compounds whose effects they are intended to mimic.