- Open Access
Splicosomal and serine and arginine-rich splicing factors as targets for TGF-β
Fibrogenesis & Tissue Repair volume 5, Article number: 6 (2012)
Transforming growth factor-β1 (TGF-β1) is a potent regulator of cell growth and differentiation. TGF-β1 has been shown to be a key player in tissue remodeling processes in a number of disease states by inducing expression of extracellular matrix proteins. In this study a quantitative proteomic analysis was undertaken to investigate if TGF-β1 contributes to tissue remodeling by mediating mRNA splicing and production of alternative isoforms of proteins.
The expression of proteins involved in mRNA splicing from TGF-β1-stimulated lung fibroblasts was compared to non-stimulated cells by employing isotope coded affinity tag (ICATTM) reagent labeling and tandem mass spectrometry. A total of 1733 proteins were identified and quantified with a relative standard deviation of 11% +/− 8 from enriched nuclear fractions. Seventy-six of these proteins were associated with mRNA splicing, including 22 proteins involved in splice site selection. In addition, TGF-β1 was observed to alter the relative expression of splicing proteins that may be important for alternative splicing of fibronectin. Specifically, TGF-β1 significantly induced expression of SRp20, and reduced the expression of SRp30C, which has been suggested to be a prerequisite for generation of alternatively spliced fibronectin. The induction of SRp20 was further confirmed by western blot and immunofluorescence.
The results show that TGF-β1 induces the expression of proteins involved in mRNA splicing and RNA processing in human lung fibroblasts. This may have an impact on the production of alternative isoforms of matrix proteins and can therefore be an important factor in tissue remodeling and disease progression.
Remodeling of the airway wall, which involves altered extracellular matrix deposition, is an important feature in airway diseases such as asthma and chronic obstructive pulmonary disease (COPD) . This process has been suggested to be associated with aberrant wound healing, dependent on the presence of myofibroblasts [2, 3]. Differentiated myofibroblasts can be distinguished from fibroblasts by de novo synthesis of α-smooth muscle actin (α-SMA), increased expression of alternatively spliced fibronectin (EDA) and assembly of stress fibers . The growth factor TGF-β1 has been shown to play an important role in the differentiation process inducing the expression of alternatively spliced fibronectin, which leads to a subsequent increased expression of α-SMA  and other cytoskeletal proteins . In addition, TGF-β1 is a potent inducer of various extracellular matrix components such as collagen , fibronectin , and the proteoglycans: biglycan [9, 10] and versican [11–13].
During constitutive and alternative splicing of gene products, splice site selection is regulated by altering initial binding of serine-arginine-rich splicing factors (SR proteins) to pre-mRNA. These factors contain an N-terminal RNA recognition motif that allows binding to pre-mRNA and a C-terminal serine-arginine-rich domain that mediates protein-protein interactions. Different exon-splicing enhancers and silencers are recognized by specific subsets of SR proteins , which include SRp20, SRp30a (ASF/SF2) SRp30c, 9 G8, SRp40, SRp55, SRp70, SRp75, and SC35 [15–18]. The ratio of different SR proteins and the presence of exon-splicing enhancers and silencers are factors that influence further assembly of splicosomal proteins. SR proteins generally have nuclear localization but some members such as ASF/SF2, 9 G8, and SRp20 also function as mRNA transporters between nucleus and the cytoplasm . The activity of SR proteins is tightly regulated via dynamic events of phosphorylations and dephosphorylations in different domains of the proteins . The phosphorylation pattern of SR proteins not only influence their activity and function but also play a role in sorting SR proteins within the nucleus . Moreover, hypo-phosphorylation of one domain of SR proteins serves as a nuclear export signal .
One important aspect of TGF-β1-driven myofibroblast differentiation is the exon inclusion of EDA in fibronectin , a process that is not fully understood. However, induced expressions of the splicing factors SRp40, SRp20, or ASF/SF2 have been suggested to stimulate inclusion of EDA suggesting that splice site selection is regulated by quantitative changes in multiple factors [24, 25]. Several other matrix molecules have been shown to have different splice variants such as biglycan , versican , decorin , and collagen . The exact role of these splice forms has not yet been established.
To investigate the mechanism of TGF-β1-induced alternative splicing, we employed isotope coded affinity tag (ICATTM) reagent labeling and tandem mass spectrometry  to identify nuclear proteins and characterize the changes in their expression upon TGF-β1 stimulation and focus on proteins involved in the splicing process. We were able to provide a detailed quantitative expression pattern of 76 proteins involved in mRNA splicing and RNA processing. The results showed that TGF-β1 altered the relative expression of serine and arginine-rich splicing factors that control splice site selection and promote alternative splicing.
TGF-β1 induces myofibroblast-like characteristics in fibroblasts
TGF-β1 stimulation for 24 h increased the immuno-reactivity for α-SMA in human embryonic lung fibroblasts (HFL-1) cells, which was accompanied by a change in phenotype as shown by immunofluorescence (Figure 1A). These results were further confirmed by western blot that showed a significant two-fold increase of α-SMA upon TGF-β1 stimulation for 48 h (P < 0.05) (Figure 1B). Following TGF-β1 stimulation HFL-1 cells also had an increased immuno-reactivity for prolyl 4-hydroxylase (Figure 1C), which catalyzes post-translational formation of proline to 4-hydroxyproline in collagens. These results could not fully be confirmed by western blot, which showed a two-fold increase after 48 h (P < 0.06) (Figure 1D).
TGF-β1 significantly increased the expression of both fibronectin and EDA fibronectin. However, following TGF-β1 stimulation the relative ratio between EDA fibronectin and fibronectin was significantly increased over time as shown by q-PCR (Figure 2A). This was confirmed by western blot showing that TGF-β1 increased the relative expression of EDA fibronectin compared to fibronectin from 269% at 24 h to (P < 0.01) to 526% at 48 h (P < 0.001) (Figure 2B). These data show that TGF-β1 may induce myofibroblast differentiation and this is accompanied by an altered splicing pattern, exemplified by the increase in alternatively spliced isoforms of fibronectin.
Strategy for identification and relative quantification of nuclear proteins
To address the question whether TGF-β1 stimulation affects nuclear proteins that are involved in the splicing process, we employed isotope coded affinity tag (ICATTM) reagent labeling and tandem mass spectrometry. Our experiments showed that the expression of EDA fibronectin increased from 6 to 48 h of TGF-β1 stimulation (Figure 2A), which indicates that an alternative splice site selection was induced after 24 h. We therefore decided to examine the expression of nuclear proteins at this time point. Figure 3 shows a schematic overview of the workflow used for the identification and relative quantification of proteins in the nuclear fractions [30–32]. Around 2500 proteins were identified in multiple LC-MS/MS experiments. This list was reduced to approximately 2000 unique proteins after consolidating the peptide-protein assignments. However, approximately 1,700 of these could be quantified after the proper normalization of the relative abundances of ‘heavy’ and ‘light’ ICATTM reagent labeled peptides. After classifying the proteins based on gene ontology , 76 proteins involved in pre-mRNA splicing and RNA processing were selected and divided into 13 functional groups as shown in Figure 4 and in Additional file 1: Table S1. The most abundant group was classified as heterogeneous ribonucleoproteins and contained 19 proteins (hnRNP). The second most abundant group (12 proteins) was proposed to be involved in splice site selection and the third most abundant group, containing 10 proteins, was classified as splicing factors. Nineteen proteins were subunits of the snRNPs or associated with the U1, U5, or U4/U6 snRNPs. In addition, helicases and peptidyl-prolyl cis-isomerases were detected. The relative standard deviation (RSD) was calculated from all ratios of the total list of identified proteins matched by more than one peptide and the average of this error was found to be 11% +/− 8. The proteome wide error was less than 20%, and in the case of the splicing factors the majority of RSDs was less than 20%.
Additional file 1: Table S1 show the relative expression levels (defined as TGF-β1 stimulated/control) of the individual splicing related proteins calculated from four unique experiments from independent cell cultures and ICAT workflow runs.
Interestingly, TGF-β1 altered the expression of splicing factors and additional proteins involved in splice site selection. The expression of splicing factor U2 small nuclear ribonucleoproteins auxiliary factor (65 kDa) (U2AF), and SRp20 were significantly increased by TGF-β1 (1.09-fold and 1.24-fold, respectively) (Additional file 1: Table S1). Furthermore, splicing factor SRp30c was significantly repressed (0.79-fold) following TGF-β1 stimulation. The relative expression of all proteins involved in splice site selection (grouped as splice site selection and splicing factors in Additional file 1: Table S1) was further statistically analyzed as shown in Figure 5. The data show that TGF-β1 significantly repressed the expression of SRp30C labeled ‘2d’ compared to all other splicing factors except SRp 9 G8 (2b). SRp20 (2c) was significantly increased compared to SRp1 (2a) and SRp30c (2d). When comparing the levels of SRp20 with SRp30c, the actual difference between these two splicing factors was 1.6-fold. Several other proteins were significantly changed upon TGF-β1 stimulation, such as RNA-binding region containing proteins, U5 snRNP 100 kDa protein, U5 small nuclear ribonucleoprotein 200 kDa, CGI-59 protein, and Cisplatin resistance-associated over expressed protein. In addition the expression of the helicase Nucleolar RNA helicase II (Nucleolar RNA helicase Gu) was also significantly different.
Western blot analysis of individual SR protein expression
Phosphorylated SR proteins from TGF-β1-stimulated HFL-1 cells were analyzed by western blots using an antibody as previously described [34, 35]. This antibody detects a conserved phospho-epitope on SR proteins, which does not coincide with absolute protein levels. We detected a complete array of SR proteins, including SRp75, SRp55, SRp40, SRp20, and an additional band that corresponds to proteins that co-migrate around 30 kDa (ASF/SF2, SC35, or SRp30c)  (Figure 6A and Table 1). TGF-β1 induced an increase of all the detected SR proteins. A moderate increase was observed at 6 h but at 24 and 48 h the increase was more pronounced (Figure 6A and B). Moreover, TGF-β1 triggered a 3.2-fold increase of the SRp75 at 24 h (P < 0.05) that was preserved at 48 h. SRp55 was 3.0-fold increased at 24 h (P < 0.05) and then slightly decreased at 48 h. SRp40 was continuously increased over time from a 3.5-fold elevation at 24 h (P < 0.05) to a 4.2-fold increase at 48 h. There was 3.4-fold increase of the band that was detected at 30 kDa at 24 h (P < 0.05) and the same increase was retained at 48 h. SRp20 was elevated 8.1-fold compared to untreated cells at 24 h (P < 0.05) which declined to 6.7-fold at 48 h (Figure 6B). To verify the TGF-β1-induced increase of SRp20 we performed separate western blots using an antibody that recognizes the actual protein and does not discriminate between phosphorylated and non-phosphorylated variants (Figure 6C). With this antibody there was a 1.8-fold increase of SRp20 at 24 h (P < 0.05) and a 2.4-fold increase at 48 h (P < 0.05), which supports the results from Additional file 1: Table S1.
Cellular localization of SR proteins and SRp20 following TGF-β1 stimulation
Next, we investigated how TGF-β1 stimulation influenced the cellular localization of SR proteins and SRp20 by immunofluorescence. The staining pattern of the splicing factors, using the anti-phospho SR proteins antibody, was exclusively nuclear (Figure 7). The staining was more intense at 48 h but this could surprisingly not be observed at 24 h of TGF-β1 stimulation compared to untreated cells. In addition the staining at 48 h was more speckled but not to the same extent at 24 h TGF-β1 stimulation. The staining when using the SRp20 antibody was mainly nuclear in untreated cells and after 24 h of TGF-β1 stimulation although some faint extra-nuclear staining also could be observed ( 8). However, after 48 h TGF-β1 stimulation SRp20 was both located intra- and extra-nuclear and in addition the staining was more speckled and intense.
In the present study the role of TGF-β1 on the expression levels of proteins involved in mRNA splicing and RNA processing was examined with a quantitative proteomic approach. We observed that TGF-β1 altered the relative ratio of splicing factors that may be important for alternative splicing of proteins. One such example was that TGF-β1 affected the levels of splicing factors possibly of importance in EDA fibronectin production, suggesting a regulatory role in myofibroblast differentiation. These results indicate that TGF-β1 may contribute to tissue remodeling and disease progression by meditating mRNA splicing and the production of alternative isoforms of proteins.
TGF-β1 plays an important role in normal wound healing but is also a central player in the development of fibrosis and tissue remodeling. TGF-β1 has been shown to induce the production of various extracellular matrix components, such as collagen , fibronectin , and proteoglycans [11–13, 36], that are elevated during disease. In the present study we verified that TGF-β1 triggered a cellular phenotypic switch of lung fibroblasts resulting in a myofibroblast-like phenotype that express α-SMA, as previously described . In addition, TGF-β1 induced production of alternative splicing variants of fibronectin. These events were accompanied by alterations in the relative ratios of proteins involved in mRNA splicing and RNA processing. Alternative splicing is an important aspect of gene regulation and results in dramatic biological consequences. It has been estimated that as much as 60% of genes undergo alternative splicing  and 15% of human genetic diseases are caused by mutations that destroy functional splice sites or generate new sites . Splicing of mRNA is carried out by the spliceosome, a large nuclear macromolecular complex of five small nuclear ribonucleic particles (snRNPs) and 50–100 polypeptides . In the current study TGF-β1 stimulation altered the relative expression of 76 proteins involved in RNA splicing and processing which indicate that TGF-β1 may be an important regulator for this process.
The ICAT results were verified by western blots that showed a general increase of phosphorylated SR proteins following TGF-β1 stimulation. The increased levels of SRp20, SRp40, and SRp75 from the ICAT experiments were consistent with the western blots (Table 1 and Additional file 1: Table S1). SRp20 was found to be induced by both ICAT and western blot using the antibody detecting the absolute protein level. However, when using the antibody that recognized phospho-epitopes of SRp20 then it was further induced. These data may suggest that TGF-β1 may influence the level of phosphorylation of SR proteins which is important for their function and localization. These results were further confirmed with immunofluorescence that indicated an increase of SRp20 accompanied by extra-nuclear localization. Some SR proteins, including SRp20, have in addition to their nuclear functions also been shown to be involved in shuttling mRNA to extra-nuclear localizations , which explains the staining pattern. Moreover, when using the antibody that detect phosphorylated SR proteins then the staining was strictly nuclear which may seem contradictory as SRp20 is one of the protein targets for the antibody. However, it has been shown that hypo-phosphorylation is a signal for nuclear export which may explain the difference in staining pattern.
There was a discrepancy in the expression levels of SRp55 as it was induced in the western blots and repressed in the ICAT dataset. A possible explanation for this is that the used antibody is directed against a conserved phospho-epitope and does not coincide with absolute protein levels. In addition, TGF-β1 changed the expression of several other proteins such as U5 associated proteins, U5 small nuclear ribonucleoprotein 200 kDa, U5 snRNP 100 kDa protein, and helicases, RNA-dependent helicase p72 and the RNA helicase II/Gu protein, all which have been shown to induce conformational changes in the spliceosome [41–43]. This suggests that TGF-β1 also can affect the splicing process via conformational changes of the spliceosome. In addition, we found one member of the hnRNPs family to be repressed, which is of interest since members of the hnRNPs competitively inhibits binding of the splicing factors to the immature mRNA . Splicing of mRNA is a complex operation which involves the activity of multiple proteins. It has been suggested that the relative ratios of proteins involved in selection of splice-sites and splicing factors may be determinants of splice site selection and alternative splicing [45, 46]. The experimental setup in this study enabled direct comparison of relative expression levels within these groups of protein (Figure 5). Our data support the idea that relatively small up- and down-regulation of different splicing factors may regulate splicing of a specific mRNA.
The ICAT experiments were chosen at a time-point where the initial changes in fibronectin splicing pattern was observed (t = 24 h) and thus, the quantification of the splicing factors and hnRNPs was made at a time point where alternative spliced sites were selected. We found that the expression of SRp20 was induced and that the expression of SRp30c was repressed. The role of SRp30c in alternative splicing of fibronectin is unclear. However, SRp20 has previously been shown to promote alternative splicing of EDB in fibronectin when induced and to inhibit EDA splicing in chondrocytes [26, 47]. In HeLa cells both the levels of EDA + and EDA- fibronectin mRNA were suppressed when over expressing SRp20, . It has been reported in other studies that SRp30a (ASF/SF2) [48, 49], 9 G8 , and SRp40 [25, 47] have positive effects on EDA inclusion. We propose that TGF-β1 mediates differential splicing of fibronectin by altering the relative expression and/or phosphorylation pattern of several of these splicing factors, which interact to promote alternative splicing. During the remodeling processes, EDA and EDB are included into the mature mRNA to generate splice isoforms . These alternative splice isoforms promote cell attachment and facilitates cell migration  and have been found to be elevated in fibrotic tissue  and malignant human tumors . TGF-β1 is known to induce an increase of EDA and EDB fibronectin in both fetal and adult fibroblasts . Collectively, these data indicate that TGF-β1 not only stimulates myofibroblast differentiation and the expression of ECM proteins, but also may contribute to alternative splicing.
In summary, we have shown that TGF-β1 may alter the expression levels of the splicing factors that regulate alternative splicing of matrix proteins. This may have an impact on the production of alternative isoforms of matrix proteins and suggests a novel mechanism of how TGF-β1 mediates tissue remodeling and disease progression.
Cell culturing and TGF-β1 stimulation
Human embryonic lung fibroblasts (HFL-1) (ATCC, Manassas, VA, USA) were sub-cultured in Eagles minimum essential medium (EMEM) supplemented with 1% glutamine and 10% fetal calf serum (FCS) and PEST. Before experiments cells were grown to confluency and were starved overnight in Dulbecco’s modified Eagle medium (DMEM) with 0.4% FCS. Cells were washed in PBS and were then incubated with or without TGF-β1 (10 ng/mL) (R&D Systems Abingdon, UK) for the time-points indicated in the figures. Experiments were performed in passage 17–22.
Cells were grown under standardized conditions with or without TGF-β1 (10 ng/mL) for 6, 24, or 48 h and whole cell lysates were prepared using lysis buffer (50 mM Tris–HCl, 500 mM NaCl, 1% NP-40, 10% glycerol, 10 mM MgCl2, pH 7.4) containing the protein inhibitor cocktail complete mini (1 mM PMSF, 1 μg/mL Aprotinin, 1 μg/mL Pepstatin, 1 μg/mL Leopeptin, Roche, Manheim, Germany). Samples were solubilized in Laemmli’s buffer and equal amounts of total protein (10 μg) were loaded and separated by electrophoresis on 4–12% Bis-Tris Gels (Invitrogen, Gibro, Carlsbad, CA, USA). The proteins were blotted to PVDF membranes (Immobilon-P Transfer Membrane, Millipore Corporation, Billerica, MA, USA). Membranes were incubated with antibodies against: a-SMA (Abcam, Cambridge, UK), prolyl 4-hydroxylase (Acris antibodies, Hiddenhausen, Germany), fibronectin (Dako, Glostrup, Denmark), EDA-fibronectin (Abcam, Cambridge, UK), GAPDH (Santa Cruz Biotechnology, Inc. Santa Cruz, CA, USA), Phospho-SR proteins (Zymed Laboratories, San Francisco, CA, USA), and SRp20 (Zymed Laboratories, San Francisco, CA, USA). Bound antibodies were visualized by peroxidase-conjugated secondary antibodies and enhanced luminescence (AmershamTM western blotting Detection Reagents, GE Healthcare, Uppsala, Sweden) with exception for the blot against phospho-SR proteins where Dy-light 800 nm conjugated secondary antibodies (Cell Signaling Technology Inc., Boston, MA, USA) was used. The luminescence/fluorescence signal was detected on Odyssey® FC imaging system (LI-COR Biosciences, Lincoln, NE, USA). Exposure times were standardized so that all samples were treated the same way for each antibody. Individual bands were quantified with densitometry using the Quantity One software version 4.6.1 (BIORAD Laboratories, Hercules, CA, USA). Data are based on four individual sets of experiments.
Fibroblasts (7000/well) were grown overnight on chamber slides and were then incubated with or without TGF-β1 24 and 48 h. Cells were then fixed in 4% formaldehyde for 15 min and permeabilized with 0.1% Triton X for 30 min. After blocking in 2% BSA-TBS containing 5% goat serum (Vector laboratories, Burlingame, CA, USA) for 30 min, cells were incubated with primary antibodies against: a-SMA (Abcam, Cambridge, UK), prolyl 4-hydroxylase (Acris antibodies, Hiddenhausen, Germany), Phospho-SR proteins (Zymed Laboratories, San Francisco, CA, USA), and SRp20 (Zymed Laboratories, San Francisco, CA, USA) and with secondary antibodies: Alexafluor 555-conjugated goat anti-mouse antibody and Alexafluor 555-conjugated goat anti-rabbit antibody (both from Molecular Probes Invitrogen, Eugene, OR, USA). To stain nuclei, cells were incubated with DAPI (Molecular Probes Invitrogen, Eugene, OR, USA). Glasses were mounted with mounting media (Dako, Glostrup, Denmark) and photographed using a TE2000-E fluorescence microscope (Nikon, Tokyo, Japan) equipped with a DXM1200C camera (Nikon).
RNA extraction and cDNA synthesis
Cells were grown under standardized conditions with or without TGF-β1 (10 ng/mL) for 6, 24, or 48 h. Total RNA was isolated from cells using RNeasy (Qiagen, GmBH, Hilden, Germany) according to the manufacturer´s instructions. The quantity of RNA was measured by spectrophotometry using a NanoDrop ND-100 (Nano Drop Technologies, Delaware, MD, USA). Total RNA (1 μg) was reverse-transcribed using superscript II according to the manufacturer’s manual (Invitrogen, Carlsbad, CA, USA) and stored at −70°C.
Five μL of cDNA (diluted 1:250) was mixed with 15 μL SYBR-green mixture (PE Biosystems, Foster City, CA, USA) and amplified by real-time RT-PCR using Stratagene MX3005P QPCR system (Agilent Technologies, Santa Clara, CA, USA). Initially the samples were held for 2 min at 50°C then for 10 min at 95°C; they were then cycled for 40 cycles of 30 s at 95°C, 1 min at 58°C, and 1 min at 72°C. Each sample was analyzed in triplicate. Reactions were performed using MX3000P 96-well plates (Agilent Technologies, Santa Clara, CA, USA). All primers were constructed using the online Primer 3 program (http://frodo.wi.mit.edu/primer3/) and they were ordered from A/S DNA Technology (Risskov, Denmark). The following primers were used. Fibronectin forward: CGA TCA CTG GCT TCC AAG TT, and reverse: TCC GAG CAT TGT CAT TCA AG. Fibronectin-EDA forward: AAT CCA AGC GGA GAG AGT CA, and reverse: CGT AAA GGG CTC AGC TCA AG. S18 forward: CGA ACG TCT GCC CTA TCA AC, and reverse: TGC CTT CCT TGG ATG TGG TA. All primers were tested for specificity by sequence alignment in the PubMed nucleic acid database (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Data are based on three individual sets of experiments.
Purification of nuclei
The nuclei were purified according from a protocol previously described . Briefly, the cells were harvested in 60 mM KCl, 15 mM NaCl, 0.15 mM Spermine, 0.5 mM Spermidine, 15 mM Hepes, and 14 mM Mercaptoethanol supplemented with 0.2% (v/v) Nonidet p40, aprotinin (1 μg/mL), leupeptin (1 μg/mL), pepstatin A (1 μg/mL), PMSF (10 μg/mL) and 0.3 M sucrose. The cell suspension was then homogenized with 60 strokes at 2,000 rpm (Labortechnik, Berlin, Germany) and the homogenate was filtered with 100 μm filter paper (Schleicher&Schuell, Dassel, Germany). The nuclei were counted in a Bürker chamber and the purity was assessed and protein content was determined by Bradford protein reagent kit (Pierce, Rockford, IL, USA).
Labeling with the acid-cleavable ICATTM reagent and isolation of cysteine containing peptides
Fibroblast nuclei were lysed in a buffer containing 6 M Guanidium-HCl (pH 8.5), 1% Triton X-100, and 50 mM Tris HCl, followed by sonication. Starting with 500 μg for control and TGF-β1 stimulated, each sample was reduced by adding 10 μl of 50 mM TCEP (Tris(2-carboxyethyl)phosphine) and boiled for 10 min. The samples were allowed to cool and the acid cleavable ICATTM reagent (all the materials in this section are from the ICATTM reagent kit Applied Biosystems, Framingham, MA, USA) was added: the light reagent to the control and heavy reagent containing nine 13 C to the TGF-β1-treated sample. Alkylation was allowed to complete for 2 h, at 37°C. The two samples are combined and acetone precipitated in order to remove the guanidium-HCl and the unreacted ICATTM reagent. The pellet was dissolved in a buffer consisting of 50 mM Tris (pH 8.5), 5 mM CaCl2, and 10% acetonitrile. Trypsin was added at a 1:40 enzyme/substrate ratio in two additions once at the start of the digestion and once more, 2 h later. Digestion was completed at 37°C overnight.
Following digestion the sample was diluted into 25% acetonitrile, pH 3.0 in order to reduce the buffer concentration below 10 mM. The resulting peptide mixture was injected to a PolyLC (4.6 × 100 mm Polysulfoethyl A) SCX column on Vision workstation (Applied Biosystems, Framingham, MA, USA) at a flow rate of 1 mL/min using a binding buffer (buffer A) 10 mM KH2PO4, 25% acetonitrile, pH 3 and an elution buffer (buffer B) of 350 mM KCL, 10 mM KH2PO4, 25% acetonitrile, pH 3. The gradient was 0% B to 10% B in 2 min, 20% B in 15 min, 45% B in 3 min, 100% B in 10 min, and an additional 8 min hold at 100% B. Twenty-three SCX fractions of 1.5 mL volume were collected.
The pH was adjusted for each SCX fraction to 7.2 with 10× PBS buffer (pH 10) and injected to the avidin affinity column as prescribed by the manufacturer (Applied Biosystems, Framingham, MA, USA). Cysteine-containing peptides bound to the avidin column were washed three times: 1 mL of Wash 1, 1 mL of Wash 2, and 1 mL of de-ionized water. Elution of the cysteine-containing peptides was performed with 800 μL of avidin elution buffer. The samples were then concentrated by a speed-vac to dry, cleaved with the ICATtm cleaving reagent containing 95% TFA and concentrated again to remove the cleaving reagent. The samples were then taken up in 2% acetonitrile, 0.1% TFA for re-injection for a nanoHPLC MS and MS/MS analysis.
Protein identification and quantification by LC-MS and -MS/MS
Avidin purified SCX fractions were subjected to MALDI and ESI HPLC-MS and MS/MS analysis in a 50:50 split. For the MALDI based workflow, these fractions were injected in the HPLC loading buffer onto a 100 μm × 15 mm C18 Magic column (Auburn, Michrom Bioresources, CA, USA) using a CapTrap pre-column (Auburn, Michrom Bioresources, CA, USA). Mobile phase A was 2% acetonitrile, 0.1% TFA, mobile phase B was 85% acetonitrile, 5% n-PrOH, 10% water, 0.1% TFA. HPLC elution was carried out at a 1-μL/min flow rate on an Ultimate nanoHPLC workstation (Dionex-LC Packings, Hercules, CA, USA). The HPLC elution from the column was collected at 20-s intervals on the MALDI plate using a Probot fraction collector (Dionex-LC Packings). Forty-eight-min HPLC elution was collected to the MALDI plates as an array of 12 × 12 sample spots. The HPLC eluent was mixed with the MALDI matrix (7.5 mg/mL α-cyano-4-hydroxycinnamic acid dissolved in 60:40 acetonitrile-water containing 0.15 mg/mL dibasic ammonium-citrate) through a mixing tee (Upchurch, WA, USA) at a flow rate of 2-μL/min. The most abundant, middle-fractions of the SCX separation were spotted onto two plates using a 90-min HPLC gradient.
MALDI plates were analyzed in automated mode on the AB4700 Proteomics Analyzer (Applied Biosystems, Framingham, MA, USA). First the MS spectra were collected from the entire HPLC run. Then, using an in-house developed program, MS/MS precursors were selected by applying an exclusion algorithm to eliminate: (a) redundant precursors carrying over multiple HPLC fractions; and (b) using only the more abundant members of peptide pairs for MS/MS analysis. MS/MS spectra were acquired using up to 2,500 laser shots/precursor unless the predefined signal-to-noise level in the MS/MS acquisitions was achieved sooner. The MS/MS data were submitted for database searching as a batch to Mascot (http://www.matrixscience.com) through its automation interface of Mascot (Mascot Daemon). The non-redundant NCBI protein database was used. A detailed description of the acceptance criteria for the database searching results will be described elsewhere. In brief, tryptic peptides containing arginine residues were accepted at a Mascot score >20, peptides not containing arginine at a Mascot score >25. Peptides with less-than-significant Mascot score were thoroughly inspected, considering the correlation of peptide basicity with SCX fraction numbers, presence of characteristic high-energy CID fragments, and accurate mass measurements through internal calibration of the MS spectra using the masses of confidently identified peptides as internal mass references.
ESI based LC-MS/MS analyses were carried out using an Ultimate nanoHPLC system (Dionex-LC Packings, CA, USA) on a 75 μM × 150 mm Picofrit C18 column at a 300-nl/min flow rate with a gradient of 5% B to 30% B over 60 min. Mobile phase A was 2% acetonitrile, 0.1% formic acid, mobile phase was 85% acetonitrile, 5% n-PrOH, 10% water, 0.1% formic. A CapTrap (Michrom Bioresources, CA, USA) precolumn was used to preconcentrate the sample.
A platinum electrode was placed behind the HPLC column using a microtee (Upchurch, WA, USA) in order to apply the electrospray voltage (3 kV) for LC-MS/MS analysis. LC-MS/MS was performed using a QSTAR quadrupole time-of-flight instrument (Applied Biosystems, CA, USA). The instrument was set up to perform a 1-s MS scan (300–1500 Da) followed by three most abundant components (two to four charges were allowed) exceeding an intensity threshold of 35 counts. To improve the protein coverage the samples were halved and the analysis was replicated. LC-MS and MS/MS analyses were processed by the ProICAT software (Applied Biosystems, Foster City, CA, USA). Database search results were accepted at >95% confidence interval. Database searching and quantification results from multiple MS platforms were consolidated by parsing all the qualitative and quantitative peptide results into an Oracle database. The set of all the identified peptides were assigned to a minimum set of proteins that could explain all the confidently identified peptide sequences. The abundance ratios of peptide pairs labeled with the heavy (9 × 13 C) and light (0 × 13 C) ICATTM reagents were normalized to the median of all peptide ratios in order to generate normalized expression ratios. Expression ratios of peptides matching to the same protein were averaged to generate expression ratios at the protein level.
Data are expressed as mean ± SEM. Student’s t-test was used to evaluate the differences of the means between groups. Differences were considered significant at P < 0.05. All analyses were performed using GraphPad Prism software version 4.00 (GraphPad Software, San Diego, CA, USA).
James AL, Wenzel S: Clinical relevance of airway remodelling in airway diseases. Eur Respir J. 2007, 30: 134-155. 10.1183/09031936.00146905.
Selman M, Pardo A: Idiopathic pulmonary fibrosis: an epithelial/fibroblastic cross-talk disorder. Respir Res. 2002, 3: 3-10.1186/rr175.
Gauldie J, Kolb M, Sime PJ: A new direction in the pathogenesis of idiopathic pulmonary fibrosis?. Respir Res. 2002, 3: 1-10.1186/rr158.
Tomasek JJ, Gabbiani G, Hinz B, Chaponnier C, Brown RA: Myofibroblasts and mechano-regulation of connective tissue remodelling. Nat Rev Mol Cell Biol. 2002, 3: 349-363. 10.1038/nrm809.
Serini G, Bochaton-Piallat ML, Ropraz P, Geinoz A, Borsi L, Zardi L, Gabbiani G: The fibronectin domain ED-A is crucial for myofibroblastic phenotype induction by transforming growth factor-beta1. J Cell Biol. 1998, 142: 873-881. 10.1083/jcb.142.3.873.
Leask A, Abraham DJ: TGF-beta signaling and the fibrotic response. FASEB J. 2004, 18: 816-827. 10.1096/fj.03-1273rev.
Roberts AB, Sporn MB, Assoian RK, Smith JM, Roche NS, Wakefield LM, Heine UI, Liotta LA, Falanga V, Kehrl JH, Fauci AS: Transforming growth factor type beta: rapid induction of fibrosis and angiogenesis in vivo and stimulation of collagen formation in vitro. Proc Natl Acad Sci U S A. 1986, 83: 4167-4171. 10.1073/pnas.83.12.4167.
Ignotz RA, Endo T, Massague J: Regulation of fibronectin and type I collagen mRNA levels by transforming growth factor-beta. J Biol Chem. 1987, 262: 6443-6446.
Westergren-Thorsson G, Sarnstrand B, Fransson LA, Malmstrom A: TGF-beta enhances the production of hyaluronan in human lung but not in skin fibroblasts. Exp Cell Res. 1990, 186: 192-195. 10.1016/0014-4827(90)90227-2.
Westergren-Thorsson G, Schmidtchen A, Sarnstrand B, Fransson LA, Malmstrom A: Transforming growth factor-beta induces selective increase of proteoglycan production and changes in the copolymeric structure of dermatan sulphate in human skin fibroblasts. Eur J Biochem. 1992, 205: 277-286. 10.1111/j.1432-1033.1992.tb16778.x.
Hallgren O, Nihlberg K, Dahlback M, Bjermer L, Eriksson LT, Erjefalt JS, Lofdahl CG, Westergren-Thorsson G: Altered fibroblast proteoglycan production in COPD. Respir Res. 2010, 11: 55-10.1186/1465-9921-11-55.
Nihlberg K, Andersson-Sjoland A, Tufvesson E, Erjefalt JS, Bjermer L, Westergren-Thorsson G: Altered matrix production in the distal airways of individuals with asthma. Thorax. 2010, 65: 670-676. 10.1136/thx.2009.129320.
Andersson-Sjoland A, Thiman L, Nihlberg K, Hallgren O, Rolandsson S, Skog I, Mared L, Hansson L, Eriksson L, Bjermer L, Westergren-Thorsson G: Fibroblast phenotypes and their activity are changed in the wound healing process after lung transplantation. J Heart Lung Transplant. 2011, 30: 945-954.
Shepard PJ, Hertel KJ: The SR protein family. Genome Biol. 2009, 10: 242-10.1186/gb-2009-10-10-242.
Graveley BR: Sorting out the complexity of SR protein functions. RNA. 2000, 6: 1197-1211. 10.1017/S1355838200000960.
Zahler AM, Lane WS, Stolk JA, Roth MB: SR proteins: a conserved family of pre-mRNA splicing factors. Genes Dev. 1992, 6: 837-847. 10.1101/gad.6.5.837.
Zahler AM, Neugebauer KM, Lane WS, Roth MB: Distinct functions of SR proteins in alternative pre-mRNA splicing. Science. 1993, 260: 219-222. 10.1126/science.8385799.
Smith CW, Valcarcel J: Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem Sci. 2000, 25: 381-388. 10.1016/S0968-0004(00)01604-2.
Caceres JF, Screaton GR, Krainer AR: A specific subset of SR proteins shuttles continuously between the nucleus and the cytoplasm. Genes Dev. 1998, 12: 55-66. 10.1101/gad.12.1.55.
Mermoud JE, Cohen PT, Lamond AI: Regulation of mammalian spliceosome assembly by a protein phosphorylation mechanism. EMBO J. 1994, 13: 5679-5688.
Lin S, Xiao R, Sun P, Xu X, Fu XD: Dephosphorylation-dependent sorting of SR splicing factors during mRNP maturation. Mol Cell. 2005, 20: 413-425. 10.1016/j.molcel.2005.09.015.
Huang Y, Yario TA, Steitz JA: A molecular link between SR protein dephosphorylation and mRNA export. Proc Natl Acad Sci U S A. 2004, 101: 9666-9670. 10.1073/pnas.0403533101.
Balza E, Borsi L, Allemanni G, Zardi L: Transforming growth factor beta regulates the levels of different fibronectin isoforms in normal human cultured fibroblasts. FEBS Lett. 1988, 228: 42-44. 10.1016/0014-5793(88)80580-5.
Lim LP, Sharp PA: Alternative splicing of the fibronectin EIIIB exon depends on specific TGCATG repeats. Mol Cell Biol. 1998, 18: 3900-3906.
Han F, Gilbert JR, Harrison G, Adams CS, Freeman T, Tao Z, Zaka R, Liang H, Williams C, Tuan RS, Norton PA, Hickok NJ: Transforming growth factor-beta1 regulates fibronectin isoform expression and splicing factor SRp40 expression during ATDC5 chondrogenic maturation. Exp Cell Res. 2007, 313: 1518-1532. 10.1016/j.yexcr.2007.01.028.
Tufvesson E, Malmstrom J, Marko-Varga G, Westergren-Thorsson G: Biglycan isoforms with differences in polysaccharide substitution and core protein in human lung fibroblasts. Eur J Biochem. 2002, 269: 3688-3696. 10.1046/j.1432-1033.2002.03058.x.
Dours-Zimmermann MT, Zimmermann DR: A novel glycosaminoglycan attachment domain identified in two alternative splice variants of human versican. J Biol Chem. 1994, 269: 32992-32998.
Danielson KG, Fazzio A, Cohen I, Cannizzaro LA, Eichstetter I, Iozzo RV: The human decorin gene: intron-exon organization, discovery of two alternatively spliced exons in the 5’ untranslated region, and mapping of the gene to chromosome 12q23. Genomics. 1993, 15: 146-160. 10.1006/geno.1993.1022.
Pihlajaniemi T, Myllyla R, Seyer J, Kurkinen M, Prockop DJ: Partial characterization of a low molecular weight human collagen that undergoes alternative splicing. Proc Natl Acad Sci U S A. 1987, 84: 940-944. 10.1073/pnas.84.4.940.
Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R: Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol. 1999, 17: 994-999. 10.1038/13690.
Griffin TJ, Han DK, Gygi SP, Rist B, Lee H, Aebersold R, Parker KC: Toward a high-throughput approach to quantitative proteomic analysis: expression-dependent protein identification by mass spectrometry. J Am Soc Mass Spectrom. 2001, 12: 1238-1246. 10.1016/S1044-0305(01)00316-6.
Smolka M, Zhou H, Aebersold R: Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry. Mol Cell Proteomics. 2002, 1: 19-29. 10.1074/mcp.M100013-MCP200.
Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW: SeqHound: biological sequence and structure database as a platform for bioinformatics research. BMC Bioinforma. 2002, 3: 32-10.1186/1471-2105-3-32.
Barnard DC, Patton JG: Identification and characterization of a novel serine-arginine-rich splicing regulatory protein. Mol Cell Biol. 2000, 20: 3049-3057. 10.1128/MCB.20.9.3049-3057.2000.
Sanford JR, Bruzik JP: Regulation of SR protein localization during development. Proc Natl Acad Sci U S A. 2001, 98: 10184-10189. 10.1073/pnas.181340498.
Malmstrom J, Larsen K, Hansson L, Lofdahl CG, Norregard-Jensen O, Marko-Varga G, Westergren-Thorsson G: Proteoglycan and proteome profiling of central human pulmonary fibrotic tissue utilizing miniaturized sample preparation: a feasibility study. Proteomics. 2002, 2: 394-404. 10.1002/1615-9861(200204)2:4<394::AID-PROT394>3.0.CO;2-6.
Desmouliere A, Geinoz A, Gabbiani F, Gabbiani G: Transforming growth factor-beta 1 induces alpha-smooth muscle actin expression in granulation tissue myofibroblasts and in quiescent and growing cultured fibroblasts. J Cell Biol. 1993, 122: 103-111. 10.1083/jcb.122.1.103.
Modrek B, Lee C: A genomic view of alternative splicing. Nat Genet. 2002, 30: 13-19. 10.1038/ng0102-13.
Cooper TA, Mattox W: The regulation of splice-site selection, and its role in human disease. Am J Hum Genet. 1997, 61: 259-266. 10.1086/514856.
Kramer A: The structure and function of proteins involved in mammalian pre-mRNA splicing. Annu Rev Biochem. 1996, 65: 367-409. 10.1146/annurev.bi.65.070196.002055.
Teigelkamp S, Mundt C, Achsel T, Will CL, Luhrmann R: The human U5 snRNP-specific 100-kD protein is an RS domain-containing, putative RNA helicase with significant homology to the yeast splicing factor Prp28p. RNA. 1997, 3: 1313-1326.
Lauber J, Fabrizio P, Teigelkamp S, Lane WS, Hartmann E, Luhrmann R: The HeLa 200 kDa U5 snRNP-specific protein and its homologue in Saccharomyces cerevisiae are members of the DEXH-box protein family of putative RNA helicases. EMBO J. 1996, 15: 4001-4015.
Valdez BC, Henning D, Busch RK, Woods K, Flores-Rozas H, Hurwitz J, Perlaky L, Busch H: A nucleolar RNA helicase recognized by autoimmune antibodies from a patient with watermelon stomach disease. Nucleic Acids Res. 1996, 24: 1220-1224. 10.1093/nar/24.7.1220.
Guil S, Gattoni R, Carrascal M, Abian J, Stevenin J, Bach-Elias M: Roles of hnRNP A1, SR proteins, and p68 helicase in c-H-ras alternative splicing regulation. Mol Cell Biol. 2003, 23: 2927-2941. 10.1128/MCB.23.8.2927-2941.2003.
Long JC, Caceres JF: The SR protein family of splicing factors: master regulators of gene expression. Biochem J. 2009, 417: 15-27. 10.1042/BJ20081501.
Lin S, Fu XD: SR proteins and related factors in alternative splicing. Adv Exp Med Biol. 2007, 623: 107-122. 10.1007/978-0-387-77374-2_7.
Kuo BA, Uporova TM, Liang H, Bennett VD, Tuan RS, Norton PA: Alternative splicing during chondrogenesis: modulation of fibronectin exon EIIIA splicing by SR proteins. J Cell Biochem. 2002, 86: 45-55. 10.1002/jcb.10188.
Cramer P, Caceres JF, Cazalla D, Kadener S, Muro AF, Baralle FE, Kornblihtt AR: Coupling of transcription with alternative splicing: RNA pol II promoters modulate SF2/ASF and 9 G8 effects on an exonic splicing enhancer. Mol Cell. 1999, 4: 251-258. 10.1016/S1097-2765(00)80372-X.
Lavigueur A, La Branche H, Kornblihtt AR, Chabot B: A splicing enhancer in the human fibronectin alternate ED1 exon interacts with SR proteins and stimulates U2 snRNP binding. Genes Dev. 1993, 7: 2405-2417. 10.1101/gad.7.12a.2405.
Schwarzbauer JE, Tamkun JW, Lemischka IR, Hynes RO: Three different fibronectin mRNAs arise by alternative splicing within the coding region. Cell. 1983, 35: 421-431. 10.1016/0092-8674(83)90175-7.
Xia P, Culp LA: Adhesion activity in fibronectin's alternatively spliced domain EDa (EIIIA) and its neighboring type III repeats: oncogene-dependent regulation. Exp Cell Res. 1994, 213: 253-265. 10.1006/excr.1994.1197.
Jarnagin WR, Rockey DC, Koteliansky VE, Wang SS, Bissell DM: Expression of variant fibronectins in wound healing: cellular source and biological activity of the EIIIA segment in rat hepatic fibrogenesis. J Cell Biol. 1994, 127: 2037-2048. 10.1083/jcb.127.6.2037.
Oyama F, Hirohashi S, Shimosato Y, Titani K, Sekiguchi K: Deregulation of alternative splicing of fibronectin pre-mRNA in malignant human liver tumors. J Biol Chem. 1989, 264: 10331-10334.
Borsi L, Castellani P, Risso AM, Leprini A, Zardi L: Transforming growth factor-beta regulates the splicing pattern of fibronectin messenger RNA precursor. FEBS Lett. 1990, 261: 175-178. 10.1016/0014-5793(90)80664-5.
Malmstrom J, Larsen K, Malmstrom L, Tufvesson E, Parker K, Marchese J, Williamson B, Patterson D, Martin S, Juhasz P, Westergren-Thorsson G, Marko-Varga G: Nanocapillary liquid chromatography interfaced to tandem matrix-assisted laser desorption/ionization and electrospray ionization-mass spectrometry: mapping the nuclear proteome of human fibroblasts. Electrophoresis. 2003, 24: 3806-3814. 10.1002/elps.200305619.
This work was supported by grants from the Swedish Medical Research Council (11550), the Swedish Cancer Fund, the Swedish Society for Medical Research, the Swedish Heart-Lung foundation the JA Persson, G Nilsson, Greta and John Kock, A Österlund and Anna-Greta Crafoord Foundations, Lars Hiertas Minne foundation, the Konsul Bergh Foundation, Riksföreningen mot Rheumatism, the Royal Physiographic Society in Lund Gustaf V.s 80 Årsfond and the Medical Faculty, University of Lund. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
The authors declare that they have no competing interests.
OH, JM, AAS, MW, LM, ET, PJ, GMV, and GWT conceived and designed the experiments; OH, JM, LM, AAS, MW, GMV, and GWT performed the experiments; OH, JM, LM, AAS, MW, GMV, and GWT analyzed the data; OH, JM, LM, ET, GMV, PJ, and GWT contributed materials; OH, JM, AAS, and GWT wrote the paper. All authors read and approved the final manuscript.
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Hallgren, O., Malmström, J., Malmström, L. et al. Splicosomal and serine and arginine-rich splicing factors as targets for TGF-β. Fibrogenesis Tissue Repair 5, 6 (2012). https://doi.org/10.1186/1755-1536-5-6
- Alternative Splice
- Splice Factor
- mRNA Splice
- Myofibroblast Differentiation
- Alternative Isoforms