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Integrated Analysis of a Gene Correlation Network Identifies Critical Regulation of Fibrosis by lncRNAs and TFs in Idiopathic Pulmonary Fibrosis
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Publication date (Electronic):
2 June 2020
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BioMed Research International
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Hindawi
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Abstract
Idiopathic pulmonary fibrosis (IPF), the most frequent form of irreversible interstitial pneumonia with unknown etiology, is characterized by massive remodeling of lung architecture and followed by progressive loss of lung function. However, the key regulatory genes and the specific signaling pathways involved in the onset and progression of IPF still remain unclear. The present study is aimed at investigating the key role of long noncoding RNAs (lncRNAs) and transcription factors (TFs) involved in the pathogenesis of IPF through the integrated analysis of three gene expression profiles from the GEO dataset (GSE2052, GSE44723, and GSE24206). A total of 8483 differentially expressed genes (DEGs) including 988 upregulated and 7495 downregulated genes were filtered. Subsequently, following the intersection of these DEGs, 29 overlapping genes were identified and further analyzed using a bioinformatics approach. Furthermore, the protein-protein interaction (PPI) network was used to obtain 18 modules of related genes. The hub genes were identified through hypergeometric testing, which were closely associated with ubiquitin-mediated proteolysis, the spliceosome, and the cell cycle. The significant difference was observed in the expression of these key genes, such as lncRNA MALAT1, E2F1, and YBX1, in the peripheral blood of IPF patients when compared with those normal control subjects by real-time polymerase chain reaction (RT-PCR) analysis. This study indicated that lncRNA MALAT1, E2F1, and YBX1 may be key regulators for the pathogenesis of IPF.
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Up-Regulation and Profibrotic Role of Osteopontin in Human Idiopathic Pulmonary Fibrosis
Annie Pardo, Kevin F. Gibson, José Luis Cisneros … (2005)
Introduction Idiopathic pulmonary fibrosis (IPF) is a chronic fibrosing interstitial pneumonia of unknown etiology characterized by alveolar epithelial cell injury/activation, fibroblast proliferation, and exaggerated accumulation of extracellular matrix in the lung parenchyma [1,2]. The disease is usually progressive and largely unresponsive to corticosteroid and immunosuppressive therapy [2,3]. A distinctive morphological feature of IPF is the development of fibroblastic/myofibroblastic foci, represented by widely scattered, small aggregates of subepithelial mesenchymal cells immersed within a myxoid-appearing extracellular matrix [4]. These fibroblastic/myofibroblastic foci represent areas of active fibrogenesis and play a crucial role in the progressive fibrotic response [1,5]. These sites are characterized by inappropriate re-epithelialization and impaired extracellular matrix remodeling. Although significant advances have been made in the characterization of the clinical and morphological features of this disease, the molecular mechanisms that underlie IPF pathogenesis in humans are still largely unknown [1,4–7]. Osteopontin (also termed secreted phosphoprotein 1) is a phosphorylated acidic glycoprotein that contains an Arg-Gly-Asp motif that binds to the integrin family of adhesion molecules [8]. It functions as a cell adhesion and migration molecule that can bind to several ligands, including αvβ3 integrin, some CD44 isoforms, and fibronectin [9,10]. Osteopontin has been implicated in a number of physiological and pathological processes including bone resorption, malignant transformation, and metastasis [11,12]. It is also considered a key cytokine regulating inflammation, cellular immune response, and tissue repair, with a unique effect on T cell function [11,12]. Using oligonucleotide microarrays we previously demonstrated that osteopontin is highly up-regulated in bleomycin-induced lung fibrosis in mice, and we reported similar results in a preliminary report involving five IPF lungs and four control samples [13,14]. Interestingly, osteopontin seems to have a profibrotic effect in the development of bleomycin-induced pulmonary fibrosis [15]. After bleomycin instillation, osteopontin-null mice developed reduced lung fibrosis characterized by dilated distal air spaces with decreased active transforming growth factor-beta 1 (TGF-β1) and reduced type I collagen expression compared with wild-type controls [16]. The mechanisms by which osteopontin, a cytokine with primarily TH1 effects (i.e., antifibrotic) on T lymphocytes [11,17,18], may cause profibrotic effects are not fully understood. In this study, we applied microarrays to analyze gene expression patterns in a larger cohort of IPF lungs (13 IPF samples and 11 controls), and we analyzed the direct effects of osteopontin on human lung fibroblasts, alveolar epithelial cell migration and proliferation, and matrix metalloprotease (MMP) gene expression in vitro. Methods Study Population Patients from the National Institute of Respiratory Diseases, Mexico City, México (Protocol S1), and the University of Pittsburgh, Pittsburgh, Pennsylvania, United States (Protocol S2), were included in this study. The protocol was approved by both Institutions, and written informed consent was obtained where required. Samples for oligonucleotide microarray were obtained from the tissue bank of the Department of Pathology at the University of Pittsburgh. The use of archived tissue has been approved by the local Institutional review board. Diagnosis of IPF was supported by history, physical examination, pulmonary function studies, chest HRCT, and bronchoalveolar lavage (BAL) findings, and was corroborated by open lung biopsy. The morphologic diagnosis of IPF was based on typical microscopic findings consistent with usual interstitial pneumonia [4]. The patients fulfilled the criteria of the American Thoracic Society and European Respiratory Society [7]. BAL samples were obtained at first consult as part of the initial diagnostic work-up. None of the patients had been treated with corticosteroids or immunosuppressive drugs at the time of BAL. Demographic data, pulmonary function data, and BAL differential cell counts are provide in Table 1. Levels of osteopontin in BAL fluids were evaluated in ten healthy individuals (two current smokers, two former smokers, and six that had never smoked). All had normal chest X-rays and spirometries. Likewise, histologically normal lung tissues obtained at necropsy from six nonsmoking adult individuals who had died of causes unrelated to lung diseases were utilized for immunohistochemistry. For oligonucleotide microarrays, control samples included normal histology lung samples resected from patients with lung cancer obtained from the Pittsburgh Tissue Bank (Pittsburgh, Pennsylvania, United States). Oligonucleotide Microarrays Surgical remnants of biopsies or lungs explanted from patients with IPF that underwent pulmonary transplant were the sources of 13 IPF samples. Lung samples resected from patients with lung cancer, obtained from the tissue bank of the Department of Pathology at the University of Pittsburgh, were the sources of 11 normal samples. None of these samples had been included in our previous study. Total RNA was extracted and used as a template to generate double-stranded cDNA and biotin-labeled cRNA, as recommended by the manufacturer of the arrays and previously described [11]. Fragmented cRNA was hybridized to Codelink Uniset I slides. After hybridization, arrays were washed and stained with streptavidin-AlexaFluor 647. The arrays were scanned using a Genepix 4000B microarray scanner. Images were analyzed using Codelink expression II analysis suite. They were visually inspected for defects and quality control parameters as recommended by the manufacturer. Data files were imported into a microarray database and linked with updated gene annotations using SOURCE (http://genome-www5.stanford.edu/cgi-bin/SMD/source/sourceSearch) and then median scaled. Based on our previous experience, all expression levels below 0.01 were brought to 0.01. Statistical analysis was performed using Scoregene gene expression package (http://www.cs.huji.ac.il/labs/compbio/scoregenes, and data visualization was performed using Genexpress (http://genexpress.stanford.edu) and Spotfire Decision Site 8.0 (Spotfire, Göteborg, Sweden). The complete set of gene array data has been deposited in the Gene Expression Omnibus database with GEO serial accession number GSE2052 (http://www.ncbi.nlm.nih.gov/geo) according to MIAME guidelines. The general approach to analysis was previously described by us [19]. Weakest link models [20,21] were fitted using the Weaklink package for the R statistical software system (http://www.r-project.org). The p-value was obtained from fitting a logistic regression model with a single independent variable that is the minimum of the percentiles for the expression levels for the two genes. A Bonferroni correction was applied for multiple testing. Bronchoalveolar Lavage BAL was performed through flexible fiberoptic bronchoscopy under local anesthesia. Briefly, 300 ml of normal saline was instilled in 50-ml aliquots, with an average recovery of 60%–70%. The recovered BAL fluid was centrifuged at 250 g for 10 min at 4 °C. The cell pellet was resuspended in 1 ml of PBS and an aliquot was used to evaluate the total number of cells. Other aliquots were fixed in carbowax, stained with hematoxylin and eosin, and used for differential cell count. Supernatants were kept at −70 °C until use. ELISA Quantification of osteopontin was performed in BAL fluid samples from 18 IPF patients and 10 healthy individual controls, by using a commercial sensitive and specific ELISA following the instructions of the manufacturer (Calbiochem, La Jolla, California, United States). Immunohistochemistry Tissue sections were deparaffinized, rehydrated, and then blocked with 3% H2O2 in methanol for 30 min, then antigen was retrieved with citrate buffer (10 mM, pH 6.0) for 5 min in a microwave. Rabbit polyclonal antibody to human osteopontin (2 ng/ml; Calbiochem) was applied and samples were incubated at 4 °C overnight. A secondary biotinylated anti-immunoglobulin followed by horseradish peroxidase-conjugated streptavidin (BioGenex, San Ramon, California, United States) was used according to manufacturer's instructions. AEC (BioGenex) in acetate buffer containing 0.05% H2O2 was used as substrate [15,19]. The sections were counterstained with hematoxylin. The primary antibody was replaced by non-immune serum for negative control slides. Two-Color Immunofluorescence Analysis A standard two-stage double-immunofluorescence labeling technique was used. Briefly, frozen sections were washed in PBS (0.01 M [pH 7.4]) for 5 min and then fixed in cold acetone for 10 min, twice. Tissues were incubated in blocking buffer (1% BSA, 5% normal serum, 0.05% NP-40, in PBS) for 30 min. The slides were then incubated with a rabbit antibody to osteopontin (1:100; Abcam, Cambridge, Massachusetts, United States) for 1 h at room temperature and washed in PBST (0.05% Tween-20 in 0.01 M PBS [pH 7.4]) for 10 min, three times. A mouse anti-MMP-7 monoclonal antibody (1:1,000; Chemicon International, Temecula, California, United States) was added and the slides were incubated for an additional 1 h at room temperature. After three 10-min washes in PBST, slides were incubated with secondary antibodies (sheep anti-rabbit IgG-Cy3, 1:1,000; and goat anti-mouse IgG-FITC, 1:1,000; Sigma-Aldrich, St. Louis, Missouri, United States) for 30 min. Slides were then washed in the same buffer and mounted with antifade medium (containing DAPI to stain cell nuclei). Cell Culture Primary human normal lung fibroblasts were obtained as previously described [22], and the A549 cell line was obtained from ATCC (Rockville, Maryland, United States). Growth Rate Assay Lung fibroblasts or A549 cells were seeded in 96-well culture plates at a cell density of 7.5 × 103 and 5 × 103 cells/well respectively, and incubated in Ham's F-12 and DMEM media, respectively (GIBCO-BRL, Grand Island, New York, United States), supplemented with 10% FBS at 37 °C in 5% CO2 and 95% air. After 12 h, the medium was replaced by medium with 0.1% FBS alone or 0.1% FBS plus increasing concentrations of osteopontin (0.4, 1, and 2 μg/ml) and the cells were maintained in culture for another 48 h. Cell growth was determined using the cell proliferation reagent WST-1 (Boehringer Mannheim, Mannheim, Germany) as previously described [19]. All assays were performed in triplicate. In parallel experiments, fibroblasts and A549 cells were pretreated for 25 min with antibody to human αvβ3 integrin (10 μg/ml; Chemicon), the pentapeptide Gly-Arg-Gly-Asp-Ser (GRGDS; Calbiochem), or antibody to human CD44 (NeoMarkers, Fremont, California, United States), and then osteopontin was added (2 μg/ml). Additionally, A549 cells were pretreated with antibody to human epidermal growth factor receptor (EGFR; 10 μg/ml; Chemicon). Cell Migration Assay Migration of fibroblasts and A549 cells was assayed using commercially available 24-well collagen-coated Boyden chambers (Chemicon) with an 8-μm pore size. Briefly, a semi confluent (∼80%) monolayer of lung fibroblasts or A549 cells was harvested with trypsin-EDTA, centrifuged, and resuspended in Ham's F-12 medium containing 5% BSA. The cell suspensions (3 × 105 cells/well) were added to the upper chamber. The lower chamber contained 0.3 ml of medium with 5% BSA alone or with 10 μg/ml of recombinant human osteopontin (Calbiochem). PDGF (8 ng/ml) and epidermal growth factor (EGF; 50 ng/ml) were used as positive controls for fibroblasts and for A549 cells, respectively. Additional BSA-coated chambers were used as blanks for each sample. After incubation for 8 h at 37 °C in a humidified incubator with 5% CO2 and 95% air, the nonmigrating cells on the top of Boyden chamber were scraped and washed. The migrating cells were quantitated according to manufacturer's instructions. Briefly, the cells were stained and the color eluted with 300 μl of extraction buffer, and 150-μl aliquots were measured in an ELISA plate reader at 545 nm. All assays were performed in duplicate. In parallel experiments, A549 cells and fibroblasts were pretreated as described above for growth rate. RNA Isolation and Northern Blot Analysis Total RNA was extracted from lung fibroblasts and A549 epithelial cells using the RNeasy Mini Kit (Qiagen GmbH, Germany). Cells were lysed and homogenized in the presence of a highly denaturing guanidine isothiocyanate-containing buffer. The samples were then applied to an RNeasy minicolumn, and RNA was eluted in 30 μl of water. Total RNA (20 μg/lane) was fractionated on a 1% agarose gel containing 0.66 M formaldehyde [21]. Ribosomal RNA was visualized with ethidium bromide, and the fractionated RNA was transferred onto a Nytran transfer membrane (NEN Life Science Products, Boston, Massachusetts, United States) by capillary blotting overnight. RNA was immobilized by baking at 80 °C for 2 h, and then prehybridized at 42 °C for 18 h in 5× SSC, 50% formamide, 5× Denhardt's solution, and 0.5% SDS, containing 100 μg/ml of denatured salmon sperm DNA. Hybridization was carried out at 42 °C for 18 h in hybridization buffer composed of formamide, 0.5% SDS, and heat-denatured 32P-labeled cDNA probes. After washing, membranes were dried and exposed to Kodak BIOMAX MS film at −70 °C with an intensifying screen. The cDNA clones for human MMP-1, TIMP-1, α1 type I collagen, and RNA ribosomal 18S were obtained from ATCC. Human MMP-7 cDNA was a kind gift of Lynn Matrisian, Vanderbilt University, Nashville, Tennessee, United States. The cDNA probes were radiolabeled with 32P-dCTP to a specific activity of 200 × 106 dpm/μg using a Random Primer Labeling Kit (Stratagene, La Jolla, California, United States). All experiments were repeated twice. Quantitative Real-Time RT-PCR 1 μg of RNA was treated with 1 unit of DNAase (Life Technologies, Grand Island, New York, United States). First-strand cDNA was synthesized by reverse transcription with random primers and Moloney-murine leukemia virus reverse transcriptase according to manufacturer's protocol (Advantage RT-for-PCR Kit; Clontech, Palo Alto, California, United States). Real-time PCR amplification was performed using i-Cycler iQ Detection System (BioRad, Hercules, California, United States), using TAQMAN probes (PE Applied Biosystems, Wellesley, California, United States) labeled with FAM and TET. PCR was performed with the cDNA working mixture in a 25-μl reaction volume containing 3 μl of cDNA, 20 mM Tris-HCl (pH 8.3), 50 mM KCl, 2 mM MgCl2, 200 μM dNTPs, 0.2 μM specific 5′ and 3′ primers for 18S rRNA, 0.6 μM specific 5′ and 3′ primers for gene target, 0.2 μM of each probe TAQMAN (18S rRNA and gene target), and 1.25 units of AmpliTaq GOLD DNA polymerase (PE Applied Biosystems). A dynamical range was built with each product of PCR on copy number serial dilutions from 1 × 108 to 1 × 101; all PCRs were performed in triplicate. Standard curves were calculated referring the threshold cycle (Ct) to the log of each cDNA dilution step. Results were expressed as the number of copies of the target gene normalized to 18S rRNA. Some primers used in PCR reactions were designed using Beacon Designer software 2.1 (BioRad) and checked for homology in BLAST. The cycling conditions for PCR amplification were performed using the following protocol: Initial activation of AmpliTaq Gold DNA polymerase at 95 °C for 7 min; and 40 cycles of denaturation at 95 °C for 30s, annealing at 60 °C for 30 s, and extension at 72 °C for 30 s. The sequences of the PCR primer pairs and probes for each gene are shown in Table 2. All PCR experiments were done in duplicate. PAGE Zymography For MMP-7 analysis, conditioned media was electrophoresed in 12.5% SDS gels containing as substrate bovine CM-transferrin (0.3 mg/ml) and heparin [22]. After electrophoresis, gels were washed in a solution of 2.5% Triton X-100, and incubated overnight at 37 °C in 100 mM glycine (pH 7.6), plus 10 mM CaCl2 and 50 nM ZnCl2. Identical gels were incubated but in the presence of 20 mM EDTA. Gels were stained with Coomassie Brilliant Blue R250 and destained in a solution of 7.5% acetic acid and 5% methanol. Recombinant human MMP-7 (Chemicon) was used as positive control. Western Blot Analysis Serum-free conditioned media was centrifuged at 300 g at 4 °C for 30 min to remove cell debris, then concentrated by lyophilization. Samples were solubilized in water, and aliquots containing 5 μg of protein were mixed with Laemmli sample buffer and electrophoresed on 10% or 12.5% SDS-polyacrylamide gels. Proteins were transferred to nitrocellulose filters at 15 V for 20 min using semi-dry transfer cell (BioRad). Nonspecific sites were blocked overnight with 4% (w/v) nonfat dried milk in PBS, and membranes were incubated with rabbit antibody to human interstitial collagenase IgG (1:250 in PBS with 1% BSA; Santa Cruz Biotechnology, California, United States), antibody to human TIMP-1 (Chemicon), antibody to human MMP-7 (Oncogene, San Diego, California, United States), or monoclonal antibody to human α-smooth muscle actin (2 μg/ml; Cymbus Biotechnology, Chandlers Ford, Hants, United Kingdom) for 2 h at room temperature. Filters were incubated with secondary antibody conjugated to peroxidase for 1 h at room temperature. Finally, the filters were developed with the Enhanced Chemiluminescence detection system (Amersham Pharmacia Biotech, Piscataway, New Jersey, United States) using radiograph film (Hyperfilm, Amersham Pharmacia Biotech) according to the instructions of the manufacturer. Western blots were repeated twice. Results Osteopontin Gene Expression Is Highly Up-Regulated in IPF Lungs The complete microarray dataset is available at the Gene Expression Omnibus database with GEO serial accession number GSE2052 (http://www.ncbi.nlm.nih.gov/geo). Gene expression patterns clearly distinguished IPF lungs from normal lungs. Osteopontin was the most up-regulated gene among the genes that distinguished IPF lungs (Figure 1A). Osteopontin levels were increased more than 20-fold (mean expression 0.62 in control lungs, 16.8 in IPF lungs; Figure 1B). This increase was statistically significant whether we applied threshold number of misclassifications (TNoM) score (p = 0.000221), or Student's t-test (p = 0.0000035). We corrected for multiple testing by controlling the false discovery rate at the 5% level [23]. Osteopontin expression levels were higher in most IPF lungs than in any control lung (Figure 1B). Osteopontin Is Increased in BAL Fluid from IPF Patients Osteopontin protein was quantified in BAL fluids from 18 IPF patients and 10 healthy controls. As shown in Figure 2, ELISA measurement revealed a significant increase in the immunoreactive protein in the fluids derived from IPF lungs (148.8 ± 83 ng/ml in IPF lungs versus 3.8 ± 2.0 ng/ml in healthy controls, p < 0.01). Immunoreactive Osteopontin Is Localized Primarily in Epithelial Cells To examine the cellular source of osteopontin we analyzed IPF and control lungs by immunohistochemistry. As illustrated in Figure 3A–3C, osteopontin was localized primarily in alveolar epithelial cells that exhibited an intense cytoplasmic staining in IPF lungs. Occasionally, clusters of alveolar macrophages were also positive (Figure 3C). Immunohistochemical staining for osteopontin was negative in normal lungs as well as in lung tissue samples incubated with nonimmune sera (Figure 3D). Osteopontin Induces Fibroblast and Epithelial Cell Growth Rate To determine the effect of osteopontin on the growth rates of fibroblasts and epithelial cells, cells were stimulated with increasing concentrations of osteopontin, and the cell number was determined after 48 h using the cell proliferation reagent WST-1. Significant dose-dependent increases in cell proliferation were observed with 1 μg/ml and 2 μg/ml. Two different fibroblast lines reached 220% and 380% over controls (p < 0.01), while in two different experiments A549 cell lines exhibited 60% and 80% increases of growth rate over control (p < 0.01). Osteopontin-induced fibroblast proliferation (2 μg/ml) was significantly suppressed by GRGDS-pentapeptide, which interrupts binding of RGD-containing proteins to cell surface integrins (p < 0.01) and by antibody to αvβ3 integrin (p < 0.05), suggesting that the effect of osteopontin on growth rate was mediated by the interaction of the GRGDS domain of osteopontin with αvβ3 integrin (Figure 4A). In contrast, epithelial cell growth was partially inhibited by antibody to CD44 (p < 0.05) (Figure 4B). Epithelial cell growth was also significantly suppressed by GRGDS but not by antibodies to αvβ3 (Figure 4B). Osteopontin Induces Fibroblast and Epithelial Cell Migration To examine the effect of osteopontin on cell migration, we used collagen-coated Boyden chambers, a well-established in vitro assay system. The number of cells that migrated in absence of osteopontin was used as control (0% migration). As revealed in Figure 5A, fibroblasts significantly moved toward osteopontin compared with cells exposed to medium plus 5% BSA alone in the lower chamber. Osteopontin (10 μg) enhanced fibroblast migration by 120% ± 11% (p < 0.01), an enhancement similar to that obtained with the potent fibroblast mitogen platelet-derived growth factor, used as a positive control (157% ± 12%, unpublished data). To analyze possible mechanisms by which osteopontin stimulates migration, different blockers were used. Fibroblast migration was significantly reduced by GRGDS and antibody to αvβ3 integrin (p < 0.01), and by antibody to CD44 (p < 0.05). The inhibition of cell migration was specific, since incubation with IgG had no effect (unpublished data). A549 lung cells also showed a significant increase in cell migration in response to osteopontin (Figure 5B). After 8 h of incubation, A549 cells passing through the membrane increased by 114% ± 25% compared to control cells (p < 0.01). Epidermal growth factor, used as a positive control, induced a 168% ± 14% increase in cell migration (unpublished data). Osteopontin-induced migration was abolished when the epithelial cells were pretreated individually with GRGDS, anti-αvβ3 integrin, or anti-CD44 (p < 0.01; Figure 5B). Osteopontin Induces an Environment That Favors Extracellular Matrix Deposition in Fibroblasts MMP-1 expression by fibroblasts Under basal conditions, some primary human lung fibroblast cell lines may express MMP-1, while others express the enzyme only when stimulated, for example, by aminophenylmercuric acetate (APMA). In this context, the effect of osteopontin on MMP-1 expression was examined by Northern blot analysis in a cell line producing MMP-1 under basal conditions, and in a cell line that did not produce MMP-1 but was stimulated by APMA (Figure 6A and 6B). Osteopontin down-regulated both the basal and the APMA-induced MMP-1 transcript level. When the signal of MMP-1 mRNA was normalized to the level of 18S RNA and quantified by densitometry, a reduction of ∼50% was noticed. This result was confirmed by real-time PCR that showed ∼40% inhibition (p < 0.05; Figure 6C). Inhibition of MMP-1 expression was partially blocked by antibody to CD44, while it was not affected by antibody to αvβ3 integrin. The inhibitory effect of osteopontin on MMP-1 was also observed at the protein level by Western blot analysis. As shown in Figure 6D, the level of immunoreactive MMP-1 present in the conditioned medium was decreased in the fibroblasts stimulated with osteopontin as compared with control cells. Osteopontin increases TIMP-1 expression by fibroblasts The effect of osteopontin on TIMP-1 gene expression in fibroblasts is illustrated in Figure 7. Northern blot analysis (Figure 7A) revealed an increase in TIMP-1 gene expression at 0.4 μg/ml and 1 μg/ml osteopontin when compared to control. This result was confirmed by real-time PCR (Figure 7B). Osteopontin increased the TIMP-1/18S ribosomal RNA from 55.7 ± 14.2 copies to 121.2 ± 13.1 copies (p < 0.01). Both anti-CD44 and anti-αvβ3 integrin abolished this increase. Osteopontin also increased TIMP-1 protein expression in conditioned medium as illustrated in Figure 7C. Osteopontin induces collagen gene expression in fibroblasts The effect of osteopontin on collagen gene expression is depicted in Figure 8. Northern blot analysis (Figure 8A) revealed a 2-fold increase in α1 type I collagen gene expression. Expression of α-smooth muscle actin in fibroblasts was induced by TGF-β1 but not by osteopontin (Figure 8B). Osteopontin Increases MMP-7 Expression by Epithelial Cells Stimulation of A549 cells with osteopontin (0.4 μg/ml and 2.0 μg/ml) induced an up-regulation of MMP-7 gene expression as illustrated by Northern blot in Figure 9A. Real-time PCR revealed a 6-fold increase at 6 h after osteopontin stimulation, which was abolished by treatment with anti-αvβ3, anti-CD44, anti-EGFR, or GRGDS as shown in Figure 9B. Pro-MMP-7 overexpression was confirmed at the protein level by Western blot analysis of the epithelial cells conditioned medium (Figure 9C). As recombinant MMP-7 used as control showed a lower molecular weight band to that of conditioned medium, this one was treated with APMA to activate pro-MMP-7. Activated proenzyme showed a similar molecular weight band to the recombinant protein. Zymography using CM-transferrin as substrate showed that treatment of A549 epithelial cells with 0.4 μg/ml and 1 μg/ml osteopontin induced an increase of both the pro-MMP-7 and MMP-7 activity bands (Figure 9D). Osteopontin Colocalizes with MMP-7 in Alveolar Epithelial Cells from IPF Lungs Since we have previously demonstrated that IPF lungs strongly express MMP-7 in alveolar epithelial cells [14], we evaluated whether the staining pattern of this enzyme is associated with that of osteopontin. Figure 10 illustrates confocal microscopy images showing that MMP-7 (Figure 10A) is partially overlapped with that of osteopontin (Figure 10B), giving substantial double labeling (Figure 10C and 10D). Normal lungs did not exhibit any significant staining for MMP-7 or osteopontin (unpublished data). Weakest Link Models Identify a Statistically Significant Interaction between Osteopontin and MMP-7 To determine whether MMP-7 and osteopontin expression levels jointly distinguish IPF and control samples, we applied weakest link statistical models [20]. Weakest link models assume that two genes jointly impact the probability that a randomly selected sample belongs to a certain phenotype (IPF in this case) only if expression levels of the two genes lie on a low-dimensional curve whose form is specified by the model and estimated using the observed quantiles of the data. Our analysis detected a statistically significant joint effect of MMP-7 and osteopontin on the IPF phenotype (p < 0.001). This joint relationship is illustrated in Figure 11 for both the gene expression values (Figure 11A) and the sample percentiles (Figure 11B). To assess the relevance of this association, we chose both substantively meaningful genes and a more general set of genes to evaluate the contribution of the weakest link model relating osteopontin and MMP-7 (Figure 11). Among 14 matrix metalloproteases and their inhibitors represented on the Human Uniset I chip, osteopontin and MMP-7 exhibited the most significant biological interaction. Osteopontin also had significant interactions (weakest link models with p < 0.05) with MMP-1, MMP-2, and MMP-11 but none was as statistically significant as MMP-7. We also ran weakest link models combining osteopontin with each of 400 genes that passed the false discovery rate of less than 0.05 for differential expression between IPF and control samples. The interaction of osteopontin with MMP-7 in a weakest link model was more significant than 371 of these 400 genes. Discussion In the present study we focused on the profibrotic effects of osteopontin, a multifunctional cytokine that mediates diverse biological functions, including cell adhesion, chemotaxis, and signaling, as well as tissue reparative processes [8,11,12]. We demonstrated that osteopontin was the most up-regulated gene in lungs of IPF patients, and that it was mainly expressed by alveolar epithelial cells. To better understand the potential local profibrotic effects of osteopontin, we studied its effects on lung fibroblasts and epithelial cells. Functionally, osteopontin induced fibroblast and epithelial cell proliferation and migration. The effect on fibroblast migration and proliferation was dependent mainly on integrins, while in epithelial cells proliferation was mainly dependent on CD44 and migration was dependent on CD44 and integrin signaling. Osteopontin exhibited profibrotic effects on molecules involved in extracellular matrix remodeling. Thus, in fibroblasts, osteopontin increased TIMP-1 and type I collagen and inhibited MMP-1 expression, while in alveolar epithelial cells it induced MMP-7. The effects on TIMP-1 and MMP-1 expression appeared to be mostly dependent on CD44, while the effect on MMP-7 expression was dependent on CD44 and integrin signaling. Interestingly, osteopontin was colocalized with MMP-7 in alveolar epithelial cells of IPF lungs, and application of the weakest link models to microarray data suggested that the genes of both interacted to affect the IPF phenotype. Our results provide a potential mechanism by which osteopontin secreted from epithelial cells exerts its profibrotic effects through direct signaling on fibroblasts and epithelial cells. Several studies in experimental tissue fibrosis have suggested a possible profibrotic role of osteopontin. In kidney fibrosis, osteopontin enhances macrophage recruitment and stimulates the development of renal scarring after an acute ischemic insult [24]. Also, osteopontin expression is increased in the myocardium after myocardial infarction, and the lack of this mediator is associated with decreased collagen accumulation [25]. Similarly, osteopontin appears to be an important mediator of the cardiac profibrotic effects of angiotensin II by promoting collagen synthesis and remodeling in the interstitial myocardium [26]. In experimental lung fibrosis it has been suggested that osteopontin produced by alveolar macrophages functions as a fibrogenic cytokine [15,16]. In granulomatous lung diseases, osteopontin is also up-regulated and its main sources are macrophages and T lymphocytes [27,28]. We observed that in human IPF lungs, hyperplastic alveolar epithelial cells seemed to be a source of osteopontin, which is consistent with the findings of Berman et al. [15,16]. These observations support the key role of alveolar epithelial cells as regulators of the lung profibrotic microenvironment in IPF, thus emphasizing the critical difference between the mechanisms of fibrosis in IPF compared with animal models or with lung fibrosis associated with inflammatory disorders. Positive feedback mechanisms have been previously proposed for osteopontin and MMP-2 [29], where osteopontin induces MMP-2 expression [30] and is cleaved and activated by MMP-2 [29]. The same mechanism has been proposed for osteopontin and MMP-3, where osteopontin binds and activates MMP-3, which in turn can cleave and activate it [31]. Similarly, osteopontin is cleaved and activated by MMP-7 [31], and we observe that MMP-7 is induced by osteopontin in epithelial cells, suggesting that this positive feedback mechanism is also applicable to osteopontin and MMP-7. This is also supported by the colocalization of MMP-7 and osteopontin in IPF epithelial cells, and by the computational relationship of the expression levels of osteopontin and MMP-7. Interestingly, MMP-7 and osteopontin are β-catenin target genes [32,33]. Recently, Chilosi et al. reported impressive activation of WNT/β-catenin in IPF lungs [34]. They have mainly observed β-catenin nuclear localization in proliferative bronchiolar lesions, where it colocalized with MMP-7 [34]. Collectively, these results could indicate a mechanism by which osteopontin and MMP-7 are induced by aberrant activation of the WNT/β-catenin pathway, and each affects the function and expression of the other gene, thus representing a local positive feedback mechanism that facilitates a chronic, relentless lung disease. Although intriguing, this proposed positive, self-perpetuating loop in itself cannot explain increased collagen deposition, the critical hallmark of fibrosis. In this context, our results suggest that osteopontin affects the critical balance between MMPs and their inhibitors through its cell-specific effects. In agreement with the inhibition of interleukin 1β-stimulated increases in MMP-2 and MMP-9 observed by Xie et al. [35], we observed that in human lung fibroblasts, osteopontin caused a significant reduction of baseline as well as APMA-stimulated MMP-1, an MMP responsible for fibrillar collagen degradation. Additionally, we observed a concomitant increase in TIMP-1, the main inhibitor of MMP-1 (as well as MMP-2 and −9), and in type I collagen gene expression, suggesting that osteopontin may facilitate a profibrotic environment not only by its effect on epithelial cells but also by inducing a nondegradative microenvironment similar to the one observed in IPF and experimental lung fibrosis [36,37]. Interestingly, osteopontin did not induce α-smooth muscle actin in lung fibroblasts in vitro, suggesting that although it had a role in facilitating the profibrotic environment in IPF, it had weaker role in the formation of myofibroblast foci. However, further experiments will be needed to determine this point. Migration and proliferation of fibroblasts are essential for the expansion of their populations and the formation of the fibroblastic foci that seem to represent the “leading edge” of the progressive fibrotic process [5]. The observation that osteopontin induced both migration and proliferation of primary human lung fibroblasts suggests that osteopontin may be involved in this process and is supported by previous observations in murine and human fibroblast cell lines [15]. Osteopontin promotes fibroblast collagen gel contraction and rat cardiac fibroblast proliferation, and it has been suggested that it is an important mediator of angiotensin II regulation of fibroblast behavior in the cardiac remodeling process [38]. It also induced proliferation of vessel smooth muscle cells, suggesting that it is involved in vascular remodeling during the development of atherosclerosis [39,40]. These results highlight the sufficiency of a cytokine secreted from alveolar epithelial cell to induce many of the phenotypic changes associated with lung fibrosis. The mechanisms by which osteopontin influences epithelial and fibroblast cells are not fully understood. In general it has been proposed that osteopontin affects cells by binding to CD44 isoforms, certain integrins, and EGFR [41,42]. It is unknown whether the expression of these receptors is changed in IPF; CD44 is expressed on lung fibroblasts and epithelial cells [43], is induced in radiation- and bleomycin-induced pulmonary fibrosis [44] and in acute alveolar fibrosis [45], and is critical for resolution of noninfectious lung inflammation [46]. The integrin receptors for osteopontin are widely expressed in lung epithelial cells and fibroblasts [47], but a change in their repertoire has not been reported yet with IPF. In this paper we did not seek to fully dissect these mechanisms; however, we explored some of the possible receptors that may be important to osteopontin effect on fibroblasts and epithelial cells. Our results support some of the previous observations regarding the importance of integrin-mediated signaling in fibroblast migration. Interestingly, we observed a differential effect in epithelial and fibroblasts cells. Inhibition of CD44 significantly reduced the effects of osteopontin on cell proliferation in epithelial cells, while αvβ3 inhibition seemed to affect mostly fibroblasts. This integrin is a receptor for a wide variety of extracellular matrix ligands with an exposed RGD sequence, including vitronectin, fibronectin, fibrinogen, thrombospondin, proteolyzed collagen, von Willebrand factor, as well as osteopontin, and appears to play a critical role in cell migration [48]. The hyaluronic acid receptor CD44 is also a receptor for osteopontin, and it has been implicated in chemotaxis mediated by this mediator [10,49,50]. In our experiments, the pan-integrin antagonist GRGDS-pentapeptide added to the culture medium abolished the effects in fibroblasts and epithelial cells, suggesting that different integrins may be involved in both cell types, and that for some effects, both integrins and CD44 are required. Detailed studies of the effects of variant osteopontin isoforms as well as cells that express different receptors will be needed to elucidate these mechanisms. Our study focused on human tissues and human cell lines because of the unique features of IPF that are not readily mimicked by any animal models. We insisted on using primary human lung fibroblasts in our experiments; therefore, we are confident that these results represent a mechanism that may actually occur in the human lung. Unfortunately, it is nearly impossible to work with primary alveolar epithelial cells, and we had to resort to the epithelial cell line A549. However, we present evidence obtained from human lungs that suggest that the mechanisms that we proposed in vitro do exist in the human IPF lung. In summary, in this study we highlight the role of osteopontin in human IPF. Although previous studies have suggested that osteopontin has a potential profibrotic effect in animal models of lung fibrosis, its role in human IPF was unclear. We demonstrated that osteopontin is highly expressed in IPF lungs, and that it is primarily expressed by hyperplastic alveolar epithelial cells. We demonstrated that osteopontin affected fibroblast and epithelial cell proliferation and migration, and that it had fibrosis-relevant effects on MMP and TIMP expressions. Our results suggest a mechanism explaining most of the profibrotic effects of osteopontin by its direct effects on fibroblasts and epithelial cells in the lungs. Furthermore, our results suggest that in IPF the interaction between MMP-7 and osteopontin may be involved in the relentlessly progressive nature of the disease, and highlight osteopontin as a potential target for therapeutic intervention in this incurable disease. Supporting Information Protocol S1 Sample Mexico (746 KB ZIP). Click here for additional data file. Protocol S2 Microarrays (2.1 MB ZIP). Click here for additional data file. Accession Numbers The GenBank (http://www.ncbi.nlm.nih.gov/) accession numbers of the genes discussed in this paper are R18S (X03205), MMP-1 (NM_002421), MMP-7 (XM_017384), and TIMP-1 (X03124). Patient summary Background Idiopathic pulmonary fibrosis is a chronic progressive disease of the lung that leads to increasing amounts of scar tissue with subsequent destruction of the lung. There is no specific cure at present. Patients may be treated with corticosteroids or drugs to suppress their immune system, although these drugs are usually not effective. Some patients receive lung transplants. Why Was This Study Done? Previous work has suggested that a protein called osteopontin is increased in mice that have lung fibrosis and that mice that do not have the gene for osteopontin are protected from lung fibrosis. The researchers wanted to investigate if osteopontin was also involved in the human disease. What Did the Researchers Do and Find? They looked at samples taken from the lungs of people with idiopathic pulmonary fibrosis and other diseases and measured many genes that are expressed there. They found that osteopontin was increased in the lungs of people with idiopathic pulmonary fibrosis. They then looked at cultures of lung cells and found that osteopontin caused an increase in the number and movement of cells that are involved in lung fibrosis. Its presence also affected other proteins that seem to be involved in fibrosis. What Do These Findings Mean? Osteopontin may have a key role in the pathway that causes fibrosis to occur in the lungs of people with idiopathic pulmonary fibrosis. Further work will need to be done to confirm these results, but in the future drugs directed against osteopontin or one of the related proteins might be a possible treatment for the disease. Currently there are no such drugs. Additionally osteopontin may be useful in the diagnosis and early detection of the disease, but further studies are required. Where Can I Get More Information Online? Medline Plus has links to many pages with information on the disease: http://www.nlm.nih.gov/medlineplus/pulmonaryfibrosis.html The Coalition for Pulmonary Fibrosis is a nonprofit organization that has information for patients as well as physicians: http://www.coalitionforpf.org/ The Dorothy P. and Richard P. Simmons Center for Interstitial Lung Diseases contains information about IPF for patients and their families: http://simmonscenterild.upmc.com/
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MicroRNAs in idiopathic pulmonary fibrosis.
In this review, we describe the recent advances in the understanding of the role of microRNAs in idiopathic pulmonary fibrosis (IPF), a chronic progressive and lethal fibrotic lung disease. Approximately 10% of the microRNAs are significantly changed in IPF lungs. Among the significantly downregulated microRNAs are members of let-7, mir-29, and mir-30 families as well as miR-17∼92 cluster among the upregulated mir-155 and mir-21. Downregulation of let-7 family members leads to changes consistent with epithelial mesenchymal transition in lung epithelial cells both in vitro and in vivo, whereas inhibition of mir-21 modulates fibrosis in the bleomycin model of lung fibrosis. Perturbations of mir-155 and mir-29 have profibrotic effects in vitro but have not yet been assessed in vivo in the context of lung fibrosis. A recurrent global theme is that many microRNAs studied in IPF are both regulated by transforming growth factor β1 (TGFβ1) and regulate TGFβ1 signaling pathway by their target genes. As a result, their aberrant expression leads to a release of inhibitions on the TGFβ1 pathway and to the creation of feed-forward loops. Coanalysis of published microRNA and gene expression microarray data in IPF reveals enrichment of the TGFβ1, Wnt, sonic hedgehog, p53, and vascular endothelial growth factor pathways and complex regulatory networks. The changes in microRNA expression in the IPF lung and the evidence for their role in the fibrosis suggest that microRNAs should be evaluated as therapeutic targets in IPF. Copyright © 2011 Mosby, Inc. All rights reserved.
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Long noncoding RNAs (lncRNAs) and the molecular hallmarks of aging
During aging, progressive deleterious changes increase the risk of disease and death. Prominent molecular hallmarks of aging are genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, cellular senescence, stem cell exhaustion, and altered intercellular communication. Long noncoding RNAs (lncRNAs) play important roles in a wide range of biological processes, including age-related diseases like cancer, cardiovascular pathologies, and neurodegenerative disorders. Evidence is emerging that lncRNAs influence the molecular processes that underlie age-associated phenotypes. Here, we review our current understanding of lncRNAs that control the development of aging traits.
Author and article information
Contributors
Feng-sen Li:
ORCID: https://orcid.org/0000-0002-8012-3769
Journal
Journal ID (nlm-ta): Biomed Res Int
Journal ID (iso-abbrev): Biomed Res Int
Journal ID (publisher-id): BMRI
Title:
BioMed Research International
Publisher:
Hindawi
ISSN
(Print):
2314-6133
ISSN
(Electronic):
2314-6141
Publication date Collection: 2020
Publication date
(Electronic):
2
June
2020
Volume: 2020
Electronic Location Identifier: 6537462
Affiliations
Author notes
Author information
Feng-sen Li
https://orcid.org/0000-0002-8012-3769
Article
DOI: 10.1155/2020/6537462
PMC ID: 7290873
PubMed ID: 32596346
SO-VID: 51abf4c5-5a75-41a1-8db4-361a9322fe8b
Copyright © Copyright © 2020 Fan Wang et al.
License:
This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
History
Date
received
: 3
February
2020
Date
accepted
: 1
May
2020
Funding
Funded by: Xinjiang Uygur Autonomous Region Graduate Research and Innovation project
Award ID: XJ2019G175
Funded by: Natural Science Foundation of Xinjiang Uygur Autonomous Region
Award ID: 2019D01A06
Categories
Subject:
Research Article
Data availability: