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1.  Evolving Concepts of Apoptosis in Idiopathic Pulmonary Fibrosis 
Idiopathic pulmonary fibrosis (IPF) is a chronic, relentlessly progressive fibrosing disease of the lung of unknown etiology. Significant progress has been made in recent years in elucidating key aspects of the pathobiology of IPF. Insights into disease pathogenesis have come from studies of cell biology, growth factor/cytokine signaling, animal models of pulmonary fibrosis, and human IPF cells and tissue. A consistent finding in the ultrastructural pathology of IPF is alveolar epithelial cell injury and apoptosis. Another consistent finding in the histopathology of human IPF, described as usual interstitial pneumonia, is the accumulation of aggregates of myofibroblasts in fibroblastic foci. The extent or profusion of fibroblastic foci in lung biopsies is strongly correlated with increased mortality in patients with IPF. There is emerging evidence that myofibroblasts in IPF/usual interstitial pneumonia, both in the in vivo microenvironment and during the process of differentiation in vitro, acquire resistance to apoptosis. Here, we review the current evidence and mechanisms for this apparent “apoptosis paradox” in the pathogenesis of IPF.
doi:10.1513/pats.200601-001TK
PMCID: PMC2231523  PMID: 16738200
epithelial cells; fibroblasts; oxidative stress; transforming growth factor β; wound healing
2.  Evolving Concepts of Apoptosis in Idiopathic Pulmonary Fibrosis 
Idiopathic pulmonary fibrosis (IPF) is a chronic, relentlessly progressive fibrosing disease of the lung of unknown etiology. Significant progress has been made in recent years in elucidating key aspects of the pathobiology of IPF. Insights into disease pathogenesis have come from studies of cell biology, growth factor/cytokine signaling, animal models of pulmonary fibrosis, and human IPF cells and tissue. A consistent finding in the ultrastructural pathology of IPF is alveolar epithelial cell injury and apoptosis. Another consistent finding in the histopathology of human IPF, described as usual interstitial pneumonia, is the accumulation of aggregates of myofibroblasts in fibroblastic foci. The extent or profusion of fibroblastic foci in lung biopsies is strongly correlated with increased mortality in patients with IPF. There is emerging evidence that myofibroblasts in IPF/usual interstitial pneumonia, both in the in vivo microenvironment and during the process of differentiation in vitro, acquire resistance to apoptosis. Here, we review the current evidence and mechanisms for this apparent “apoptosis paradox” in the pathogenesis of IPF.
doi:10.1513/pats.200601-001TK
PMCID: PMC2231523  PMID: 16738200
epithelial cells; fibroblasts; oxidative stress; transforming growth factor β; wound healing
3.  Gene Expression Profiles Distinguish Idiopathic Pulmonary Fibrosis from Hypersensitivity Pneumonitis 
Rationale: Many of the interstitial lung diseases represent a diagnostic and therapeutic challenge because their clinical and even histologic features are often nonspecific. Likewise, the transcriptional signatures of most of them are unknown.
Objective: To compare the gene expression patterns from patients with idiopathic pulmonary fibrosis (IPF) hypersensitivity pneumonitis (HP), and nonspecific interstitial pneumonia (NSIP) using custom oligonucleotide microarrays.
Methods: We profiled lung biopsies from 15 patients with IPF, 12 with HP, and eight with NSIP. Labeled complementary ribonucleic acid was hybridized to a custom Affymetrix oligonucleotide DNA microarray using standard Affymetrix protocols. The custom array, Hu03, contained 59,619 probe sets representing an estimated 46,000 gene clusters.
Results: We identified statistically significant gene expression signatures that characterize HP and IPF. The HP gene expression signature was enriched for genes that are functionally associated with inflammation, T-cell activation, and immune responses, whereas the IPF signature was characterized by the expression of tissue remodeling, epithelial, and myofibroblast genes. We then compared these gene expression signatures to classify NSIP, a histologic pattern that is often difficult to differentiate consistently from HP and IPF. Two cases exhibited an IPF-like gene expression, another one could be more properly classified as HP, whereas others did not resemble HP or IPF, suggesting that they may represent idiopathic NSIP.
Conclusions: Our results underscore the value of gene expression signatures to classify the interstitial lung diseases and to understand pathogenic mechanisms, and suggest new ways to improve the diagnosis and treatment of patients with these diseases.
doi:10.1164/rccm.200504-644OC
PMCID: PMC2662988  PMID: 16166619
global transcription analysis; interstitial lung diseases; lung fibrosis; microarrays; nonspecific interstitial pneumonia
4.  Gene Expression Profiling as a Window into Idiopathic Pulmonary Fibrosis Pathogenesis 
Expression microarrays that provide genome-level, transcriptional, high-resolution profiles have been applied successfully to multiple diseases. Although microarrays provide information regarding thousands of genes, many investigators prefer to focus on a single gene and validate its role, an approach often supported by grant and journal reviewers. Only a minority of investigators focus on global changes in gene expression. Here, we describe and contrast two general approaches to the use of microarray data: the reductionist “cherry picking” approach and the more global, quantitative “systems” approach. We describe microarray analysis experiments relevant to idiopathic pulmonary fibrosis (IPF) in the context of these two approaches. Although it seems that the cherry-picking approaches have been successful in identifying new relevant genes in IPF, we suggest that to fulfill the discovery potential of microarrays in IPF and to create a working model of IPF, unbiased integrative systems approaches are required.
doi:10.1513/pats.200601-011TK
PMCID: PMC2658685  PMID: 16738198
FIZZ1; matrix metalloprotease; microarrays; osteopontin; systems biology
5.  High Resolution Multi-Detector CT Aided Tissue Analysis and Quantification of Lung Fibrosis 
Academic radiology  2007;14(7):772-787.
Rational and Objectives
Volumetric high-resolution scans can be acquired of the lungs with multi-detector CT (MDCT). Such scans have potential to facilitate useful visualization, characterization, and quantification of the extent of diffuse lung diseases, such as Usual Interstitial Pneumonitis or Idiopathic Pulmonary Fibrosis (UIP/IPF). There is a need to objectify, standardize and improve the accuracy and repeatability of pulmonary disease characterization and quantification from such scans. This paper presents a novel texture analysis approach toward classification and quantification of various pathologies present in lungs with UIP/IPF. The approach integrates a texture matching method with histogram feature analysis.
Materials and Methods
Patients with moderate UIP/IPF were scanned on a Lightspeed 8-detector GE CT scanner (140kVp, 250mAs). Images were reconstructed with 1.25mm slice thickness in a high-frequency sparing algorithm (BONE) with 50% overlap and a 512 × 512 axial matrix, (0.625 mm3 voxels). Eighteen scans were used in this study. Each dataset is pre-processed which includes segmentation of the lungs and the broncho-vascular trees. Two types of analysis were performed, first an analysis of independent volume of interests (VOIs) and second an analysis of whole lung datasets.
1.) Fourteen of the eighteen scans were used to create a database of independent 15×15×15 cubic voxel VOIs. The VOIs were selected by experts as having greater than 70% of the defined class. The database was composed of the following: Honeycombing (# of VOIs 337), Reticular (130), Ground glass (148), Normal (240), and Emphysema (54). This database was used to develop our algorithm. Three progressively challenging classification experiments were designed to test our algorithm. All three experiments were performed using a 10-fold cross validation method for error estimation. Experiment 1 consisted of a two class discrimination: Normal and Abnormal. Experiment 2 consisted of a four class discrimination: Normal, Reticular, Honeycombing, and Emphysema. Experiment 3 consisted of a five class discrimination: Normal, Ground glass, Reticular, Honeycombing, and Emphysema.
2.) The remaining four scans were used to further test the algorithm on new data in the context of a whole lung analysis. Each of the four datasets was manually segmented by three experts. These datasets included Normal, Reticular and Honeycombing regions and did not include Ground glass or Emphysema. The accuracy of the classification algorithm was then compared with results from experts.
Results
Independent VOIs: 1.) Two class discrimination problem (sensitivity, specificity): Normal versus Abnormal (92.96%,93.78%). 2.) Four class discrimination problem: Normal (92%,95%), Reticular (86%,87%), Honeycombing (74%,98%), and Emphysema (93%,98%). 3.) Five class discrimination problem: Normal(92%,95%), Ground glass (75%,89%), Reticular (22%,92%), Honeycombing (74%,91%), and Emphysema (94%,98%).
Whole lung datasets: 1.) William's Index shows that algorithm classification of lungs agrees with the experts as well as the experts agree with themselves. 2.) Student-T test between overlap measures of algorithm and expert (AE) and expert and expert (EE) : Normal (t=-1.20, p = 0.230), Reticular (t=-1.44, p = 0.155), Honeycombing (t=-3.15, p = 0.003). 3.) Lung Volumes Intra-class correlation: Dataset 1 (ICC = 0.9984, F = 0.0007); Dataset 2 (ICC = 0.9559, F = 0); Dataset 3 (ICC = 0.8623, F= 0.0015); Dataset 4 (ICC = 0.7807, F = 0.0136).
Conclusions
We have demonstrated that our novel method is computationally efficient and produces results comparable to expert radiologic judgment. It is effective in the classification of normal versus abnormal tissue and performs as well as the experts in distinguishing among typical pathologies present in lungs with UIP/IPF. The continuing development of quantitative metrics will improve quantification of disease and provide objective measures of disease progression.
doi:10.1016/j.acra.2007.03.009
PMCID: PMC2701291  PMID: 17574128
Multi-Detector CT; Lung imaging; Tissue Classification; Quantitative Lung Analysis; Texture Analysis
6.  Immunoglobulin Free Light Chains Are Increased in Hypersensitivity Pneumonitis and Idiopathic Pulmonary Fibrosis 
PLoS ONE  2011;6(9):e25392.
Background
Idiopathic pulmonary fibrosis (IPF), a devastating lung disorder of unknown aetiology, and chronic hypersensitivity pneumonitis (HP), a disease provoked by an immunopathologic reaction to inhaled antigens, are two common interstitial lung diseases with uncertain pathogenic mechanisms. Previously, we have shown in other upper and lower airway diseases that immunoglobulin free light chains (FLCs) are increased and may be involved in initiating a local inflammation. In this study we explored if such a mechanism may also apply to HP and IPF.
Methods
In this study we examined the presence of FLC in serum and BAL fluid from 21 IPF and 22 HP patients and controls. IgG, IgE and tryptase concentrations were measured in BAL fluid only. The presence of FLCs, plasma cells, B cells and mast cells in lung tissue of 3 HP and 3 IPF patients and 1 control was analyzed using immunohistochemistry.
Results
FLC concentrations in serum and BAL fluid were increased in IPF and HP patients as compared to control subjects. IgG concentrations were only increased in HP patients, whereas IgE concentrations were comparable to controls in both patient groups. FLC-positive cells, B cells, plasma cells, and large numbers of activated mast cells were all detected in the lungs of HP and IPF patients, not in control lung.
Conclusion
These results show that FLC concentrations are increased in serum and BAL fluid of IPF and HP patients and that FLCs are present within affected lung tissue. This suggests that FLCs may be involved in mediating pathology in both diseases.
doi:10.1371/journal.pone.0025392
PMCID: PMC3182208  PMID: 21980441
7.  Clinical Characteristics of Idiopathic Pulmonary Fibrosis Patients with Diabetes Mellitus: the National Survey in Korea from 2003 to 2007 
Journal of Korean Medical Science  2012;27(7):756-760.
Evidence suggests that diabetes mellitus (DM) is associated with idiopathic pulmonary fibrosis (IPF). According to the new IPF guidelines, high-resolution computed tomography (HRCT) is an essential means of diagnosing IPF. We investigated the relationship between IPF and DM in patients treated between 2003 and 2007. Newly diagnosed IPF patients in large university teaching hospitals in Korea were enrolled from January 2003 to December 2007. We retrospectively analyzed 1,685 patients using the interstitial lung disease (ILD) registry. In total, 299 IPF patients (17.8%) also had DM. The mean age of our subjects was 68.0 ± 9.4 yr. HRCT showed significantly more reticular and honeycomb patterns in IPF patients with DM than in IPF patients without DM (P = 0.014, P = 0.028, respectively). Furthermore, significantly higher incidences of hypertension, cardiovascular diseases, and other malignancies (except lung cancer) were found in IPF patients with DM than in IPF patients without DM. In conclusion, IPF patients with DM are more likely to have the usual interstitial pneumonia (UIP) pattern, including reticular and honeycomb patterns, on HRCT than are those without DM.
doi:10.3346/jkms.2012.27.7.756
PMCID: PMC3390723  PMID: 22787370
Idiopathic Pulmonary Fibrosis; Diabetes Mellitus; High Resolution Computed Tomography
8.  Cleaved cytokeratin-18 is a mechanistically informative biomarker in idiopathic pulmonary fibrosis 
Respiratory Research  2012;13(1):105.
Background
Stress of the endoplasmic reticulum (ER) leading to activation of the unfolded protein response (UPR) and alveolar epithelial cell (AEC) apoptosis may play a role in the pathogenesis of idiopathic pulmonary fibrosis (IPF). Our objectives were to determine whether circulating caspase-cleaved cytokeratin-18 (cCK-18) is a marker of AEC apoptosis in IPF, define the relationship of cCK-18 with activation of the UPR, and assess its utility as a diagnostic biomarker.
Methods
IPF and normal lung tissues were stained with the antibody (M30) that specifically binds cCK-18. The relationship between markers of the UPR and cCK-18 was determined in AECs exposed in vitro to thapsigargin to induce ER stress. cCK-18 was measured in serum from subjects with IPF, hypersensitivity pneumonitis (HP), nonspecific interstitial pneumonia (NSIP), and control subjects.
Results
cCK-18 immunoreactivity was present in AECs of IPF lung, but not in control subjects. Markers of the UPR (phosphorylated IRE-1α and spliced XBP-1) were more highly expressed in IPF type II AECs than in normal type II AECs. Phosphorylated IRE-1α and cCK-18 increased following thapsigargin-induced ER stress. Serum cCK-18 level distinguished IPF from diseased and control subjects. Serum cCK-18 was not associated with disease severity or outcome.
Conclusions
cCK-18 may be a marker of AEC apoptosis and UPR activation in patients with IPF. Circulating levels of cCK-18 are increased in patients with IPF and cCK-18 may be a useful diagnostic biomarker.
doi:10.1186/1465-9921-13-105
PMCID: PMC3547729  PMID: 23167970
Idiopathic interstitial pneumonia; idiopathic pulmonary fibrosis; lung fibrosis; ER stress; apoptosis
9.  Multiplex protein profiling of bronchoalveolar lavage in idiopathic pulmonary fibrosis and hypersensitivity pneumonitis 
Annals of Thoracic Medicine  2013;8(1):38-45.
CONTEXT:
Idiopathic pulmonary fibrosis (IPF) and chronic hypersensitivity pneumonitis (HP) are diffuse parenchymal lung diseases characterized by a mixture of inflammation and fibrosis, leading to lung destruction and finally death.
AIMS:
The aim of this study was to compare different pathophysiological mechanisms, such as angiogenesis, coagulation, fibrosis, tissue repair, inflammation, epithelial damage, oxidative stress, and matrix remodeling, in both disorders using bronchoalveolar lavage (BAL).
METHODS:
At diagnosis, patients underwent bronchoscopy with BAL and were divided into three groups: Control (n = 10), HP (n = 11), and IPF (n = 11), based on multidisciplinary approach (clinical examination, radiology, and histology): Multiplex searchlight technology was used to analyze 25 proteins representative for different pathophysiological processes: Eotaxin, basic fibroblast growth factor (FGFb), fibronectin, hepatocyte growth factor (HGF), interleukine (IL)-8, IL-12p40, IL-17, IL-23, monocyte chemotactic protein (MCP-1), macrophage-derived chemokine (MDC), myeloperoxidase (MPO), matrix metalloproteinase (MMP)-8, MMP-9, active plasminogen activating inhibitor 1 (PAI-1), pulmonary activation regulated chemokine (PARC), placental growth factor (PlGF), protein-C, receptor for advanced glycation end products (RAGE), regulated on activation normal T cells expressed and secreted (RANTES), surfactant protein-C (SP-C), transforming growth factor-β1 (TGF-β1), tissue inhibitor of metalloproteinase-1 (TIMP-1), tissue factor, thymic stromal lymphopoietin (TSLP), and vascular endothelial growth factor (VEGF).
RESULTS:
All patients suffered from decreased pulmonary function and abnormal BAL cell differential compared with control. Protein levels were increased in both IPF and HP for MMP-8 (P = 0.022), MMP-9 (P = 0.0020), MCP-1 (P = 0.0006), MDC (P = 0.0048), IL-8 (P = 0.013), MPO (P = 0.019), and protein-C (P = 0.0087), whereas VEGF was decreased (P = 0.0003) compared with control. HGF was upregulated in HP (P = 0.0089) and active PAI-1 was upregulated (P = 0.019) in IPF compared with control. Differences in expression between IPF and HP were observed for IL-12p40 (P = 0.0093) and TGF-β1 (P = 0.0045).
CONCLUSIONS:
Using BAL, we demonstrated not only expected similarities but also important differences in both disorders, many related to the innate immunity. These findings provide new clues for further research in both disorders.
doi:10.4103/1817-1737.105718
PMCID: PMC3573557  PMID: 23440593
Bronchoalveolar lavage; enzyme-linked immunosorbent assay; hypersensitivity pneumonitis; interstitial lung disease; idiopathic pulmonary fibrosis
10.  IDIOPATHIC PULMONARY FIBROSIS: A DISORDER OF EPITHELIAL CELL DYSFUNCTION 
Idiopathic pulmonary fibrosis (IPF) is characterized by progressive dyspnea, interstitial infiltrates in lung parenchyma, and restriction on pulmonary function testing. IPF is the most common and severe of the idiopathic interstitial pneumonias (IIPs), with most individuals progressing to respiratory failure. Multiple lines of evidence reveal prominent roles for alveolar epithelial cells (AECs) in disease. Our current disease paradigm is that ongoing or repetitive injurious stimuli in the presence of a genetic or acquired dysfunctional type II AEC phenotype results in increased AEC injury/apoptosis, deficiencies in regeneration of normal alveolar structure, and aberrant lung repair and fibroblast activation, leading to progressive fibrosis. While the nature of injurious events and processes involved in aberrant repair of the alveolar epithelium are not well understood, ongoing investigations provide hope to better understand mechanisms by which AECs maintain homeostasis or contribute to fibrosis. These strategies may hold promise for developing novel treatment approaches for IPF.
doi:10.1097/MAJ.0b013e31821a9d8e
PMCID: PMC3103044  PMID: 21613930
alveolar epithelial cell; familial interstitial pneumonia; idiopathic pulmonary fibrosis; lung
11.  Challenges in pulmonary fibrosis · 1: Use of high resolution CT scanning of the lung for the evaluation of patients with idiopathic interstitial pneumonias 
Thorax  2007;62(6):546-553.
High resolution CT (HRCT) scanning has contributed significantly to the evaluation of patients with interstitial lung disease and is particularly useful in the diagnosis of idiopathic pulmonary fibrosis (IPF). The characteristic radiographic features of the idiopathic interstitial pneumonias on HRCT scans have been increasingly analysed and are now fairly well described. Based on current data, HRCT scanning can provide a confident, highly specific diagnosis of IPF in many patients with diffuse lung disease. This article reviews an organised approach to HRCT scanning and identifies the features that allow an accurate diagnosis of the idiopathic interstitial pneumonias to be made. The role of surgical lung biopsy is discussed in the diagnosis of cases when a definite HRCT diagnosis cannot be made.
doi:10.1136/thx.2004.040022
PMCID: PMC2117220  PMID: 17536033
12.  Genetic studies provide clues on the pathogenesis of idiopathic pulmonary fibrosis 
Disease Models & Mechanisms  2013;6(1):9-17.
Idiopathic pulmonary fibrosis (IPF) is a progressive and often fatal lung disease for which there is no known treatment. Although the traditional paradigm of IPF pathogenesis emphasized chronic inflammation as the primary driver of fibrotic remodeling, more recent insights have challenged this view. Linkage analysis and candidate gene approaches have identified four genes that cause the inherited form of IPF, familial interstitial pneumonia (FIP). These four genes encode two surfactant proteins, surfactant protein C (encoded by SFTPC) and surfactant protein A2 (SFTPA2), and two components of the telomerase complex, telomerase reverse transcriptase (TERT) and the RNA component of telomerase (TERC). In this review, we discuss how investigating these mutations, as well as genetic variants identified in other inherited disorders associated with pulmonary fibrosis, are providing new insights into the pathogenesis of common idiopathic interstitial lung diseases, particularly IPF. Studies in this area have highlighted key roles for epithelial cell injury and dysfunction in the development of lung fibrosis. In addition, genetic approaches have uncovered the importance of several processes – including endoplasmic reticulum stress and the unfolded protein response, DNA-damage and -repair pathways, and cellular senescence – that might provide new therapeutic targets in fibrotic lung diseases.
doi:10.1242/dmm.010736
PMCID: PMC3529334  PMID: 23268535
13.  Genetic mutations in surfactant protein C are a rare cause of sporadic cases of IPF 
Thorax  2004;59(11):977-980.
Background: While idiopathic pulmonary fibrosis (IPF) is one of the most common forms of interstitial lung disease, the aetiology of IPF is poorly understood. Familial cases of pulmonary fibrosis suggest a genetic basis for some forms of the disease. Recent reports have linked genetic mutations in surfactant protein C (SFTPC) with familial forms of pulmonary fibrosis, including one large family in which a number of family members were diagnosed with usual interstitial pneumonitis (UIP), the pathological correlate to IPF. Because of this finding in familial cases of pulmonary fibrosis, we searched for SFTPC mutations in a cohort of sporadic cases of UIP and non-specific interstitial pneumonitis (NSIP).
Methods: The gene for SFTPC was sequenced in 89 patients diagnosed with UIP, 46 patients with NSIP, and 104 normal controls.
Results: Ten single nucleotide polymorphisms in the SFTPC sequence were found in IPF patients and not in controls. Only one of these created an exonic change resulting in a change in amino acid sequence. In this case, a T to C substitution resulted in a change in amino acid 73 of the precursor protein from isoleucine to threonine. Of the remaining polymorphisms, one was in the 5' UTR, two were exonic without predicted amino acid sequence changes, and six were intronic. One intronic mutation suggested a potential enhancement of a splicing site.
Conclusions: Mutations in SFTPC are identified infrequently in this patient population. These findings indicate that SFTPC mutations do not contribute to the pathogenesis of IPF in the majority of sporadic cases.
doi:10.1136/thx.2004.026336
PMCID: PMC1746860  PMID: 15516475
14.  Signaling pathways in the epithelial origins of pulmonary fibrosis 
Cell Cycle  2010;9(14):2769-2776.
Pulmonary fibrosis complicates a number of disease processes and leads to substantial morbidity and mortality. Idiopathic pulmonary fibrosis (IPF) is perhaps the most pernicious and enigmatic form of the greater problem of lung fibrogenesis with a median survival of three years from diagnosis in affected patients. In this review, we will focus on the pathology of IPF as a model of pulmonary fibrotic processes, review possible cellular mechanisms, review current treatment approaches and review two transgenic mouse models of lung fibrosis to provide insight into processes that cause lung fibrosis. We will also summarize the potential utility of signaling pathway inhibitors as a future treatment in pulmonary fibrosis. Finally, we will present data demonstrating a minimal contribution of epithelial-mesenchymal transition in the development of fibrotic lesions in the transforming growth factor-alpha transgenic model of lung fibrosis.
doi:10.4161/cc.9.14.12268
PMCID: PMC3040960  PMID: 20676040
epithelial mesenchymal transition; epidermal growth factor receptor; transforming growth factor alpha
15.  Clinical Predictors of a Diagnosis of Idiopathic Pulmonary Fibrosis 
Rationale: Idiopathic pulmonary fibrosis (IPF) and other idiopathic interstitial pneumonias (IIPs) have similar clinical and radiographic features, but their histopathology, response to therapy, and natural history differ. A surgical lung biopsy is often required to distinguish between these entities.
Objectives: We sought to determine if clinical variables could predict a histopathologic diagnosis of IPF in patients without honeycomb change on high-resolution computed tomography (HRCT).
Methods: Data from 97 patients with biopsy-proven IPF and 38 patients with other IIPs were examined. Logistic regression models were built to identify the clinical variables that predict histopathologic diagnosis of IPF.
Measurements and Main Results: Increasing age and average total HRCT interstitial score on HRCT scan of the chest may predict a biopsy confirmation of IPF. Sex, pulmonary function, presence of desaturation, or distance walked during a 6-minute walk test did not help discriminate pulmonary fibrosis from other IIPs.
Conclusions: Clinical data may be used to predict a diagnosis of IPF over other IIPs. Validation of these data with a prospective study is needed.
doi:10.1164/rccm.200906-0959OC
PMCID: PMC2854332  PMID: 20056903
idiopathic pulmonary fibrosis; idiopathic interstitial pneumonia; diagnosis; computed tomography of the chest
16.  A review of current and novel therapies for idiopathic pulmonary fibrosis 
Journal of Thoracic Disease  2013;5(1):48-73.
Idiopathic pulmonary fibrosis (IPF) is a progressively fibrotic interstitial lung disease that is associated with a median survival of 2-3 years from initial diagnosis. To date, there is no treatment approved for IPF in the United States, and only one pharmacological agent has been approved outside of the United States. Nevertheless, research over the past 10 years has provided us with a wealth of information on its histopathology, diagnostic work-up, and a greater understanding of its pathophysiology. Specifically, IPF is no longer thought to be a predominantly pro-inflammatory disorder. Rather, the fibrosis in IPF is increasingly understood to be the result of a fibroproliferative and aberrant wound healing cascade. The development of therapeutic targets has shifted in accord with this paradigm change. This review highlights the current understanding of IPF, and the recent as well as novel therapeutics being explored in clinical trials for the treatment of this devastating disease.
doi:10.3978/j.issn.2072-1439.2012.12.07
PMCID: PMC3548009  PMID: 23372951
Idiopathic pulmonary fibrosis/drug therapy; idiopathic pulmonary fibrosis/pathology; molecular targeted therapy; clinical trials
17.  Clinical review: Idiopathic pulmonary fibrosis acute exacerbations - unravelling Ariadne's thread 
Critical Care  2010;14(6):246.
Idiopathic pulmonary fibrosis (IPF) is a dreadful, chronic, and irreversibly progressive fibrosing disease leading to death in all patients affected, and IPF acute exacerbations constitute the most devastating complication during its clinical course. IPF exacerbations are subacute/acute, clinically significant deteriorations of unidentifiable cause that usually transform the slow and more or less steady disease decline to the unexpected appearance of acute lung injury/acute respiratory distress syndrome (ALI/ARDS) ending in death. The histological picture is that of diffuse alveolar damage (DAD), which is the tissue counterpart of ARDS, upon usual interstitial pneumonia, which is the tissue equivalent of IPF. ALI/ARDS and acute interstitial pneumonia share with IPF exacerbations the tissue damage pattern of DAD. 'Treatment' with high-dose corticosteroids with or without an immunosuppressant proved ineffective and represents the coup de grace for these patients. Provision of excellent supportive care and the search for and treatment of the 'underlying cause' remain the only options. IPF exacerbations require rapid decisions about when and whether to initiate mechanical support. Admission to an intensive care unit (ICU) is a particular clinical and ethical challenge because of the extremely poor outcome. Transplantation in the ICU setting often presents insurmountable difficulties.
doi:10.1186/cc9241
PMCID: PMC3220036  PMID: 21235829
18.  Early Interstitial Lung Disease in Familial Pulmonary Fibrosis 
Rationale: Identification of early, asymptomatic interstitial lung disease (ILD) in populations at risk of developing idiopathic pulmonary fibrosis (IPF) may improve the understanding of the natural history of IPF.
Objectives: To determine clinical, radiographic, physiologic, and pathologic features of asymptomatic ILD in family members of patients with familial IPF.
Methods: One hundred sixty-four subjects from 18 kindreds affected with familial IPF were evaluated for ILD. Bronchoalveolar lavage fluid cells were analyzed using flow cytometry. Lung biopsies were performed in six subjects with asymptomatic ILD.
Measurements and Main Results: High-resolution computed tomography abnormalities suggesting ILD were identified in 31 (22%) of 143 asymptomatic subjects. Subjects with asymptomatic ILD were significantly younger than subjects with known familial IPF (P < 0.001) and significantly older than related subjects without lung disease (P < 0.001). A history of smoking was identified in 45% of subjects with asymptomatic ILD and in 67% of subjects with familial IPF; these percentages were significantly higher than that of related subjects without lung disease (23%) (P = 0.02 and P < 0.001, respectively). Percentages of activated CD4+ lymphocytes were significantly higher in bronchoalveolar lavage fluid cells from subjects with asymptomatic ILD compared with related subjects without lung disease (P < 0.001). Lung biopsies performed in subjects with asymptomatic ILD revealed diverse histologic subtypes.
Conclusions: Asymptomatic ILD in individuals at risk of developing familial IPF can be identified using high-resolution computed tomography scan of the chest, especially in those with a history of smoking. Lung biopsies from individuals in this cohort with early asymptomatic lung disease demonstrate various histologic subtypes of ILD.
doi:10.1164/rccm.200702-254OC
PMCID: PMC1994234  PMID: 17641157
idiopathic pulmonary fibrosis; interstitial lung disease; high-resolution computed tomography; bronchoalveolar lavage; asymptomatic interstitial lung disease
19.  Platelet-derived growth factor in idiopathic pulmonary fibrosis. 
Journal of Clinical Investigation  1990;86(4):1055-1064.
Fibrosis is a complex process involving an inflammatory reaction, fibroblast proliferation, and abnormal accumulation of interstitial collagens. Mononuclear cells are usually present in lung fibrosis. Activated monocytes and macrophages in culture have been shown to produce several growth factors including platelet-derived growth factor (PDGF). PDGF is a potent mitogen and chemoattractant for fibroblasts and smooth muscle cells and a stimulator of collagen synthesis. We have studied the expression of c-sis/PDGF-2 mRNA in lung tissues derived from five patients with idiopathic pulmonary fibrosis (IPF) and from four control individuals without IPF. Northern blot analysis of specimens obtained from four patients with IPF revealed the expression of the c-sis/PDGF-2 protooncogene. A control lung tissue without IPF did not express the c-sis protooncogene. In situ hybridization extended these studies demonstrating the expression of the c-sis mRNA in the five specimens with IPF but not in the four control specimens without IPF. The expression of c-sis mRNA was localized primarily in the epithelial cells. Invading alveolar macrophages also expressed c-sis mRNA. The expression of c-sis mRNA was accompanied by the expression of PDGF-like proteins in lung specimens with IPF but not in control lung specimens. These findings demonstrate the in vivo expression of the c-sis/PDGF-2 protooncogene and the production of PDGF-like proteins in the epithelial cells and macrophages of the fibrotic tissue. This localized and sustained production of PDGF-like mitogen may constitute an important contributing factor in the abnormal fibroblast proliferation and collagen production, events associated with pulmonary fibrosis.
Images
PMCID: PMC296832  PMID: 2170444
20.  Morphologic-physiologic correlates of the severity of fibrosis and degree of cellularity in idiopathic pulmonary fibrosis. 
Journal of Clinical Investigation  1979;63(4):665-676.
Idiopathic pulmonary fibrosis (IPF) is a progressive disease of lung parenchyma characterized by a chronic inflammatory cellular infiltration and varying degrees of interstitial fibrosis. Current data indicate that the severity of fibrosis and the degree of cellularity determine, in part, the prognosis of IPF and the response to therapy. Whereas lung biopsy gives the best assessement of fibrosis and cellularity, physiologic studies are used to stage and monitor the disease process. To determine which physiologic studies correlate best with severity of fibrosis and degree of cellularity, these parameters were graded in lung biopsies of 23 patients with IPF and compared with a variety of physiologic studies. Although vital capacity, total lung capacity, and diffusing capacity are commonly used as objective monitors of the disease process, none of these parameters correlated with either the severity of fibrosis or the degree of cellularity in biopsy specimens. In contrast, almost all parameters of lung distensibility correlated with the morphologic assessment of degree of fibrosis; compliance had the best correlation. Parameters of distensibility, however, correlated poorly with the degree of cellularity. In comparison, gas exchange during exercise correlated with both morphologic parameters; the exercise-induced changes in arterial oxygen pressure per liter of oxygen consumed had a high correlation with the degree of fibrosis (r = 0.89; P less than 0.001) and correlated to a lesser extent with the degree of cellularity (r = 0.56; P = 0.009). In contrast, neither the resting arterial oxygen tension nor the arterial oxygen tension at maximal exercise correlated with the morphologic assessment of degree of fibrosis or the degree of cellularity. These morphologic-physiologic comparisons suggest that (a) lung volumes and diffusing capacity are poor monitors of both the degree of fibrosis and the degree of cellularity; (b) the fibrotic process contributes, at least in part, to parameters of lung distensibility, and both fibrosis and cellularity contribute to gas exchange alterations during exercise; and (c) parameters of lung distensibility and exercise-induced gas exchange alterations may be useful in staging the severity of disease in IPF.
PMCID: PMC372001  PMID: 438328
21.  Macrophage derived chemokine (CCL22), thymus and activation-regulated chemokine (CCL17), and CCR4 in idiopathic pulmonary fibrosis 
Respiratory Research  2009;10(1):80.
Background
Idiopathic pulmonary fibrosis (IPF) is a chronically progressive interstitial lung disease of unknown etiology. Previously, we have demonstrated the selective upregulation of the macrophage-derived chemokine CCL22 and the thymus activation-regulated chemokine CCL17 among chemokines, in a rat model of radiation pneumonitis/pulmonary fibrosis and preliminarily observed an increase in bronchoalveolar (BAL) fluid CCL22 levels of IPF patients.
Methods
We examined the expression of CCR4, a specific receptor for CCL22 and CCL17, in bronchoalveolar lavage (BAL) fluid cells, as well as the levels of CCL22 and CCL17, to elucidate their pathophysiological roles in pulmonary fibrosis. We also studied their immunohistochemical localization.
Results
BAL fluid CCL22 and CCL17 levels were significantly higher in patients with IPF than those with collagen vascular diseases and healthy volunteers, and there was a significant correlation between the levels of CCL22 and CCL17 in patients with IPF. CCL22 levels in the BAL fluid did not correlate with the total cell numbers, alveolar lymphocytes, or macrophages in BAL fluid. However, the CCL22 levels significantly correlated with the numbers of CCR4-expressing alveolar macrophages. By immunohistochemical and immunofluorescence analysis, localization of CCL22 and CCR4 to CD68-positive alveolar macrophages as well as that of CCL17 to hyperplastic epithelial cells were shown. Clinically, CCL22 BAL fluid levels inversely correlated with DLco/VA values in IPF patients.
Conclusion
We speculated that locally overexpressed CCL22 may induce lung dysfunction through recruitment and activation of CCR4-positive alveolar macrophages.
doi:10.1186/1465-9921-10-80
PMCID: PMC2741459  PMID: 19715610
22.  Reactive Oxygen Species Are Required for Maintenance and Differentiation of Primary Lung Fibroblasts in Idiopathic Pulmonary Fibrosis 
PLoS ONE  2010;5(11):e14003.
Background
Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal illness whose pathogenesis remains poorly understood. Recent evidence suggests oxidative stress as a key player in the establishment/progression of lung fibrosis in animal models and possibly in human IPF. The aim of the present study was to characterize the cellular phenotype of fibroblasts derived from IPF patients and identify underlying molecular mechanisms.
Methodology/Principal Findings
We first analyzed the baseline differentiation features and growth ability of primary lung fibroblasts derived from 7 histology proven IPF patients and 4 control subjects at different culture passages. Then, we focused on the redox state and related molecular pathways of IPF fibroblasts and investigated the impact of oxidative stress in the establishment of the IPF phenotype. IPF fibroblasts were differentiated into alpha-smooth muscle actin (SMA)-positive myofibroblasts, displayed a pro-fibrotic phenotype as expressing type-I collagen, and proliferated lower than controls cells. The IPF phenotype was inducible upon oxidative stress in control cells and was sensitive to ROS scavenging. IPF fibroblasts also contained large excess of reactive oxygen species (ROS) due to the activation of an NADPH oxidase-like system, displayed higher levels of tyrosine phosphorylated proteins and were more resistant to oxidative-stress induced cell death. Interestingly, the IPF traits disappeared with time in culture, indicating a transient effect of the initial trigger.
Conclusions/Significance
Robust expression of α-SMA and type-I collagen, high and uniformly-distributed ROS levels, resistance to oxidative-stress induced cell death and constitutive activation of tyrosine kinase(s) signalling are distinctive features of the IPF phenotype. We suggest that this phenotype can be used as a model to identify the initial trigger of IPF.
doi:10.1371/journal.pone.0014003
PMCID: PMC2982828  PMID: 21103368
23.  Mimics in chest disease: interstitial opacities 
Insights into Imaging  2012;4(1):9-27.
Septal, reticular, nodular, reticulonodular, ground-glass, crazy paving, cystic, ground-glass with reticular, cystic with ground-glass, decreased and mosaic attenuation pattern characterise interstitial lung diseases on high-resolution computed tomography (HRCT). Occasionally different entities mimic each other, either because they share identical HRCT findings or because of superimposition of patterns. Idiopathic pulmonary fibrosis (IPF), fibrosis associated with connective tissue disease, asbestosis, end-stage sarcoidosis or chronic hypersensitivity pneumonitis (HP) may present with lower zone, subpleural reticular pattern associated with honeycombing. Lymphangiomyomatosis may be indistinguishable from histiocytosis or extensive emphysema. Both pulmonary oedema and lymphangitic carcinomatosis may be characterised by septal pattern resulting from thickened interlobular septa. Ill-defined centrilobular nodular pattern may be identically present in HP and respiratory bronchiolitis–associated with interstitial lung disease (RBILD). Sarcoidosis may mimic miliary tuberculosis or haematogenous metastases presenting with miliary pattern, while endobronchial spread of tuberculosis may be indistinguishable from panbronchiolitis, both presenting with tree-in-bud pattern. Atypical infection presenting with ground-glass mimics haemorrhage. Ground-glass pattern with minimal reticulation is seen in desquamative interstitial pneumonia (DIP), RBILD and non-specific interstitial pneumonia (NSIP). Obliterative bronchiolitis and panlobular emphysema may present with decreased attenuation pattern, while obliterative bronchiolitis, chronic pulmonary embolism and HP may manifest with mosaic attenuation pattern. Various mimics in interstitial lung diseases exist. Differential diagnosis is narrowed based on integration of predominant HRCT pattern and clinical history.
Teaching Points
• To learn about the different HRCT patterns, which are related to interstitial lung diseases.
• To be familiar with the more “classical” entities presenting with each HRCT pattern.
• To discuss possible overlap of different HRCT patterns and the more common mimics in each case.
• To learn about some clues that help differentiate the various diagnostic mimics on HRCT.
doi:10.1007/s13244-012-0207-7
PMCID: PMC3579994  PMID: 23247773
Interstitial lung diseases; HRCT patterns; Mimics; Reticular; Nodular; Ground-glass opacity; Cystic
24.  Interleukin-13 and Its Receptors in Idiopathic Interstitial Pneumonia: Clinical Implications for Lung Function 
Journal of Korean Medical Science  2009;24(4):614-620.
Idiopathic interstitial pneumonia (IIP) is characterized by varying degrees of interstitial fibrosis. IL-13 and IL-4 are strong inducers of tissue fibrosis, whereas IFN-γ has antifibrotic potential. However, the roles of these substances in IIP remain unknown. IL-13, IL-4, and IFN-γ were measured in the BAL fluid of 16 idiopathic pulmonary fibrosis (IPF) patients, 10 nonspecific interstitial pneumonia (NSIP) patients, and 8 normal controls. The expression of IL-13 and IL-13Rα1/α2 in lung tissues was analyzed using ELISA and immunohistochemistry. IL-13 levels were significantly higher in IPF patients than the others (P<0.05). IL-4 levels were higher in both IPF and NSIP patients than in normal controls (P<0.05), and IFN-γ levels were lower in NSIP patients than in normal controls (P=0.047). IL-13 levels correlated inversely with FVC% (r=-0.47, P=0.043) and DLCO% (r=-0.58, P=0.014) in IPF and NSIP patients. IL-13 was strongly expressed in the smooth muscle, bronchial epithelium, alveolar macrophages and endothelium of IPF patients. IL-13Rα1, rather than IL-13Rα2, was strongly expressed in the smooth muscle, bronchial epithelium, and endothelium of IPF patients. IL-13 and its receptors may contribute to the pathogenesis of fibrosis in IIP and appear to be related to the severity of the disease.
doi:10.3346/jkms.2009.24.4.614
PMCID: PMC2719183  PMID: 19654941
Interleukin-13; Interleukin-13 Receptor Alpha1 Subunit; Interleukin-13 Receptor Alpha2 Subunit; Idiopathic Pulmonary Fibrosis; Lung Function; NSIP
25.  Analysis of cellular and protein content of broncho-alveolar lavage fluid from patients with idiopathic pulmonary fibrosis and chronic hypersensitivity pneumonitis. 
Journal of Clinical Investigation  1977;59(1):165-175.
To evaluate cellular and protein components in the lower respiratory tract of patients with idiopathic pulmonary fibrosis (IPF) and chronic hypersensitivity pneumonitis (CHP), limited broncho-alveolar lavage was done in 58 patients (19 IPF, 7 CHP, and 32 controls). Analysis of the cells and protein in the lavage fluids from patients with IPF revealed an inflammatory and eosinophilic response and a significant elevation of IgG in the lungs. With corticosteroid therapy, inflammation diminished but eosinophils remained. Lavage fluid from patients with CHP also had eosinophils and elevated levels of IgG. However, in contrast to IPF, lavage fluid from CHP patients contained IgM, fewer inflammatory cells, and a strikingly increased number (38-74%) of lymphocytes. Identification of lavage lymphocytes in CHP showed that T lymphocytes were significantly elevated and B lymphocytes were decreased compared to peripheral blood. These studies suggest nthat the lung in IPF and CHP may function as a relatively independent immune organ, and that analysis of cells and proteins in broncho-alveolar lavage fluid may be of diagnostic, therapeutic, and investigative value in evaluating patients with fibrotic lung disease.
PMCID: PMC333344  PMID: 830661

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