Article pubs.acs.org/jpr
Chrono-Proteomics of Human Saliva: Variations of the Salivary Proteome during Human Development Irene Messana,† Tiziana Cabras,† Federica Iavarone,‡ Barbara Manconi,† Liling Huang,‡ Claudia Martelli,‡ Alessandra Olianas,† Maria Teresa Sanna,† Elisabetta Pisano,§ Monica Sanna,† Morena Arba,† Alfredo D’Alessandro,† Claudia Desiderio,∥ Alberto Vitali,∥ Davide Pirolli,‡ Chiara Tirone,⊥ Alessandra Lio,⊥ Giovanni Vento,⊥ Costantino Romagnoli,⊥ Massimo Cordaro,# Armando Manni,# Patrizia Gallenzi,# Antonella Fiorita,▽ Emanuele Scarano,▽ Lea Calò,▽ Giulio Cesare Passali,▽ Pasqualina Maria Picciotti,▽ Gaetano Paludetti,▽ Vassilios Fanos,§ Gavino Faa,§ and Massimo Castagnola*,‡,∥ †
Dipartimento di Scienze della Vita e dell’Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy ‡ Istituto di Biochimica e Biochimica Clinica, Università Cattolica, Largo Francesco Vito 1, Roma 00168, Italy § Dipartimento di Scienze Chirurgiche, Università di Cagliari, Cittadella Universitaria di Monserrato, S. P. Monserrato Sestu Km 0.700, Monserrato (CA) 09042, Italy ∥ Istituto di Chimica del Riconoscimento Molecolare, CNR, Largo Francesco Vito 1, Roma 00168, Italy ⊥ Istituto di Clinica Pediatrica, Università Cattolica, Roma 00168, Italy # Istituto di Clinica Odontostomatologica, Università Cattolica, Roma 00168, Italy ▽ Istituto di Clinica Otorinolaringoiatrica, Università Cattolica, Roma 00168, Italy S Supporting Information *
ABSTRACT: An important contribution to the variability of any proteome is given by the time dimension that should be carefully considered to define physiological modifications. To this purpose, whole saliva proteome was investigated in a wide age range. Whole saliva was collected from 17 preterm newborns with a postconceptional age at birth of 178−217 days. In these subjects sample collection was performed serially starting immediately after birth and within about 1 year follow-up, gathering a total of 111 specimens. Furthermore, whole saliva was collected from 182 subjects aged between 0 and 17 years and from 23 adults aged between 27 and 57 years. The naturally occurring intact salivary proteome of the 316 samples was analyzed by low- and high-resolution HPLC−ESI−MS platforms. Proteins peculiar of the adults appeared in saliva with different time courses during human development. Acidic proline-rich proteins encoded by PRH2 locus and glycosylated basic proline-rich proteins encoded by PRB3 locus appeared following 180 days of postconceptional age, followed at 7 months (±2 weeks) by histatin 1, statherin, and P−B peptide. The other histatins and acidic proline-rich proteins encoded by PRH1 locus appeared in whole saliva of babies from 1 to 3 weeks after the normal term of delivery, S-type cystatins appeared at 1 year (±3 months), and basic proline-rich proteins appeared at 4 years (±1 year) of age. All of the proteinases involved in the maturation of salivary proteins were more active in preterm than in atterm newborns, on the basis of the truncated forms detected. The activity of the Fam20C kinase, involved in the phosphorylation of various proteins, started around 180 days of postconceptional age, slowly increased reaching values comparable to adults at about 2 years (±6 months) of age. Instead, MAPK14 involved in the phosphorylation of S100A9 was fully active since birth also in preterm newborns. KEYWORDS: chrono-proteomics, saliva, human, proline-rich proteins, statherin, histatin, S-type cystatins, S100A9 protein, preterm newborns
1. INTRODUCTION Human saliva is a bodily fluid that is very attractive for diagnostic and prognostic purposes because it is characterized by an easy and noninvasive specimen collection.1 For this © 2015 American Chemical Society
Received: September 10, 2014 Published: March 11, 2015 1666
DOI: 10.1021/pr501270x J. Proteome Res. 2015, 14, 1666−1677
Article
Journal of Proteome Research
after discharge from the neonatal unit, during the periodical check visits within about 1 year follow-up. In this way 111 saliva specimens were analyzed covering a period from 178 to 545 days of PCA. (b) 182 donors (92 males, 90 females) with an age comprised between 0 to 17 years of age. (c) 23 adults (10 males, 13 females) with an age comprised between 27 and 57 years. Collection time was usually established between 10:00 and 12:00 a.m. The donors were under healthy clinical conditions. Except for preterm newborns, donors did not eat or drink 2 h before the collection. Whole saliva was collected with a soft plastic aspirator as it flowed into the anterior floor of the mouth. After collection, each salivary sample was immediately diluted 1:1 (v/v) with 0.2% aqueous 2,2,2-trifluoroacetic acid (TFA) in ice bath. The solution was then centrifuged at 8000g for 5 min (4 °C). Finally, the acidic supernatant was separated from the pellet and either immediately analyzed with the HPLC−ESI−MS apparatus or stored at −80 °C until the analysis.
reason, in the last years many groups have studied by a large variety of -omic platforms human saliva under physiological and pathological conditions to evidence new, and possibly early, salivary biomarkers of disease with clinical utility, as reported in recent outstanding reviews and articles.2−5 Sampling of saliva can be accomplished without pain and stress for the donor, therefore, representing a suitable bodily fluid that may be collected and investigated also in pediatric age.6 In the last years our group, as well as other ones, investigated the salivary proteome of preterm newborns and subjects in the pediatric age, highlighting striking differences with respect to adults.7−11 By an integrated top-down/bottom-up platform, we evidenced that human preterm newborn saliva contains more than 40 major salivary proteins either undetectable (according to the detection limit of our analytical method) or detectable in small amount in saliva of adults.9 On the contrary, the proteins typically revealed in adult were undetectable or present in small amount in preterm newborn saliva. In the present study the human salivary proteome was investigated in a large group of subjects over a wide range of ages, starting from preterm newborns of ∼180 days of postconceptional age (PCA) up to 17 year old subjects, to define the appearance and the level changes of the proteins typically found in adult saliva from the last months of fetal development to adulthood. Several posttranslational-derived proteoforms have been also investigated as a function of age to obtain information on the time course activation of different enzymes, in particular, kinases and convertases. The present study provides reference data to assess whether abnormal expression of salivary proteins and anomalous activities of specific enzymes involved in posttranslational modifications (PTMs) occur during human development. The possibility to easily highlight abnormalities of the salivary proteome, which may be a clue of potential diseases, could have a significant impact on clinical practice, especially in pediatrics.
2.3. RP−HPLC−ESI−MS Analysis
2.3.1. RP−HPLC−High-Resolution MS/MS Characterization of Intact Protein. High-resolution HPLC−ESI−MS/ MS experiments were carried out by an Ultimate 3000 Nano/ Micro HPLC apparatus (Dionex, Sunnyvale, CA) equipped with a FLM-3000-Flow manager module and coupled to an LTQ Orbitrap XL apparatus (ThermoFisher, San Jose, CA). A Dionex C8 column (3 μm particle diameter; column dimension 300 μm i.d. × 15 cm) or a Zorbax 300 SB-C8 (3.5 μm particle diameter; column dimension 1 mm i.d. × 15 cm) were used as chromatographic columns. The following eluents were used: (A) 0.1% (v/v) aqueous formic acid (FA) and (B) 0.01% (v/v) FA in acetonitrile/water 80/20 v/v. The applied gradient was 0−4 min 5% B, 4−34 min from 5 to 50% B (linear), and 34−64 min from 50 to 90% B (linear) at a flow rate of 80 μL/min. High-resolution positive MS/MS spectra were collected in full scan using the lock mass for internal mass calibration (polydimethyl cyclosiloxane, 445.1200 m/z) with the resolution of 60 000 and 30 000, respectively, and m/z range from 350 to 2000. In data-dependent acquisition mode the three most intense multiply charged ions were selected and fragmented by using collision-induced dissociation (CID, 35% normalized collision energy) and spectra were recorded. Alternatively, fragmentation was carried out using the same analysis conditions on selected multiply charged ions corresponding to a specific protein mass. Tuning parameters were: capillary temperature 250 °C, source voltage 4.0 kV, capillary voltage 48 V, and tube lens voltage 170 V. Detailed instrumental operative conditions are reported in Supplemental S1 in the Supporting Information (SI). The inject volume was set at 20 μL, corresponding to 10 μL of saliva. 2.3.2. RP−HPLC−Low-Resolution MS Analysis of Intact Protein. For low-resolution (1/6000) MS experiments the HPLC−ESI−IT−MS apparatus used was a Surveyor HPLC system (ThermoFisher Scientific) connected by a T splitter to a photo diode-array detector and either to an LCQ Advantage ion trap mass spectrometer (ThermoFisher Scientific) or to an LCQ Deca XP Plus ion trap mass spectrometer (ThermoFisher Scientific). The chromatographic column was a 150 × 2.1 mm Vydac (Hesperia, CA) C8 column with 5 μm particle diameter. The following solutions were utilized for the RP−HPLC separation: (eluent A) 0.056% aqueous TFA and (eluent B)
2. EXPERIMENTAL SECTION 2.1. Reagents
All general chemicals and reagents of LC−MS grade were purchased from J. T. Baker (Deventer, The Netherlands), Merck (Darmstadt, Germany), and Sigma-Aldrich (St. Louis, MO). 2.2. Subjects Enrolled, Sample Collection, and Treatment
The study protocol and written consent form were approved by the Ethical Committees of the University Hospital of Cagliari, of the Catholic University of Rome, and by the Ethical Committee of the Neonatal Intensive Care Unit of the Institute of Clinical Pediatric of the Catholic University of Rome; therefore, it has been performed in accordance with the ethical standards laid down in the 1964 Declaration of Helsinki. All rules were observed, and written consent forms were signed by the donor or by one parent of each child. For ethical reasons, saliva was collected only when sample collection caused no stress. 316 samples of resting whole saliva were gathered and analyzed from the following subjects: (a) 17 preterm newborns (8 males, 9 females) with a birth weight ranging between 500 and 1250 g and a PCA at birth of 178−217 days (26−31 weeks). Newborns with major congenital malformations or prenatal infections were excluded from the study. Sample collection was performed on the same preterm newborn during several weeks after birth at fixed time intervals (1 or 2 weeks). When possible, it was also performed 1667
DOI: 10.1021/pr501270x J. Proteome Res. 2015, 14, 1666−1677
Article
Journal of Proteome Research
Figure 1. Scheme describing the approximate time course of the different salivary proteins and peptides investigated in this study. The sum of XIC peak areas of all of the members belonging to the same family of proteins/peptides, grouped on the basis of their locus, is reported as a function of age. A logarithmic scale has been used in the abscissa axis to better highlight the major changes occurring in preterm newborns during the first months of life, which correspond to the last months of fetal development, and those occurring immediately after the normal term of delivery and in the first years of life. Dashed lines represent the age range in which the proteins were detected in at least one baby. The upper limit of this range corresponds to the age in which saliva of all babies displayed the protein in the chromatographic profile, even if at small amount.
resolution HPLC−ESI−MS XIC peak areas were in agreement with those calculated by low-resolution HPLC−ESI−MS peak areas (within the limit of the experimental error). The XIC search reveals the peak associated with the protein of interest by extracting along the total ion current (TIC) chromatographic profile the intensity of the ion current of specific multiply charged ions (m/z) generated by the ESI source. The ions used to quantify the proteins and peptides were carefully selected to exclude values in common with other coeluting analytes. The area of the XIC peak was related to the saliva volume (1.0 mL), and it is proportional to protein/peptide concentration; therefore, under constant analytical conditions, it can be used for a quantitative analysis and comparative studies.14−16 The estimated percentage error of the XIC procedure was
