Study of pulmonary experimental paracoccidioidomycosis by analysis of bronchoalveolar lavage cells: Resistant vs. susceptible mice

Adult Swiss (susceptible) and BALB/c (non-susceptible) mice were inoculated by the intravenous route with 1 × 10⁶ yeast cells of Paracoccidioides brasiliensis, strain 18. Immunologic parameters, histopathology and features of the bronchoalveolar lavage (BAL) were evaluated at week 2, 4, 8 and 16 post-infection. The pulmonary infection was progressive in Swiss mice and regressive in BALB/c mice. The numbers of total cells, lymphocytes and polymorphonuclear neutrophils increased in BAL, as well as the percentages of giant cells, and CD4 and CD8 positive cells. The ultrastructural study of BAL cells revealed a predominance of macrophages and a frequency of 13.2% of type II pneumocytes. As the infection progressed, the number of fungal cells and spreading macrophages, as well as the stimulated release of H₂O₂ by macrophages, increased. The animals exhibited an exacerbation of the humoral immune response and a depression of cellular immunity during the infection. There was a good correlation between the intensity and the pattern of the pulmonary histopathology and the cellular findings in the BAL. The present model reproduces some anatomoclinical patterns of the human disease and shows that BAL may be a useful tool in monitoring the pulmonary infection caused by P. brasiliensis. This revised version was published online in June 2006 with corrections to the Cover Date.     

Cytokine profiles of bronchoalveolar lavage fluid in patients with pneumocystis pneumonia

The clinical features of PCP differ according to the factors responsible for the predisposing immunosuppression. Although the diagnosis of PCP often requires BAL, the profiles of the inflammatory mediators in the BAL fluid are not thoroughly documented. The aim of the current study was to characterize the profiles of inflammatory mediators in BAL fluid during PCP in patients with underlying autoimmune diseases, malignancies, or AIDS. The medical records of 14 patients with autoimmune diseases, 10 with malignancies, and 8 with AIDS, all of whom had been diagnosed with PCP by microscopic examination of BAL fluid, were reviewed. The concentrations of TNF‐α, MCP‐1, HMGB1, IL‐8, IL‐6, IL‐10, and IFN‐γ in the BAL fluid that had been obtained for the diagnosis of PCP were measured. The concentrations of MCP‐1, IL‐8, and IL‐6 differed according to the underlying disease, tending to be higher in patients with autoimmune diseases and lower in those with AIDS. The concentrations of HMGB1, IL‐8, and IL‐6 were positively correlated with the proportion of neutrophils in BAL fluid and inversely with the oxygenation index. Although the serum concentrations of CRP and LDH were positively correlated with those of IL‐8 and MCP‐1, none of the mediators in BAL fluid was correlated with the serum β‐D‐glucan concentration. The production of inflammatory mediators in the lung differed between the patient groups with different underlying disorders. The modest upregulation of IL‐8 and IL‐6 might be associated with the milder clinical manifestations of PCP in AIDS patients.     

Proteogenomics: needs and roles to be filled by proteomics in genome annotation

While genome sequencing efforts reveal the basic building blocksof life, a genome sequence alone is insufficient for elucidatingbiological function. Genome annotation—the process ofidentifying genes and assigning function to each gene in a genomesequence—provides the means to elucidate biological functionfrom sequence. Current state-of-the-art high-throughput genomeannotation uses a combination of comparative (sequence similaritydata) and non-comparative (ab initio gene prediction algorithms)methods to identify protein-coding genes in genome sequences.Because approaches used to validate the presence of predictedprotein-coding genes are typically based on expressed RNA sequences,they cannot independently and unequivocally determine whethera predicted protein-coding gene is translated into a protein.With the ability to directly measure peptides arising from expressedproteins, high-throughput liquid chromatography-tandem massspectrometry-based proteomics approaches can be used to verifycoding regions of a genomic sequence. Here, we highlight severalways in which high-throughput tandem mass spectrometry-basedproteomics can improve the quality of genome annotations andsuggest that it could be efficiently applied during the genecalling process so that the improvements are propagated throughthe subsequent functional annotation process.      

Th1-Th2 cytokine kinetics in the bronchoalveolar lavage fluid of mice infected with Cryptococcus neoformans of different virulences

Th1 immune response plays an important role in protection against infection with Cryptococcus neoformans in mice. We investigated the effect of virulence of C. neoformans on cytokine production in the lung of a mouse model of pulmonary cryptococcosis. BALB/c mice were inoculated intratracheally with a high or low virulence strain of C. neoformans, followed by serial measurements of Th1 and Th2 cytokine concentrations in the bronchoalveolar lavage (BAL) fluid using appropriate enzyme-linked immunosorbent assay kits. The number of colony-forming units (CFU) increased with time, and all mice infected with the highly virulent strain were dead at 28 days after inoculation. In contrast, the number of microorganisms diminished with time in the mice infected with the low virulence strain during the 4-week study. The numbers of neutrophils and lymphocytes in the BAL fluid paralleled those of CFU. High neutrophil counts were observed in the BAL fluid of mice infected with the highly virulent strain, while lymphocyte counts were increased only in the later part of the study in mice infected with the high and low virulence strains. The concentrations of Th2 cytokine, interleukin (IL)-4 were significantly higher in mice infected with the highly virulent strain at days 14 and 21 of infection, whereas the level of Th1 cytokine, interferon-gamma, was significantly higher in the latter strain at days 7 and 14. Our results suggest that strain-specific difference in the organism's ability to induce (or evade) the host immune system contributes to the outcome of infection.     

Chemiluminescence of bronchoalveolar lavage cells as an indicator of leukocyte activation in rats with a hyperreactive bronchus

Activation and generation of inflammatory mediators by different leukocytes may be important in the pathogenesis of airway hyperreactivity. We studied the effect of active sensitization with ovalbumin as antigen and i.v. treatment with Sephadex particles on bronchial reactivity (BR) in rats and its possible relation to leukocyte infiltration (LI) and activation (LA) in bronchoalveolar lavage (BAL). A marked BR to aerosols of serotonin (5-HT) and ovalbumin was found in Sephadex treated animals but not in control animals. In parallel to this a marked increase in BAL cell count from Sephadex-treated animals compared to controls was seen. This increase in BAL cell count corresponded with a clear augmentation of spontaneous, buffer-induced and C₃Z-induced, luminol-amplified CL. We deduce that detection of CL of BAL cells from rats might be used for studying inflammatory mechanisms which lead to a hyperreactive bronchus.     

Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

Next‐generation technologies generate an overwhelming amount of gene sequence data. Efficient annotation tools are required to make these data amenable to functional genomics analyses. The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences. It uses the MapMan ‘BIN’ ontology, which is tailored for functional annotation of plant ‘omics’ data. The classification procedure performs parallel sequence searches against reference databases, compiles the results and computes the most likely MapMan BINs for each query. In the current version, the pipeline relies on manually curated reference classifications originating from the three reference organisms (Arabidopsis, Chlamydomonas, rice), various other plant species that have a reviewed SwissProt annotation, and more than 2000 protein domain and family profiles at InterPro, CDD and KOG. Functional annotations predicted by Mercator achieve accuracies above 90% when benchmarked against manual annotation. In addition to mapping files for direct use in the visualization software MapMan, Mercator provides graphical overview charts, detailed annotation information in a convenient web browser interface and a MapMan‐to‐GO translation table to export results as GO terms. Mercator is available free of charge via http://mapman.gabipd.org/web/guest/app/Mercator .     

Diagnostic value of nucleic acid amplification tests on bronchoalveolar lavage fluid for smear-negative pulmonary tuberculosis: a meta-analysis

The diagnosis of smear-negative pulmonary tuberculosis (SNPT) remains a clinical challenge. Many studies suggest that nucleic acid amplification tests (NAATs) on bronchoalveolar lavage fluid (BALF) plays a role in diagnosing SNPT, but with considerable varying results. The current study aimed to summarize the overall diagnostic accuracy of NAATs assay on BALF for SNPT. A systematic literature search was performed and data were retrieved. Pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR) and diagnostic odds ratio (DOR) were calculated. A summary receiver operating characteristic curve and area under the curve (AUC) were used to evaluate the overall diagnostic performance. All the statistical analysis was performed by using STATA 12.0 and Meta-DiSc 1.4 software. A total of nine studies with 1214 subjects were included this meta-analysis. The pooled sensitivity, specificity, PLR, NLR and DOR were 0.54 [95% CI (confidence interval): 0.48–0.59], 0.97 (95% CI: 0.95–0.98), 12.13 (95% CI: 8.23–17.88), 0.36 (95% CI: 0.23–0.56) and 44.71 (95% CI: 22.30–89.63) respectively. The AUC was 0.96. Estimated positive and negative post-probability values for a SNPT prevalence of 20% were 82% and 7% respectively. No publication bias was identified. Current available evidence indicated that NAATs on BALF may play a role in diagnosing SNPT, whereas the results should be interpreted in parallel with clinical information of patients and the results of traditional tests. Further studies should be performed to confirm our findings.     

Investigation of the significance of Oil Red O‐positive macrophage excess in bronchoalveolar lavage fluid during HIV infection

L. Lacoste‐Collin, G. Martin‐Blondel, C. Basset‐Léobon, V. Lauwers‐Cancès, D. d’Aure, J. Aziza, A. Berry, B Marchou, M.B. Delisle and M. Courtade‐Saïdi Investigation of the significance of Oil Red O‐positive macrophage excess in bronchoalveolar lavage fluid during HIV infection Objective: To assess the significance of increased levels of Oil Red O‐positive macrophages (ORO‐PM) in bronchoalveolar lavage fluids (BALFs) from HIV‐positive patients. Methods: Cytological data for seventy BALF samples from 66 consecutive HIV‐infected patients were analysed according to antiretroviral therapy regimen, presence of Pneumocystis jiroveci infection, blood CD4⁺T cell count, HIV‐1 viral load and plasma lipid levels. Non‐parametric tests were used to compare the values between groups. Results: The percentages of ORO‐PM were high in this group: 40% [6–80] (median [interquartile range]). They were positively correlated with the BALF total cell count, 21% [5–48.5] for <300 cells/mm³ and 60% [26.5–80] for >300 cells/mm³ (P < 0.01) but inversely correlated with the percentage of BALF lymphocytes, 50% [20–80] for <15% lymphocytes and 11.5% [2–47] for ≥15% lymphocytes (P < 0.01). Antiretroviral therapy with or without protease inhibitors, plasma lipid levels, HIV‐1 viral load, blood CD4⁺T cell count or presence of a Pneumocystis jiroveci infection were not correlated with the ORO‐PM status. Conclusion: Significantly increased numbers of ORO‐PM were correlated with high total cell counts and low lymphocyte counts in BALF, irrespective of disease activity or treatment. Extended work on a larger series of patients needs to be conducted.     

LC-MS analysis of phospholipids and lysophospholipids in human bronchoalveolar lavage fluid

A reversed phase HPLC method was developed for the simultaneous analysis of different phospholipids and lysophospholipids in human bronchoalveolar lavage fluid (BALF). Separation was achieved using a pellicular C8 column at elevated temperatures with an increasing gradient of acetonitrile containing 0.1% formic acid. Detection was carried out by electrospray ionization ion-trap mass spectrometry. Calibration graphs for selected phospholipids (phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and lysophosphatidylcholine) showed linearity up to 50 ng allowing quantitative determinations. Identification of the individual species within each class was possible with tandem mass spectrometry. Analysis of BALF phospholipids was performed after liquid/liquid extraction with a mixture of chloroform/methanol/acetic acid. Recoveries ranged from 69 to 97% with standard deviations of less than 6%. The limit of detection varied slightly between different classes but was in the range 0.05-0.25 ng total injected amount.     

Cut‐off values and significance of Oil Red O‐positive cells in bronchoalveolar lavage fluid

C. Basset‐Léobon, L. Lacoste‐Collin, J. Aziza, J.C. Bes, S. Jozan and M. Courtade‐Saïdi
Cut‐off values and significance of Oil Red O‐positive cells in bronchoalveolar lavage fluid Objective: To evaluate the percentage and predictive value of Oil Red O‐positive macrophages (ORO‐PM) to identify lipid‐laden macrophages in bronchoalveolar lavage fluids (BALF) from patients with different pathologies. Methods: The percentage and absolute numbers of ORO‐PM were evaluated in 305 BALF. The patients were separated into ten groups: corticosteroid treatment (n = 18), amiodarone treatment (n = 8), interstitial fibrosis (n = 11), human immunodeficiency virus (HIV)‐positive (n = 25), infectious pneumonia (n = 43), severe haematological disorder (n = 25), interstitial syndrome (n = 109), suspicion of cancer (n = 17), transplant recipients (n = 50) and controls (n = 43). The total and differential cell counts in BALF were recorded. The presence of specific pathogens was also noted. Parametric and non‐parametric tests were used to compare the values between groups. Receiver–operating characteristics (ROC) curves were established in order to determine a cut‐off value. Results: The percentages of ORO‐PM were (mean ± standard deviation) 21.67 ± 29.12 in the corticosteroid group, 10.00 ± 12.49 in the amiodarone group, 19.45 ± 20.72 in the interstitial fibrosis group, 47.80 ± 30.46 in the HIV group, 19.72 ± 26.26 in the infectious pneumonia group, 27.42 ± 30.04 in the severe haematological disorder group, 25.18 ± 30.63 in the interstitial syndrome group, 17.64 ± 27.76 in the suspicion of cancer group, 22.50 ± 27.27 in the transplanted recipients group and 2.63 ± 3.48 in the control group. Significantly higher values were found in all groups when compared with the control group (P < 0.001). Only the HIV group showed higher numbers of ORO‐PM when compared with the interstitial syndrome group (P < 0.01). According to ROC curves, > 6% ORO‐PM was suggested as the positive cut‐off value. Conclusion: Significantly increased numbers of ORO‐PM were associated with various lung pathologies. However, the higher numbers observed in HIV patients require further investigations.     

Interleukin-2-administration intravenously and intrapleurally in a patient with primary pulmonary adenocarcinoma. Cellular responses in peripheral blood,intrapleural fluid and bronchoalveolar lavage

A case report of a patient who suffered from a rapidly progressive lung adenocarcinoma with malignant pleural effusions, is given. The patient failed to respond on two series of conventional cytotoxic drug therapy (Carboplatin, Etoposid). Interleukin-2 (IL-2) treatment was first started as intrapleural instillations (3.0 million IU per day in 6 days). A clear clinical response was achieved with ceasing of the pleural effusion, and the overall disease became stable. In the peripheral blood, there was an increase of CD₄ positive lymphocytes that remained elevated after finishing the installation period. Both in bronchoalveolar lavage (BAL), and in the pleural fluid, there was a marked decrease of cells recovered, possibly due to an enhanced tissue attachment of activated cells. A second analysis with subtyping of lymphocytes in BAL was impossible due to the low cell number. In the pleural fluid, the fractions of CD₃ positive cells increased from 20 to 71% while the ratio between CD₄ and CD₈ remained persistently elevated at 6.11. Because of the disappearance of the pleural effusion, the patient was thereafter treated with IL-2 given as a continuous infusion (18 million IU per square-metre during 24 hours for 5 days). Hereby a more pronounced cell response was achieved in the peripheral blood. In contrast to the intrapleural treatment route, not only CD₄ positive cells, but also the numbers of natural killer cells (NK) increased. However this treatment was also associated with a much higher degree of side effects. It can be concluded from both intrapleural and intravenous IL-2 therapy, that a clinical and immunological response was achieved. As this type of tumour is well known to respond poorly to conventional therapy, treatment with biological modifiers such as IL-2 may offer an interesting alternative in the future.Abbreviations BAL bronchoalveolar lavage - K-2 Interleukin-2     

Purification and characterization of a silica-induced bronchoalveolar lavage protein with fibroblast growth-promoting activity

Experimentally induced silicosis provides a good model for chronic interstitial pulmonary inflammation and fibrosis. In the present study, a specific single polypeptide with an apparent molecular mass of 58,000 and a pI of 4.5 was purified and characterized from the bronchoalveolar lavage fluid of silicotic rats. The same protein was also isolated from both the extract and conditioned medium of alveolar macrophages of silicotic rats. Therefore, this protein was termed an inducible silicotic (rat) bronchoalveolar lavage protein-p⁵⁸ (iSBLP⁵⁸) or an inducible silicotic (rat) pulmonary macrophage factor (iSPMF-p⁵⁸). iSBLP⁵⁸ has been purified to homogeneity by a combination of gel permeation, Mono Q ion exchange, and reverse-phase high performance liquid chromatography. This polypeptide displayed a potent fibroblast growth-promoting activity in vitro. The sequence of the first 15 NH₂-terminal amino acids was determined and was found to have high sequence homology with members of the mammalian chitinase-like protein family, which includes human cartilage gp39, mammalian oviduct-specific glycoprotein, and a secretory protein from activated mouse macrophages. J. Cell. Biochem. 67:257–264, 1997. © 1997 Wiley-Liss, Inc.     

Automated interpretation of metabolic capacity from genome and metagenome sequences

The KEGG pathway maps are widely used as a reference data set for inferring high-level functions of the organism or the ecosystem from its genome or metagenome sequence data. The KEGG modules, which are tighter functional units often corresponding to subpathways in the KEGG pathway maps, are designed for better automation of genome interpretation. Each KEGG module is represented by a simple Boolean expression of KEGG Orthology (KO) identifiers (K numbers), enabling automatic evaluation of the completeness of genes in the genome. Here we focus on metabolic functions and introduce reaction modules for improving annotation and signature modules for inferring metabolic capacity. We also describe how genome annotation is performed in KEGG using the manually created KO database and the computationally generated SSDB database. The resulting KEGG GENES database with KO (K number) annotation is a reference sequence database to be compared for automated annotation and interpretation of newly determined genomes.     

1-DE MS and 2-D LC-MS analysis of the mouse bronchoalveolar lavage proteome

Bronchoalveolar lavage fluid (BALF) is a complex mixture of proteins, which represents a unique clinically useful sampling of the lower respiratory tract. Many proteomic technologies can be used to characterize complex biological mixtures; however, it is not yet clear which technology(s) provide more information regarding the number of proteins identified and sequence coverage. In this study, we initially compared two common proteomic approaches, 2-D LC microESI MS/MS and 1-DE followed by gel slice digestion, peptide extraction and peptide identification by MS in characterization of the mouse BALF proteome; secondly, we identified 297 unique proteins from the mouse BALF proteome, greatly expanded the BALF proteome by about threefold regardless of species.     

Structural and functional analysis of rice genome

Rice is an excellent system for plant genomics as it represents a modest size genome of 430 Mb. It feeds more than half the population of the world. Draft sequences of the rice genome, derived by whole-genome shotgun approach at relatively low coverage (4-6 X), were published and the International Rice Genome Sequencing Project (IRGSP) declared high quality (> 10 X), genetically anchored, phase 2 level sequence in 2002. In addition, phase 3 level finished sequence of chromosomes 1, 4 and 10 (out of 12 chromosomes of rice) has already been reported by scientists from IRGSP consortium. Various estimates of genes in rice place the number at >50,000. Already, over 28,000 full-length cDNAs have been sequenced, most of which map to genetically anchored genome sequence. Such information is very useful in revealing novel features of macroand micro-level synteny of rice genome with other cereals. Microarray analysis is unraveling the identity of rice genes expressing in temporal and spatial manner and should help target candidate genes useful for improving traits of agronomic importance. Simultaneously, functional analysis of rice genome has been initiated by marker-based characterization of useful genes and employing functional knock-outs created by mutation or gene tagging. Integration of this enormous information is expected to catalyze tremendous activity on basic and applied aspects of rice genomics.     

重症肺炎新生儿支气管肺泡灌洗液病原菌分布及耐药性

目的 研究重症肺炎新生儿支气管肺泡灌洗液的病原菌分布和耐药性。方法 选择2016年4月至2018年4月在本院呼吸科治疗的新生儿268例,其中符合重症肺炎诊断标准的患儿142例,归为重症肺炎组;不符合重症肺炎诊断标准的患儿126例,归为对照组。检测患儿肺泡灌洗液病原菌分布情况和耐药情况。结果 重症肺炎组患儿肺炎克雷伯菌、流感嗜血菌、铜绿假单胞菌、阴沟肠杆菌、大肠埃希菌、金黄葡萄球菌、溶血葡萄球菌、表皮葡萄球菌、肺炎链球菌、草绿链球菌检出率明显高于对照组。肺炎克雷伯菌对亚胺培南,美罗培南的耐药性为0.0%,大肠埃希菌对亚胺培南,美罗培南,阿米卡星的耐药性为0.0%,阴沟肠杆菌对亚胺培南,美罗培南,左氧氟沙星的耐药性为0.0%,肺炎链球菌对万古霉素的耐药性为0.0%,金黄葡萄球菌对万古霉素的耐药性为0.0%。结论 新生儿重症肺炎患者病原菌以革兰阴性菌为主,亚胺培南、美罗培南、万古霉素可以用于治疗新生儿重症肺炎,但由于其毒副作用较大,应严格把握适应症。     

From the genome sequence to the proteome and back: evaluation of E. coli genome annotation with a 2-D gel-based proteomics approach

The ambition of systems biology to understand complex biological systems at the molecular level implies that we need to have a concrete and correct understanding of each molecular entity and its function. However, even for the best-studied organism, Escherichia coli, a large number of proteins have never been identified and characterised from wild-type cells, and/or await unravelling of their biological role. Instead, the ORF models for these proteins have been predicted by suitable algorithms and/or through comparison with known, homologous proteins from other organisms, approaches which may be prone to error. In the present study, we used a combination of 2-DE, MALDI-TOF-MS and PMF to identify 1151 different proteins in E. coli K12 JM109. Comparison of the experimental with the theoretical Mr and pI values (4000 experimental values each) allowed the identification of numerous proteins with incorrect or incomplete ORF annotations in the current E. coli genome databases. Several inconsistencies in genome annotation were verified experimentally, and up to 55 candidates await further investigation. Our findings demonstrate how an up-to-date 2-D gel-based proteomics approach can be used for improving the annotation of prokaryotic genomes. They also highlight the need for harmonization among the different E. coli genome databases.     

Analysis of bronchoalveolar lavage fluid proteome from systemic sclerosis patients with or without functional, clinical and radiological signs of lung fibrosis

Lung fibrosis is a major cause of mortality and morbidity in systemic sclerosis (SSc). However, its pathogenesis still needs to be elucidated. We examined whether the alteration of certain proteins in bronchoalveolar lavage fluid (BALF) might have a protective or a causative role in the lung fibrogenesis process. For this purpose we compared the BALF protein profile obtained from nine SSc patients with lung fibrosis (SSc_Fib+) with that obtained from six SSc patients without pulmonary fibrosis (SSc_Fib-) by two-dimensional gel electrophoresis (2-DE). Only spots and spot-trains that were consistently expressed in a different way in the two study groups were taken into consideration. In total, 47 spots and spot-trains, corresponding to 30 previously identified proteins in human BALF, showed no significant variation between SSc_Fib+ patients and SSc_Fib- patients, whereas 24 spots showed a reproducible significant variation in the two study groups. These latter spots corresponded to 11 proteins or protein fragments, including serum albumin fragments (13 spots), 5 previously recognized proteins (7 spots), and 4 proteins (3 spots) that had not been previously described in human BALF maps, namely calumenin, cytohesin-2, cystatin SN, and mitochondrial DNA topoisomerase 1 (mtDNA TOP1). Mass analysis did not determine one protein-spot. The two study groups revealed a significant difference in BALF protein composition. Whereas levels of glutathione S-transferase P (GSTP), Cu–Zn superoxide dismutase (SOD) and cystatin SN were downregulated in SSc_Fib+ patients compared with SSc_Fib- patients, we observed a significant upregulation of α1-acid glycoprotein, haptoglobin-α chain, calgranulin (Cal) B, cytohesin-2, calumenin, and mtDNA TOP1 in SSc_Fib+ patients. Some of these proteins (GSTP, Cu–Zn SOD, and cystatin SN) seem to be involved in mechanisms that protect lungs against injury or inflammation, whereas others (Cal B, cytohesin-2, and calumenin) seem to be involved in mechanisms that drive lung fibrogenesis. Even if the 2-DE analysis of BALF did not provide an exhaustive identification of all BALF proteins, especially those of low molecular mass, it allows the identification of proteins that might have a role in lung fibrogenesis. Further longitudinal studies on larger cohorts of patients will be necessary to assess their usefulness as predictive markers of disease.     

Analysis of bronchoalveolar lavage fluid proteome from systemic sclerosis patients with or without functional, clinical and radiological signs of lung fibrosis

Lung fibrosis is a major cause of mortality and morbidity in systemic sclerosis (SSc). However, its pathogenesis still needs to be elucidated. We examined whether the alteration of certain proteins in bronchoalveolar lavage fluid (BALF) might have a protective or a causative role in the lung fibrogenesis process. For this purpose we compared the BALF protein profile obtained from nine SSc patients with lung fibrosis (SScFib+) with that obtained from six SSc patients without pulmonary fibrosis (SScFib-) by two-dimensional gel electrophoresis (2-DE). Only spots and spot-trains that were consistently expressed in a different way in the two study groups were taken into consideration. In total, 47 spots and spot-trains, corresponding to 30 previously identified proteins in human BALF, showed no significant variation between SScFib+ patients and SScFib- patients, whereas 24 spots showed a reproducible significant variation in the two study groups. These latter spots corresponded to 11 proteins or protein fragments, including serum albumin fragments (13 spots), 5 previously recognized proteins (7 spots), and 4 proteins (3 spots) that had not been previously described in human BALF maps, namely calumenin, cytohesin-2, cystatin SN, and mitochondrial DNA topoisomerase 1 (mtDNA TOP1). Mass analysis did not determine one protein-spot. The two study groups revealed a significant difference in BALF protein composition. Whereas levels of glutathione S-transferase P (GSTP), Cu-Zn superoxide dismutase (SOD) and cystatin SN were downregulated in SScFib+ patients compared with SScFib- patients, we observed a significant upregulation of alpha1-acid glycoprotein, haptoglobin-alpha chain, calgranulin (Cal) B, cytohesin-2, calumenin, and mtDNA TOP1 in SScFib+ patients. Some of these proteins (GSTP, Cu-Zn SOD, and cystatin SN) seem to be involved in mechanisms that protect lungs against injury or inflammation, whereas others (Cal B, cytohesin-2, and calumenin) seem to be involved in mechanisms that drive lung fibrogenesis. Even if the 2-DE analysis of BALF did not provide an exhaustive identification of all BALF proteins, especially those of low molecular mass, it allows the identification of proteins that might have a role in lung fibrogenesis. Further longitudinal studies on larger cohorts of patients will be necessary to assess their usefulness as predictive markers of disease.