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Mol Cell Proteomics. 2010 September; 9(9): 1937–1953.
Published online 2010 May 13. doi:  10.1074/mcp.M900483-MCP200
PMCID: PMC2938108

Quantitative Proteomics Analysis of the Nuclear Fraction of Human CD4+ Cells in the Early Phases of IL-4-induced Th2 Differentiation*An external file that holds a picture, illustration, etc.
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Abstract

We used stable isotope labeling with 4-plex iTRAQ (isobaric tags for relative and absolute quantification) reagents and LC-MS/MS to investigate proteomic changes in the nucleus of activated human CD4+ cells during the early stages of Th2 cell differentiation. The effects of IL-4 stimulation upon activated naïve CD4+ cells were measured in the nuclear fractions from 6 and 24 h in three biological replicates, each using pooled cord blood samples derived from seven or more individuals. In these analyses, in the order of 800 proteins were detected with two or more peptides and quantified in three biological replicates. In addition to consistent differences observed with the nuclear localization/expression of established human Th2 and Th1 markers, there were changes that suggested the involvement of several proteins either only recently reported or otherwise not known in this context. These included SATB1 and among the novel changes detected and validated an IL-4-induced increase in the level of YB1. This unique data set from human cord blood CD4+ T cells details an extensive list of protein determinations that compares with and complements previous data determined from the Jurkat cell nucleus.

As a response to antigen encounter and their cytokine environment, naïve CD4+ cells differentiate into functionally distinct T helper (Th)1 cell subsets, the best characterized of which are Th1 and Th2 cells (13). Th1 cells produce proinflammatory cytokines and are generally acknowledged to be involved in autoimmune diseases such as multiple sclerosis and diabetes, whereas Th2 cells produce proallergic cytokines, the dysregulation of which can lead to asthma and other atopic diseases (46). Because these subsets share a common progenitor, the early events that determine lineage are important in the understanding of the pathways leading to polarization and associated disease. DNA microarrays (712) and proteomics platforms (1320) have been used in the characterization and comparison of these Th cell types.

Interleukin-4 (IL-4) is the key cytokine in Th2 differentiation; it is expressed by Th2 cells and also drives Th2 differentiation (21, 22). The binding of IL-4 to its receptor at the Th cell surface leads to the phosphorylation of signal transducer and activator of transcription 6 (STAT6) followed by STAT6 homodimerization and nuclear localization where it regulates transcription of its target genes (23, 24). The importance of IL-4 and STAT6 for the induction of the Th2 response is well documented, and similarly the transcription factor GATA3 plays an important role in several stages of Th2 cell development where it is required for the regulation of several Th2-specific cytokines (2527). Th1 differentiation is induced by IL-12 stimulation and characterized by up-regulation of T box transcription factor TBX21 (T-BET) and interferon-γ (2830).

The differentiation process leads to the specific and heritable gene expression profiles of the Th cell subtypes without alteration of the base sequence of the DNA. These thus termed epigenetic mechanisms have been shown to play a key role in the determination of the fate of Th cell specification (31, 32). Proteomic changes involving signaling and organization at the nucleus are therefore important in the early phases leading to differentiation. The aim of the present work was to apply a quantitative proteomics approach to investigate changes in the nuclear proteome of naïve CD4+ human cells during the early stages of Th2 cell differentiation. In transcriptomic measurements (12, 96), we observed a large number of distinct changes during the first 24 h of differentiation and on the basis of these selected to investigate proteomic changes at time points of 6 and 24 h. We used 4-plex iTRAQ reagents (33) to compare the abundances of proteins in the nuclear fractions of activated CD4+ cells and those activated and IL-4-stimulated (at 6 and 24 h). With these measurements, we aimed to identify protein abundance changes associated with Th2 cell differentiation with potential mechanistic relevance to the early phases of this process. Three biological replicates were made with triplicate analysis of the sample material. Proteins with consistent and statistically significant changes were considered for further validation. Further evaluations were made in terms of known protein interactions and functions and GO annotation in general.

In addition to the expected changes in relative protein abundance for Th2- and Th1/interferon-related proteins that were indicated in these data, there were a number changes that involved proteins either not previously reported or fully characterized in association with human Th2 differentiation. Furthermore, although large scale identification experiments have been made previously for the nucleus of Jurkat cells (34, 35), to our knowledge, this is the first such study for human cord blood CD4+ cells.

EXPERIMENTAL PROCEDURES

Cell Culture and Cytokine Activation

CD4+ cells were isolated from the cord blood samples (collected from healthy neonates at Turku University hospital) by Ficoll-Paque (Amersham Biosciences) density gradient centrifugation and anti-CD4 magnetic beads (Dynal). The purity of the isolated cell population was estimated using CD4 surface staining and flow cytometry as described previously (19). The mean measured purity for the gated populations was 98.5% (as illustrated in supplemental File S1.1).

Cells were cultured in Yssel's medium (provided by Dr. Hans Yssel) (36) supplemented with 1% AB serum (Red Cross Finland Blood Service). Cells were activated with plate-bound anti-CD3 (500 ng/ml) and soluble anti-CD28 (500 ng/ml) (Immunotech) and stimulated with IL-4 (10 ng/ml; R&D Systems). Activation was performed within 16 h of CD4+ cell isolation. Cells were harvested at 6 and 24 h after activation for the iTRAQ and Western blotting (WB) experiments and at 0, 0.5, 2, 4, 6, 12, 24, 48, and 72 h for the RT-PCR measurements. For the 72-h sample, an IL-2 supplement (40 units/ml; R&D Systems) was added at 48 h.

Three separate biological cell cultures were made for the iTRAQ experiments with an additional 16 cultures made for the validations. The cultures were made using CD4+ cells derived from the cord blood of ≥7 individuals for the iTRAQ labeling and were typically from five individuals in the Western blot validation experiments. The counts of CD4+ cells used in the cultures varied from 32 to 270 million. Details of these cell counts and protein isolation yields are in supplemental File S1.2.

Isolation of Nuclear Fraction

The isolation of nuclear/DNA-binding proteins was performed according to the protocol of Andrews and Faller (37) with slight modifications. In brief, the cells (in aliquots of 10–50 million cells) were harvested, washed with ice-cold PBS, and lysed for 10 min on ice using a lysis buffer of 20 mm HEPES, 0.2% Nonidet P-40, 0.5 mm DTT, 1.5 mm MgCl2, 10 mm KCl, 1 mm NaF, 1 mm Na3VO4, and Complete Mini protease inhibitors (Roche Applied Science). Lysis was controlled by trypan blue staining for which virtually all cells were positive after the 10-min incubation, indicating disruption of the plasma membrane.

The cell suspension was centrifuged at 10,000 rpm for 1 min, and the supernatant (cytoplasmic fraction) was collected. The pellet was washed using the lysis buffer and resuspended in the nuclear extraction buffer (20 mm HEPES, pH 7.9, 420 mm NaCl, 25% glycerol, 0.5 mm DTT, 1.5 mm MgCl2, 0.2 mm EDTA, 1 mm NaF, 1 mm Na3VO4, and Complete Mini protease inhibitors from Roche Applied Science) and incubated on ice for 20 min. Following incubation, the suspension was centrifuged (13,000 rpm for 15 min), and the supernatant (nuclear extract) was collected.

Enrichment of nuclear proteins in this nuclear fraction was verified by Western blotting with PARP1 antibody as indicated in Fig. 4b. To confirm that IL-4 signaling was functional, immunodetections for phospho-STAT6 and GATA3 were performed. Flow cytometry measurements of CD69 (38) and immunodetection of phospho-Erk are detailed as markers of activation in supplemental Files S1.3 and S1.4.

Fig. 4.
a, Western blot analysis for IL-4 signaling and Th2 differentiation markers in anti-CD3/CD28-activated human CD4+ cells. Immunodetection of phospho-STAT6 (p-STAT6) and GATA3 from whole cell lysates is shown. Clear IL-4-induced up-regulation is observed ...

iTRAQ Labeling and Peptide Fractionation

Based on the results of the Bradford assays (39), equal protein amounts (50–100 μg) from the four compared states, i.e. 6- and 24-h activation versus and 6- and 24-h activation with IL-4 treatment, were labeled with the separate forms of the iTRAQ reagents. Protein precipitation was achieved during 4 h at −20 °C after mixing with 6 volumes of acetone. The pelleted proteins were then dissolved in 40 μl of triethylammonium bicarbonate buffer containing 0.1% SDS and labeled with iTRAQ reagents as described in the manufacturer's protocol. Briefly, this included reduction with tris(2-carboxyethyl)phosphine and derivatization of free cysteines with methyl methanethiosulfonate (MMTS) followed by overnight digestion with trypsin (sequencing grade modified, Promega). The resulting peptides were labeled with the iTRAQ reagents for 1 h at room temperature. In all three biological replicates, the 114 and 116 reagents were used to label the peptides from the cells activated for 6 and 24 h, respectively, and likewise the 115 and 117 reagents were used to label the activated and IL-4-treated cells for 6 and 24 h, respectively. The labeled peptides were combined and acidified (pH 2.9–3.1). The resulting peptide mixtures were fractionated with a 200 × 4.6-mm-inner diameter polysulfoethyl A column (Poly LC Inc., Columbia, MD) strong cation exchange (SCX) column using a BioCADTM chromatograph (PerSeptive Biosystems, Freiburg, Germany). The peptides were eluted at 0.7 ml/min from the cation exchange column during a two-step gradient from 0 to 30% B in 14 min and then to 100% B in 10 min (held for 15 min). The A and B phases consisted of 5 mm KH2PO4 and 25% acetonitrile, pH 3 with the B phase containing 0.6 m KCl. The eluted peptides were subsequently collected in 20 sequential fractions. The SCX fractions were dried in a HetoVac vacuum centrifuge (Heto-Holten A/S, Allerød, Denmark) and desalted using EmporeTM octadecyl bonded silica sorbent material (3M, St. Paul, MN).

LC-ESI-MS/MS Analysis

Aliquots (2–6 μg) of the desalted fractions were dissolved in 0.1% HCOOH and then characterized by LC-MS/MS. The LC-MS/MS system consisted of a nanoflow LC system (Famos, Switchos-II, and Ultimate, LC Packings, Amsterdam, Netherlands) coupled to a QSTAR® Pulsar ESI-hybrid quadrupole-time of flight instrument (Applied Biosystems/MDS Sciex). Sample loading was performed using a 0.3 × 5-mm PepMap C18 μ-precolumn (LC Packings) from which the samples were back-flushed onto a reverse phase 15-cm × 75-μm-inner diameter fused silica capillary column packed with 5-μm Magic C18 (Michrom Bioresources, Inc., Auburn, CA). Peptide separation was achieved using a gradient from 5 to 40% B in 120 min at a mobile phase flow rate of 200 nl/min. The phase compositions were as follows: phase A, 5% ACN and 0.1% HCOOH; phase B, 95% ACN and 0.1% HCOOH. The mass spectrometer was set to perform survey scans of 1 s followed by two 3-s MS/MS scans of the two most intense peaks from the survey scan with dynamic exclusion for 5 min. Data acquisition and instrument control were performed using Analyst QS 1.1 software (Applied Biosystems).

Triplicate LC-MS/MS analyses were carried out for each cation exchange fraction in separate batches of 20. Overall, the data set for each biological experiment consisted of 60 runs (i.e. 3 × 20) with 180 LC-MS/MS analyses in total for the three biological replicates.

Data Processing

A data processing work flow was implemented that aimed to facilitate a broad comparison of the data from the biological replicates and indicate consistent changes in protein abundance in the nucleus of CD4+ cells induced to Th2 differentiation compared with cells that were activated only. The elements of the data analysis process are indicated in the experimental schematic depicted in Fig. 1.

Fig. 1.
Schematic of experimental work flow. Differences in protein abundance were determined for the nuclear fractions of IL-4-treated anti-CD3/CD28-activated versus anti-CD3/CD28-activated CD4+ cells at 6 and 24 h by iTRAQ labeling with LC-MS/MS analysis. For ...

ProQuant

The LC-MS/MS data were analyzed using the Applied Biosystems Analyst script ProQuant (version 1.1, Applied Biosystems). For this study using human umbilical cord blood T lymphocytes, a Swiss-Prot database (release date, December 5, 2005; 13,303 human sequences) composed of human proteins plus known contaminants (trypsin fragments and BSA; 11 entries) was concatenated with its reversed counterpart and formatted to create an interrogator that included MMTS modification of cysteine; iTRAQ labeling at the N terminus, lysine, and tyrosine; and one missed tryptic cleavage permitted. With the exception of tyrosine labeling, all the latter modifications were treated as fixed. The precursor and product ion mass tolerances were set to 0.3 and 0.2 Da, respectively, and the following variable zone modifications were specified (40): O-phosphorylation of serine, threonine, and tyrosine; deamidation of asparagine and glutamine; and methionine oxidation.

ProGroup

Protein inference (i.e. determining which proteins best describe the peptide data where degenerate peptides are present) from the ProQuant search results was made according to the ProGroup algorithm (version 1.0, Applied Biosystems). ProGroup uses the peptide identification results to determine the minimal set of proteins that can be reported for a given protein confidence threshold. Data inclusion of peptide data down to 70% confidence was used to increase the opportunities for overlap of identification across replicates, particularly in cases where the lower intensity precursor ion led to poorer scoring. For the peptide data, only peptides of 6 or more amino acids were accepted. Using these criteria, the false positive rates (FPRs) for protein identification were estimated from the number of hits for reversed peptide sequences according to the method described by Gygi and co-workers (41, 42). The estimated FPRs were typically on the order of 9% for proteins detected with two or more peptides in biological replicates 1, 2, and 3 (9.4, 9.3, and 7.3%, respectively) and 5.3 and 0.5% for proteins detected in all three biological replicates by one and two sequences, respectively.

Mascot

To add an extra measure of confidence to the protein identifications and to represent the identification data in relation to a more frequently used identification algorithm, the data from the different biological data sets were also analyzed with Mascot (43). An in-house Mascot server was used (version 2.1, Matrix Science, London, UK), and the data were searched against the same concatenated database as used with ProQuant with the same mass tolerances and enzyme specificity. iTRAQ labeling of tyrosine, deamidation of asparagine and glutamine, and methionine oxidation were specified as variable modifications, and MMTS modification of cysteine and iTRAQ labeling at the N-terminus and lysine were specified as fixed modifications. Peak lists were created in *.mgf format using ProteinPilot 2.0 software (Applied Biosystems) as described previously (44). In brief, these were created without merging of any putatively similar spectra and with no restriction of mass range for precursors applied (beyond the constraints used during acquisition).

Based on the search results where reversed sequences were identified from the concatenated database, the inclusion criteria for protein identifications were chosen such that the overall FPR was on the order of 5%. Mascot protein scores greater than or equal to 40 were accepted, and peptides with an expectation score less than 0.05 and a peptide rank of 1 were counted. The false positive rates were 3.0, 5.0, and 5.3% for the biological replicates 1, 2, and 3, respectively. With these criteria, there were no protein hits based on reversed sequences detected by Mascot in all three replicates. Furthermore, for proteins identified with ProQuant in all three biological replicates and by Mascot in at least one replicate, the estimated FPR was 0.2%. Protein inference from the Mascot searches was made according to the Mascot bold red function; the bold red option assigns degenerate peptides to the highest scoring protein. These data were subsequently summarized using the ScaffoldTM proteomic software (version Scaffold-02_05_01, Proteome Software Inc.) as described below.

Relative Quantification

Protein iTRAQ ratios and their associated standard deviations were calculated from each biological replicate. Although ProGroup provides this calculation, the ratios were purposely recalculated from the exported peptide data to establish the data used and the associated variance. These abundance ratios (IL-4-treated and activated versus activated for 6 and 24 h) were determined as weighted averages over the corresponding peptide-level iTRAQ reporter ion peak area ratios similarly to Gan et al. (45). More specifically, if xi denotes the logarithmic ratio of the peak areas of the iTRAQ reporter ions for a peptide i in a particular biological replicate, then the protein-level ratio is defined as

equation image

where the weight wi is the inverse of the percent error for the ratio of the peak areas for peptide i. The ratios and their percent errors were calculated by the ProQuant software. The corresponding weighted standard deviation was calculated as

equation image

where v is the variance across the n peptide ratios xi. In these calculations, only data from peptides with a sequence length greater than or equal to 6, with a ProGroup confidence of at least 70%, and without unlabeled residues (Lys or N terminus) were used. The exported peptide data were normalized by ProQuant to correct for possible systematic bias. In brief, the program excludes iTRAQ ratios that are blank, 0, or 9999 and those for which the sum of the peak areas is less than 40 counts. The program finds the median iTRAQ ratio and sets the applied bias so that the median ratio is 1. The normalization was confirmed for the selected data.

To identify consistent changes with these data, we used the so-called random effect meta-analysis model to estimate representative expression ratios for each protein from the three biological replicates. The approach is conceptually similar to the probe-level expression change averaging procedure that we have successfully applied to combine data across gene expression microarray experiments (46). For microarray applications, the method takes into account the probe-level information rather than a general measure of variability and enables determination of the variability of the estimated statistic directly from the data. A similar procedure has been applied to microarray data by other groups (47, 48). We selected this method to assess each value according to its own attributes and to facilitate the comparison of data of variable quality, particularly because protein quantifications are derived from unique peptides with their own physical characteristics and associated LC-MS/MS background.

The random effect model for the replicate measurements (m) can be written as

equation image

where the Gaussian components

equation image

and

equation image

correspond to the between-replicate and within-replicate variability, respectively. Following the procedure described in detail by Choi et al. (49), the parameter μ and its variance were estimated as

equation image

and

equation image

respectively. The parameter τ was estimated using the method of moments technique of DerSimonian and Laird (50) as is indicated in supplemental File S1.5. Finally, to test the null hypothesis H0: μ = 0 (i.e. that the iTRAQ ratio is unity), the statistic

equation image

that is distributed as N(0,1) under the null hypothesis was used. A two-tailed significance threshold p < 0.05 was applied (i.e. |Z| ≥ 1.96). These calculations were made for proteins that were detected and quantified in all three biological replicates. To consider potential changes for proteins with less spectral representation, iTRAQ ratios were calculated for proteins with at least five iTRAQ ratio calculations for the time point analyzed.

With iTRAQ applications in general, high confidence differences in expression on the order of 1.2-fold and greater have been reported (5153). In an evaluation of the iTRAQ reproducibility, Gan et al. (45) have demonstrated technical variation of iTRAQ measurements to be on the order of 20% and observed greater biological variation on the order of 45%. In our iTRAQ measurements three biological replicates were made, although the material did represent a wider population with the cord blood from 34 individuals. Although individual specific biases could occur with such pooling (54), we have, however, selected a threshold for change of ~20%, i.e. a log2 ratio of ±0.263, together with p < 0.05 to highlight potentially important results for further hypothesis and investigation. To estimate the false discovery rate (FDR), the Benjamini and Hochberg (55) correction was used. For this, each protein was assigned a rank according to their p values from smallest to largest, and then each was multiplied by the total number of proteins in the list and divided by its rank (56, 57). These calculations were performed using Microsoft Excel, the informatics program Kensington (InforSense Ltd., London, UK), and scripts written with R.

Data Annotation and Comparison

GO annotation of the identified proteins was done using PIGOK (58) and used for sorting and grouping. To gain an additional overview of these data in relation to published literature, the Ingenuity Pathway Analysis (version 6.5, Ingenuity Systems, Inc.) application was used.

In the context of other studies and T cell proteomics data sets, large scale measurements from the nucleus of human T cells have mostly used the Jurkat cell lines (34, 35, 59). Han and co-workers (34) have studied nuclear fractionation methods and reported 1174 proteins associated with the nuclear fraction from Jurkat cells during apoptosis. These included 829 proteins from the Swiss-Prot database (current entries) of which there were 349 proteins with GO annotation for the nucleus. In a later study (35), extensive subcellular fractionation of human Jurkat A3 T leukemic cells was carried out, and 1,750 proteins were detected from the nuclear fractions. Using a hierarchical clustering-based method to indicate organelle-specific association, a subset of 768 proteins was defined, 520 of which had GO annotation for the nucleus. For the purpose of comparison, we considered the data from the latter two studies and selected data associated with Swiss-Prot identifiers. To accommodate for changes in nomenclature and deletion of entries, all the accession numbers entries have been updated using the software from the Universal Protein Resource (UniProt) with the database released March 3, 2009 (version 14.9). Altogether, the combined set from these Jurkat studies was determined to present 1439 proteins currently listed in the Swiss-Prot database of which 629 have GO annotation for the nucleus. For the comparison with our iTRAQ data, we compared the proteins detected in all three biological replicates with the former data sets. To improve the accessibility of these data, the Mascot search results (*.dat files) from the three biological replicates were summarized using Scaffold proteomic software (version Scaffold-02_05_01, Proteome Software Inc.) The Scaffold analysis includes an empirical probability-based validation of the protein identification data based on the PeptideProphet and ProteinProphet algorithms (60, 61). The protein assignment is based on Occam's razor approach that computes the minimal protein list that best describes the data (61). For these comparisons, protein summaries of the Mascot analyses of the iTRAQ data were created by Scaffold as lists of proteins detected in all three replicates with more than one peptide with a PeptideProphet probability of 95%. For broader comparisons, all proteins detected with more than one peptide and a ProteinProphet probability of 99.9% were also considered. The Scaffold result files for these analyses are available in supplemental File S1.6 together with results from searches of version 15.13 of the Swiss-Prot database (released date, January 19, 2010; 20,277 human sequence entries) such that the data can be freely explored with the Scaffold browser.

As an additional level of reference for these data, comparisons were made with previous transcriptomic measurements from studies of Th2 versus Th0 human cord blood cells (11, 12). These data were determined with three biological replicates using cultures of human naïve CD4+ cells isolated from cord blood that were similarly activated with plate-bound anti-CD3 and soluble anti-CD-28 (Th0 state) with Th2 differentiation induced with the addition of IL-4. The cells were harvested at 2, 6, and 48 h as described previously (11, 12).

Real Time Quantitative RT-PCR

On the basis of the comparison of these proteomics data with previous transcriptomics results (11, 12), several targets were selected, and their expression was evaluated across a wider time series by RT-PCR. These RT-PCR analyses were carried out using a TaqMan ABI Prism 7900 HT instrument (Applied Biosystems) as described previously (62, 63). Primers and probes for EF1α, GATA3, YB1, STAT1, STAT6, IKZF1, SATB1, TCF7, and TBX21 were designed using Primer Express (Applied Biosystems) or Universal ProbeLibrary ProbeFinder (Roche Applied Science) and are detailed in supplemental File S1.7. The quantitative measurements were determined as the threshold cycle (Ct) and normalized using the reference gene EF1α (64) as follows.

equation image

Linear -fold differences between conditions were extrapolated from these normalized values using the following function.

equation image

Kinetic changes were measured by comparing each normalized ΔCt value with the respective base-line value from the T helper cell precursor (ThP) sample.

equation image

The statistical significance of the changes was assessed using a paired t test.

Western Blot Analysis

Western blot analyses were performed with the same sample material used in iTRAQ analysis, and 16 more cultures were made to support these data. An Odyssey system (LI-COR Biosciences, Lincoln, NE) with fluorescently labeled antibodies and direct infrared fluorescence detection was used for these determinations.

The isolated nuclear proteins (10–30 μg; quantified using the Bio-Rad detergent compatible protein assay) were boiled for 5 min with Laemmli sample buffer and resolved with 10% Bis-Tris gels (Criterion XT, Bio-Rad) using XT MOPS running buffer. Following electrophoresis, the proteins were either transferred onto nitrocellulose (Hybond ECL, Amersham Biosciences) or PVDF membranes (Immobilon FL, Millipore). For analyses with the Odyssey system, the IRDye 800- and Alexa Fluor 680-labeled secondary antibodies were used, and the signals were quantified using Odyssey software. Equal loading and transfer of proteins was confirmed by Coomassie staining (51), and quantification of the band intensities was performed with Microcomputer imaging device system software (InterFocus Imaging Ltd., Cambridge, UK) or, in case of whole cell lysate samples, by immunodetection of glyceraldehyde-3-phosphate dehydrogenase. Antibodies for the following proteins were used in these studies: IKZF1, TBX21, SATB1, and STAT1 from Santa Cruz Biotechnology; nuclease-sensitive element-binding protein 1 (Y box-binding protein 1 (YB1)) from Abcam; MAPK (Erk1/2), phospho-MAPK (Thr-202/Tyr-204), phospho-STAT6 (Tyr-641), and PARP1 from Cell Signaling Technologies; STAT6 and GATA3 from BD Biosciences; and TCF7 from Upstate.

RESULTS

Protein Identification and Relative Quantification

In this study, we investigated changes in the nuclear proteome of human naïve T helper cells in the early phases of Th2 cell differentiation using iTRAQ technology. Three biological replicates were made for iTRAQ analysis with triplicate analysis of the sample material from each experiment. Repeated analyses of this complex sample material were performed to improve the opportunities for identification and statistical analysis of the data (65). Furthermore, evaluation of the reproducibility of these protein ratios, from run to run, indicated good correlation between the values determined (detailed in supplemental Files S1.8 and S1.9). Fig. 2a illustrates the relationship between the results from the biological replicates and indicates a central core of proteins detected in all three experiments among a background of less frequently reported proteins and numerous single peptide hits. Of the 903 protein identities reported, 843 were characterized by two or more distinct peptides of which 815 were satisfactorily quantified in all three biological experiments using ProQuant. Typically, these protein determinations corresponded to a median of four peptides and seven calculations per biological experiment. The FPRs for identification were estimated from concatenated database searches to be 0.5% for the proteins that were detected and quantified by ProQuant in all three biological replicates with at least two unique peptide sequences. The attribute of specifying that these should also attain a Mascot score of ≥40 indicated an FPR of 0.2%. Moreover, the implementation of Mascot together with the Scaffold software supported several additional two-peptide identifications and provided an alternative measure of confidence with the calculation of ProteinProphet protein identification probabilities. In previous investigations, researchers have demonstrated that the use of multiple search algorithms can provide the advantage of consensus validation of the search results as well as additional identification data (20, 6668). Similarly with these analyses, there was a high level of corroboration of the qualitative data as well as a small number of results that likely reflected differences in peptide scoring and protein inference. The list of repeatedly detected proteins was assessed in terms of their GO annotations for cellular location. The distribution of GO annotation for these proteins is indicated in Fig. 2b, and their function and process are indicated in Fig. 2, b and c. Although from this annotation it was apparent that a number of cytoplasmic proteins, among others, were co-enriched in this material, a large proportion of the proteins (~50%) are associated with the nucleus. The largest groups for GO processes and functions were described with the broad terms biological process and protein binding, respectively, followed by cell differentiation and nucleic acid binding.

Fig. 2.
Comparison and classification of proteins detected in analysis of nuclear fraction of IL-4-treated anti-CD3/CD28-activated human CD4+ cells. a, the relationship between proteins from the biological replicates (Bio. 1, Bio. 2, and Bio. 3). The numbers ...

In the relation to other studies of the T cell nucleus, ~70% of the proteins detected in all three replicates were previously reported in the Jurkat nucleus data sets from Han and co-workers (34, 35). Also in similarity to the data from Han and co-workers (34, 35), proteins with GO annotation for the nucleus were well represented in these identifications (~450 proteins). Interestingly, approximately a quarter of the nuclear annotated proteins detected in all three replicates were not matched in the Jurkat data. Moreover, there were on the order of 230 nuclear annotated proteins from the Jurkat data sets not detected in our data. A comparison of the proteins that were specific to either set by associated GO terms for function and process indicated no major differences in their classifications. Notable differences from our data set were with the signaling proteins STAT1 and STAT6 (both classified with the GO function signal transducer activity) that are clearly related to the nature of our study. Some differences with proteins of the nuclear lamina (i.e. the lamin proteins) could be attributed to the isolation procedures used. Further representation of these data and their comparison as well as the full lists of peptide and protein identifications are included as supplement material to clarify the numbers of proteins reported and matched and their annotations (supplemental Files S2, S3, and S5).

To facilitate the investigation and summary of the quantitative data, we applied a statistical model that considered each protein and its individual variance in the three biological replicates. Adapting methodology we have successfully demonstrated in microarray comparisons (46), a random effect meta-analysis model was used to combine the individual estimates into an overall estimate of the -fold change and associated Z scores and p values for each protein. For these calculations the weighted protein iTRAQ ratios and their weighted standard deviations from each biological replicate were used. As a measure of the false discovery rate, the Benjamini and Hochberg (55) correction was applied. The distributions of estimated protein ratios are represented as volcano plots of log2(abundance change) versus −log10(p value) in Fig. 3. The iTRAQ ratios indicate changes in protein abundance in the nuclear fraction associated with IL-4 treatment of activated CD4+ cells in comparison with cells that were activated only.

Fig. 3.
Protein abundance ratios determined from iTRAQ labeling of nuclear fraction of IL-4-treated anti-CD3/CD28-activated versus anti-CD3/CD28-activated CD4+ cells. The data from the random effect estimations of the log2(protein ratio) are plotted versus −log ...

It was notable in the quantitative analysis of these data that, with the exception of a set of ribosomal proteins that were enriched in one of the biological replicates, the overall magnitudes of changes detected throughout these experiments were generally not greater than 2-fold. On the basis of previous observations in iTRAQ studies where expression differences greater than 1.2-fold have been confidently identified (5153), we applied an abundance change threshold of >20% together with a p statistic <0.05 to define a group of proteins of interest and potential significance; these thresholds (−log10(p value) > 1.3 and |log2(ratio)| > 0.263) are indicated in Fig. 3. A list of the proteins defined by these criteria is included in Table I, although cytoplasmic ribosomal proteins and keratins are not included in this table but are available in supplemental File S2 as Table 1S. Using these thresholds, 5% of the data is represented (including the former). With the application of the Benjamini and Hochberg (55) correction with a 5% FDR threshold, 2% of the data are retained. Additional proteins that were noted during data processing or are otherwise of general interest in our research are listed in Table I. These include the Th1-specific transcription factor TBX21 (i.e. T-BET), which was detected in one replicate with a decreased abundance indicated in the IL-4-treated cells. Also included are the interferon-related proteins STAT1 and IFI16.

Table I
Comparison of protein abundance changes determined by iTRAQ labeling of nuclear fractions from IL-4-treated anti-CD3/CD28-activated CD4+ cells versus anti-CD3/CD28-activated CD4+ cells at 6 and 24 h with LC-MS/MS analysis

To provide a wider overview of the regulation of the proteins highlighted by their quantitative data, the transcriptomic profiles of eight selected targets were determined for the first 72 h of activation and treatment. These RT-PCR data are illustrated in Fig. 5c. The analyses indicated the accepted trends and differences for the general Th1 and Th2 transcription factors GATA3, STAT1, and TBX21 and support expectations for SATB1 and TCF7. Induction by activation with IL-4 treatment, and activation alone was apparent for YB1, whilst consistent differences with IL-4 treatment were indicated for the IKZF1 data. As the changes relating to STAT6 in Th2 differentiation are associated with its phosphorylation and translocation, the absence of transcriptional differences does not indicate an inconsistency.

Fig. 5.
Proteomic and transcriptomic changes associated with IL-4 treatment of anti-CD3/CD28-activated human CD4+ cells. a, Western blot analysis for selected proteins in the nuclear fraction. The images show representative blots from cells cultured in the presence ...

iTRAQ Data Validation

On the basis of their iTRAQ ratios and associated statistics together with GO annotation, known mRNA expression (12), novelty, and antibody availability, a panel of proteins was selected for validation by WB. These were STAT6, SATB1, TCF7, IKZF1, and (least familiar in relation to T cell differentiation) YB1. Although the known Th1 transcription factors STAT1 and TBX21were not well represented in the MS data, these were also included as protein targets for WB analysis. During the primary handling of the material used for the mass spectrometry-based analysis, WB analyses were performed for phospho-STAT6 to confirm IL-4 signaling. Additional tests were performed for GATA3 to confirm Th2 differentiation status; these data are exemplified in Fig. 4a. Validation of nuclear fractionation was achieved using PARP1 (69) (Fig. 4b). The detection of GATA3 (for the nuclear fraction) also supported the efficacy of this fractionation (included as supplemental File S1.10). To improve the opportunities for detection and provide better discrimination between small changes, the Odyssey infrared fluorescence system was used for these WB measurements (70).

From the WB analyses, validations of quantification and identification were achieved for four of the proteins that were indicated from the iTRAQ data (Fig. 5). These results supported the changes in STAT6 and SATB1 in the original sample material and also in new cultures at these time points. The changes detected for YB1 in association with IL-4 treatment were also confirmed by WB as was the decreased nuclear abundance of TBX21. With the WB analysis of the DNA-binding protein Ikaros (IKZF1), multiple isoforms were detected, the strongest of which was a double band migrating at ~50 kDa. Although there appeared to be some consistency in the increase of these isoforms, the change was not statistically significant. With the mass spectrometry data for IKZF1, it was difficult to discern clear differences because of the absence of isoform-specific peptides. The decreased nuclear abundance indicated for TCF7 in the iTRAQ data was not statistically significant in the WB data. For STAT1, a familiar protein in the context of interferon-related pathways and Th1 cells, the changes in the iTRAQ and WB measurements were not significant for the nuclear fractions at 24 h.

DISCUSSION

Multiplex Relative Quantification of Early Phases of Th2 Differentiation

Using 4-plex iTRAQ methodology, protein identifications from the nuclear fraction of human CD4+ cells under Th2-promoting conditions were attained with relative quantification compared with activation alone for 6- and 24-h time points. Whereas large scale proteomics studies of the T cell nucleus have been made with Jurkat cells, to our knowledge this data set presents the largest such set of identification data from the nucleus of human cord blood CD4+ cells. Overall, there were on the order of 800 proteins detected with two or more peptides that were quantified in all three replicates, half of which had GO annotation for the nucleus. In spite of the differences in cell treatment and isolation of the nuclear fraction, in comparison with the extensive Jurkat data sets of Han and co-workers (34, 35) our measurements provide a complementary view of the T cell nuclear proteome. In consideration of all the proteins detected with more than one unique peptide and with a ProteinProphet identification probability of 99.9%, on the order of 1120 proteins were detected in these experiments of which 566 had GO annotation for the nucleus and 185 of which are not common in the comparisons with Jurkat data. Because of experimental dissimilarities, it is not appropriate to conclude that these differences indicate that the proteins may be less abundant or absent in Jurkat cells. Further comparisons with other Jurkat data, e.g. from targeted interactome studies in the Jurkat nucleus (71), did indicate additional matches (details are included in supplemental File S5).

With these measurements, we aimed to identify protein abundance changes associated with the differentiation process with potential mechanistic relevance to the early phases of the differentiation process. Notably, although some of the changes associated with this process may only be subtle or involve post-translational modifications or alternative isoforms not detected in our data, no large differences in protein abundance were observed in these analyses. Potential limitations to our observations were likely met by the challenges of the sample complexity versus the speed and dynamic range of the MS instrument. Moreover, with global peptide labeling, as achieved with the iTRAQ method, the presence of a background of highly abundant proteins can affect the normalization and thus reduce relative abundance differences calculated. Similarly, the transfer of multiple precursors from complex mixtures can affect the reporter ion signals, masking abundance changes (72). Targeted analysis, e.g. amino acid-specific labeling and fractionation, such as ICAT, or targeting post-translational modifications could have improved sensitivity. Similarly, changes in sample fractionation as well as the MS/MS data-dependent acquisition method may have resulted in additional data.

To represent the changes in the data as a whole, we used a random effect meta-analysis model and applied a significance threshold of p < 0.05 together with a fold change larger than 20% to indicate potentially interesting expression changes. In addition to the latter thresholds, we used the Benjamini and Hochberg (55) correction to estimate the FDR. On the basis of these criteria, a subset of proteins that indicated consistent change was defined (Table I). From the WB validation of a selection of these proteins, the results generally supported the direction of the iTRAQ-determined changes (i.e. increases and decreases). Notably, however, some of these determinations were close to the limit of discrimination, and accurate normalization was an important and limiting factor. The validations were based on numerous biological replicates and in general were of a similar magnitude. With STAT6, however, the iTRAQ-derived values were notably less than those suggested by the WB data. Although such differences can reflect technical reproducibility and biological variability, it was apparent that the iTRAQ reporter ions were close to the limit of quantification and only based on just a few peptide measurements (supplemental File S4). Similarly, it has been demonstrated previously that the precision of iTRAQ measurements is poorer with lower concentration analytes (73) in addition to the other limitations of iTRAQ quantification from complex mixtures as discussed above (72). Furthermore, to screen for changes of proteins with a lower spectral count, we permitted the inclusion of protein quantifications based on five measurements. Although calculation of the FDR provides an extra level of control, in cases where the data is scarce, the values should be evaluated with scrutiny. Alternatively, on a wider scale, filters based on the minimum number of calculations for each replicate could be applied.

Included in the changes that were detected within the FDR criteria (<5%) were several T cell-related cytoplasmic and membrane proteins (e.g. CD3 and CD5); some of these were also reported in the data sets of Han and co-workers (34, 35) as indicated in Table I. For these observations, it is possible that with the concentration of lysis buffer used (0.2% Nonidet P-40) some of the hydrophobic membrane proteins were not sufficiently dissolved and thus co-isolated with the nuclear pellet. Among the proteins highlighted, there are also associations reported for GLU2B (74) and GRB2 (75) in T cell activation and differentiation. Other observations reported in Table I included an increased abundance of the dual specificity mitogen-activated protein kinase kinase 3 (MP2K3) indicated at 6 h that is known to catalyze phosphorylation of mitogen-activated protein kinase p38 and has been reported previously in the nucleus (76). An increase was also indicated for transcription initiation factor TFIID subunit 10 (TAF10) at 6 h. TAF10 is associated with several complexes involved with the modulation of transcription, and although a number of the other known components of these complexes were also observed in these data, i.e. TAF4, TAF6, TAF7, and TAF9, none of these showed significant changes in abundance. Among the data from the iTRAQ measurements, in general, there were no proteins that showed changes at both time points. Without further measurements, it is difficult to determine the significance of these seemingly transient changes.

In the assessment of these data, we also made comparisons with transcriptomic measurements from this system. Such proteomic and transcriptomic comparisons have been described previously (77, 78), including measurements from Jurkat T cells (35). Although the expression of proteins is often regulated at the level of transcription, differences in mRNA stability, translational regulation, and protein turnover limit the direct comparison of mRNA and proteomics data at a set point in time (79). Moreover, measurements may be difficult to account for or inappropriate when targeting subproteomes. However, from the comparisons made between our proteomics data and transcriptomic measurements across a wider time window, a number of the changes were reflected at the mRNA level (Fig. 5c). The differences are plotted as ΔΔCt as described above.

Proteomic Changes Characteristic of Th2 Differentiation

The changes observed with IL-4 treatment reflected the importance of STAT6 and the accumulation of nuclear phospho-STAT6 in Th2 differentiation (80, 81). However, although changes in the total level of nuclear STAT6 were indicated in our iTRAQ experiments, these lacked detail on the proportions of phospho-STAT6. Noticeably, in this overall data set, only a small number of phosphopeptides were detected, none of which were detected in all three biological replicates. It is likely that many of the phosphopeptides could have been lost in the SCX fractionation (82) and moreover may have been difficult to detect without any enrichment steps because of their relative stoichiometry. Nevertheless, changes for total STAT6 were confirmed by Western blotting, and similarly, the nuclear phospho-STAT6 levels were increased. In further support of the integrity of the cultures with respect to Th2 differentiation, the Western blots for GATA3 followed the expected line of change, i.e. an increased protein level with IL-4 stimulation at 6 and 24 h. The failure to detect GATA3 in the mass spectrometry data was attributed to its low level of expression in the stimulated naïve T cells at these time points and limitations of detection from such complex mixtures. Also, in consideration of Th1-related proteins, the decreasing level of TBX21 in the nuclear fraction in response to IL-4 treatment indicated in the mass spectrometric data was confirmed in the Western blot analysis. TBX21 controls the expression of the Th1 cytokine interferon-γ and directs Th1 lineage development. In keeping with this change, reduced levels of other interferon-related proteins would be expected (1517) as indicated by a number of moderate changes in these data (Table I). With the corresponding transcriptomics data for these proteins, more distinct changes were observed along the extended time series (0.5–72 h), e.g. GATA3, TCF7, and STAT1 (Fig. 5c).

Our earlier published results have also indicated that special AT-rich sequence-binding protein 1 (SATB1) is up-regulated at early stages of Th2 polarization of human CD4+ T cells, both at the mRNA and total protein level (11). In keeping with this, an increased abundance of SATB1 in the nuclear fraction of the IL-4-treated human CD4+cells was observed in the iTRAQ data and supported by the Western blot validations. Although the importance of SATB1 on IL-4-induced Th2 differentiation was first shown by its regulation of the expression of the Th2 cytokines IL-4, IL-5, and IL-13 in the mouse (83), recent studies with human CD4+ cells suggest that SATB1 mediates the expression of GATA3 and Th2 cytokines in a wnt/β-catenin-dependent manner. In relation to this, it is notable that although lymphoid enhancer factor/TCF7 transcription factors associate with β-catenin in canonical wnt signaling leading to the transcription of its target genes, SATB1 has recently been shown to competitively influence the TCF7 binding to β-catenin (84). Taken together, it has been proposed that cell fate and differentiation could be influenced through the balance of expression, post-translational modifications, and interaction of TCF7, SATB1, and β-catenin (84) as indicated by the relative abundance of TCF7 and SATB1 in Th1 and Th2 cells (11). Additionally, in recent studies in mouse, it has been demonstrated that TCF7 initiates Th2 differentiation in activated CD4+ cells through activation of the GATA3 promoter (32), further indicating the role of wnt signaling in GATA3 regulation and the balance of nuclear activity of TCF7 and SATB1 binding. Studies from our group on human Th cell differentiation (96), including SATB1 siRNA measurements (97), indicate that of the proteins highlighted in our proteomic measurements TRI22, IKZF1, IFI16, and PSB8 are both SATB1- and IL-4/STAT6-dependent, further supporting the relevance of the changes detected.

With these comparisons of activation and IL-4-induced Th2 polarization, an increased abundance of YB1 in the nuclear fraction was observed. YB1 is a multifunctional protein involved in processes such as cell proliferation, DNA repair, and stress responses as reviewed by Kohno et al. (85). In regard to these roles, it was observed from the transcriptomic measurements that YB1 was induced similarly with IL-4 and activation alone (Fig. 5c). When translocated to the nucleus, YB1 represses genes associated with cell death, including the Fas cell death-associated receptor and the p53 tumor suppressor gene (8588). In T cells, the triggering of the Fas receptor (FasR) by the Fas ligand, leading to activation of downstream caspase pathways (8992), takes place during activation-induced cell death and is regarded as a method for maintaining T cell homeostasis and eliminating autoreactive cells. Notably, in relation to this, we have also observed that IL-4 treatment of activated human CD4+ cells decreases caspase-3 activity and alters expression of several proteins involved in its upstream regulation, including FasR (19). In view of the observed changes in the nuclear levels of YB1 and its associations with FasR repression, we selected the use of YB1 siRNA (93) to investigate its effect upon FasR expression in these early phases of Th2 differentiation. However, using YB1 siRNA and measuring the expression of the FasR by fluorescence-activated cell sorting in both activated and IL-4-treated activated CD4+ cells, we did not find any consistent change in cell surface FasR expression in response to YB1 knockdown at the 24-h time point (data not shown). Details of the siRNA constructs and methods are provided in supplemental File S1.11.

Recent studies in the mouse have shown that IKZF1 is a regulator of Th2 cell differentiation where it promotes chromatin accessibility in the nucleus and thus activates Th2 gene expression (i.e. IL-4, IL-5, and IL-13) and indirectly regulates the expression of Th2- and Th1-specific transcription factors (GATA3 and cMAF and TBX21 and STAT1, respectively) (94). Additional studies (in the mouse) have indicated that IKZF1 silences TBX21 expression and production during Th2 differentiation (95). In the transcriptomic comparison of IL-4 treatment of activated human CD4+ cells, a greater expression of IKZF1 was consistently observed (Fig. 5c). With the protein measurements from the nuclear fraction, the WB validations indicated isoform-specific changes with IL-4 treatment (Fig. 5b).

In summary, from these investigations of proteomic changes in the nuclear fraction of naïve human CD4+ cells, a number of subtle differences were detected in the relative abundance of Th1- and Th2-related proteins in the early stages of IL-4-stimulated Th2 differentiation. In addition to differences in familiar proteins, some differences were indicated for proteins less well characterized or novel in this context, including changes in the nuclear abundance of SATB1, TCF7, and IKFZ1 that are in keeping with recent data from this system. Further proteomics studies of a wider time series could provide clearer detail of changes in the differentiation process. Targeted efforts, for example measuring changes in protein phosphorylation, would produce more specific information and reduce sample complexity. Overall, this data set presents a collection of 900 confident and reproducible protein identifications from human umbilical cord blood CD4+ cells that complement and supplement previous proteomics data from the study of the T cell nucleus. The spectral data from the Mascot analyses of these data are available as supplemental material that can be previewed using the Scaffold browser, and the data are available in their raw format from the Tranche project (https://proteomecommons.org/dataset.jsp?i=NQhdNouKyMteqAmy5FwkeYRSt7XG1n0f3RGPvrwWy0vQEQjKAHl7KQYXqcMQ18ROm4ThCVQCc5fHaJHi0LdeHOp%2fiz8AAAAAAAAHwg%3d%3d; see also supplemental Files S1.6 and S1.12). Additional supplemental material is cited in the text.

Supplementary Material

Supplemental Data:

Acknowledgments

We acknowledge Applied Biosystems for help and generosity (Rod Watson) and for advice with aspects of data processing (Sean Seymour and Alpesh Patel). Professor Sanjeev Galande of the National Centre for Cell Science, Pune, India, is thanked for sharing details of studies on SATB1. These studies were performed with the assistance of the Turku Centre for Biotechnology Proteomics core facility, Sarita Heinonen (RT-PCR), Marjo Hakkarainen, and the Finnish Microarray Centre.

* This work was supported by The National Technology Agency of Finland, the Academy of Finland (SysBio Program and Grant 8209083); the Sigrid Jusélius Foundation; the TurkuUniversity medical faculty research fund; The National Graduate School inComputational Biology, Bioinformatics, and Biometry; and EuropeanCommission Seventh Framework Grants EC-FP7-SYBILLA-201106, EC-FP7-NANOMMUNE-214281, and EC-FP7-DIABIMMUNE-202063.

An external file that holds a picture, illustration, etc.
Object name is sbox.jpg This article contains supplemental files S1 to S5. The supplements S1.1–S1.13 are included in S1, of which S1.13 details the contents of the other files. Table 1S is included in S2.

1 The abbreviations used are:

Th
T helper
FasR
Fas receptor
FDR
false discovery rate
FPR
false positive rate
IKZF1
Ikaros
IL
interleukin
iTRAQ
isobaric tags for relative and absolute quantification
MMTS
methyl methanethiosulfonate
SATB1
special AT-rich sequence-binding protein 1
SCX
strong cation exchange
STAT
signal transducer and activator of transcription
TCF7
transcription factor 7
YB1
nuclease-sensitive element-binding protein 1 (Y box-binding protein 1)
GO
gene ontology
WB
Western blotting
Erk
extracellular signal-regulated kinase
Ct
threshold cycle
Bis- Tris
2-[bis(2-hydroxyethyl)amino]-2-(hydroxymethyl)propane-1,3- diol
MAPK
mitogen-activated protein
siRNA
short interfering RNA
c-MAF
Transcription factor Maf
GATA3
trans-acting T-cell-specific transcription factor GATA-3
TBX21
T-box transcription factor TBX21
ThP
T helper cell precursor.

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