Classification of usual interstitial pneumonia in patients with interstitial lung disease: assessment of a machine learning approach using high-dimensional transcriptional data

2015 ◽  
Vol 3 (6) ◽  
pp. 473-482 ◽  
Author(s):  
Su Yeon Kim ◽  
James Diggans ◽  
Dan Pankratz ◽  
Jing Huang ◽  
Moraima Pagan ◽  
...  
2019 ◽  
Vol 23 (24) ◽  
pp. 13409-13421 ◽  
Author(s):  
Rabia Aziz Musheer ◽  
C. K. Verma ◽  
Namita Srivastava

2021 ◽  
Vol 9 (5) ◽  
pp. 1034
Author(s):  
Carlos Sabater ◽  
Lorena Ruiz ◽  
Abelardo Margolles

This study aimed to recover metagenome-assembled genomes (MAGs) from human fecal samples to characterize the glycosidase profiles of Bifidobacterium species exposed to different prebiotic oligosaccharides (galacto-oligosaccharides, fructo-oligosaccharides and human milk oligosaccharides, HMOs) as well as high-fiber diets. A total of 1806 MAGs were recovered from 487 infant and adult metagenomes. Unsupervised and supervised classification of glycosidases codified in MAGs using machine-learning algorithms allowed establishing characteristic hydrolytic profiles for B. adolescentis, B. bifidum, B. breve, B. longum and B. pseudocatenulatum, yielding classification rates above 90%. Glycosidase families GH5 44, GH32, and GH110 were characteristic of B. bifidum. The presence or absence of GH1, GH2, GH5 and GH20 was characteristic of B. adolescentis, B. breve and B. pseudocatenulatum, while families GH1 and GH30 were relevant in MAGs from B. longum. These characteristic profiles allowed discriminating bifidobacteria regardless of prebiotic exposure. Correlation analysis of glycosidase activities suggests strong associations between glycosidase families comprising HMOs-degrading enzymes, which are often found in MAGs from the same species. Mathematical models here proposed may contribute to a better understanding of the carbohydrate metabolism of some common bifidobacteria species and could be extrapolated to other microorganisms of interest in future studies.


2021 ◽  
Vol 10 (12) ◽  
pp. 2548
Author(s):  
Marco Sebastiani ◽  
Fabrizio Luppi ◽  
Gianluca Sambataro ◽  
Diego Castillo Villegas ◽  
Stefania Cerri ◽  
...  

Anti-neutrophil cytoplasmic antibodies (ANCA), mainly anti-myeloperoxidase (MPO) antibodies, have been frequently identified in patients with idiopathic pulmonary fibrosis (IPF). However, their role remains unclear, and only 7–23% of these patients develops clinically overt vasculitis. We aimed to investigate the clinical, serological, and radiological features and prognosis of anti-MPO-positive interstitial lung disease (ILD) patients. Fifty-eight consecutive patients firstly referred for idiopathic interstitial pneumonia and showing serological positivity of anti-MPO antibodies were retrospectively enrolled. For each patient, clinical data, lung function testing, chest high-resolution computed tomography (HRCT) pattern, and survival were recorded. Thirteen patients developed a rheumatic disease during a median follow-up of 39 months. Usual interstitial pneumonia (UIP) was the most frequent ILD pattern, significantly influencing the patients’ survival. In fact, while the 52-week survival of the overall population was 71.4 ± 7.5%, significantly higher than IPF, survivals of anti-MPO patients with UIP pattern and IPF were similar. Forced vital capacity and diffusion lung capacity for CO significantly declined in 37.7 and 41.5% of cases, respectively, while disease progression at chest HRCT was observed in 45.2%. A careful clinical history and evaluation should always be performed in ILD patients with anti-MPO antibodies to quickly identify patients who are developing a systemic rheumatic disease.


2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1222.2-1222
Author(s):  
R. Ortega Castro ◽  
P. S. Laura ◽  
F. U. Pilar ◽  
J. Calvo Gutierrez ◽  
A. Requejo-Jimenez ◽  
...  

Background:Diffuse interstitial lung disease (ILD) is frequently associated with connective tissue diseases (CTD) and is one of the main causes of morbidity and mortality in these patients. Recently, the concept of Interstitial Pneumonia with Autoimmune Features (IPAF) has been defined to characterize ILD associated with systemic manifestations limited to subtle serological and clinical autoimmune abnormalities and not fulfilling the international criteria for the diagnosis of a given CTD.Objectives:The objective of this study is to describe the clinical, serological and radiological characteristics, as well as the treatment patterns of patients with ILD referred to a Rheumatology Service for suspected CTDMethods:Observational, cross-sectional study of 43 patients with ILD referred for evaluation to the medical consultation of CTD of the Rheumatology service at the Reina Sofía Hospital. Patients were classified as patients with defined CTD, patient with IPAF and patients with other types of pneumopathy. We conducted a descriptive study of all patients and compared the clinical-analytical-radiological characteristics and treatment patterns of the first two groups.Results:Of the 43 patients, 67.40% were women with a mean age at diagnosis of 65.65 (10.42) years and 53.50% of smoking patientsOf the total of patients, 16 (37.2%) were included in the CTD group, 17 (39.5%) met criteria for IPAF and 10 (23.3%) had another type of pneumopathy.In the CTD group scleroderma was the most frequent disease (6/16), followed by inflammatory myopathy (4/16), Sjögren’s syndrome (3/16), rheumatoid arthritis (2/16) and polymyalgia rheumatic (1/16). In this group of patients, the most common symptom was Raynaud’s phenomenon (RP) (7/16), followed by arthritis (7/16) and mechanic’s hands (3/16). Regarding the most frequently antibodies were ANA (100%), anti-RO (41.7%), anti-citrullinated protein antibodies (30%) and rheumatoid factor (RF) (28.6%).In patients with IPAF, as in the CTD group, the most observed clinical criterion was RP (5/17), followed by arthritis (1/17) and mechanic’s hands (1/17). Among the serological criteria the most common antibodies were ANA (100%), followed by anti-RO (33.3%), anti-RNA synthetase (28.6%) and RF (22.2%).Regarding the radiological pattern, in both groups the most frequent was nonspecific interstitial pneumonia, followed by the indeterminate pattern and usual interstitial pneumonia (UIP) in third place. There were no significant differences by gender and age, between the group of CTD and IPAF, observing in both groups a predominance of women with a similar mean age, being the upper smoking habit in the IPAF group (70.6% vs 31.5%, p= 0.02). Regarding the treatment used, the use of immunosuppressants (IS) was more frequent in CTD group (56.3% vs 11.8%, p = 0.007).Conclusion:The clinical-serological and radiological characteristics were similar among patients with IPAF and CTD, which supports the notion of a similar pathophysiology in both groups. In our cohort patients with CTD received IS more frequently than IPAF group, however, future work would be necessary to assess whether the response to treatment is similar in these populations and if IS can benefit patients with IPAF to long term. In addition, it could be useful to include the UIP pattern within the IPAF classification criteria, not currently included, since it is the third most frequent radiological pattern.References:[1]Respirology, 21 (2016), pp. 245-258[2]Eur Respir J, 46 (2015), pp. 976-987Disclosure of Interests:Rafaela Ortega Castro: None declared, Pérez Sánchez Laura: None declared, Font Ugalde Pilar: None declared, Jerusalem Calvo Gutierrez: None declared, Antonio Requejo-Jimenez: None declared, Simona Espejo-Pérez: None declared, Teresa Gonzalez-Serrano: None declared, María del Carmen Castro Villegas: None declared, Gómez García Ignacio: None declared, Alejandro Escudero Contreras: None declared, Eduardo Collantes Estevez Grant/research support from: ROCHE and Pfizer, Speakers bureau: ROCHE, Lilly, Bristol and Celgene, Maria A Aguirre: None declared


Author(s):  
Alexis Falcin ◽  
Jean-Philippe Métaxian ◽  
Jérôme Mars ◽  
Éléonore Stutzmann ◽  
Jean-Christophe Komorowski ◽  
...  

Rheumatology ◽  
2019 ◽  
Vol 59 (7) ◽  
pp. 1626-1631 ◽  
Author(s):  
Sarah L Tansley ◽  
Zoe Betteridge ◽  
Hui Lu ◽  
Emma Davies ◽  
Simon Rothwell ◽  
...  

Abstract Objectives It has been over 10 years since the first report of autoantibodies directed against phenylalanyl tRNA synthetase (anti-Zo) in a patient with features of the anti-synthetase syndrome. In that time no further cases have been published. Here we aim to characterize more fully the clinical phenotype of anti-Zo–associated myositis by describing the clinical features of nine patients. Methods Anti-Zo was identified by protein-immunoprecipitation in patients referred for extended spectrum myositis autoantibody testing at our laboratory. Results were confirmed by immunodepletion using a reference serum. Medical records were retrospectively reviewed to provide detailed information of the associated clinical phenotype for all identified patients. Where possible, HLA genotype was imputed using Illumina protocols. Results Nine patients with anti-Zo were identified. The median age at disease onset was 51 years, and six patients were female. Seven patients had evidence of inflammatory muscle disease, seven of interstitial lung disease and six of arthritis. The reported pattern of interstitial lung disease varied with usual interstitial pneumonia, non-specific interstitial pneumonia and organizing pneumonia all described. Other features of the anti-synthetase syndrome such as RP and mechanics hands were common. HLA data was available for three patients, all of whom had at least one copy of the HLA 8.1 ancestral haplotype. Conclusion Patients with anti-Zo presenting with features of the anti-synthetase syndrome and interstitial lung disease is a common finding. Like other myositis autoantibodies, there is likely to be a genetic association with the HLA 8.1 ancestral haplotype.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Maria A. Nieto ◽  
Maria J. Rodriguez-Nieto ◽  
Olga Sanchez-Pernaute ◽  
Fredeswinda Romero-Bueno ◽  
Leticia Leon ◽  
...  

Abstract Background To assess mortality rate (MR) and standardized mortality rate (SMR) of rheumatoid arthritis-related interstitial lung disease (RA-ILD) patients and to evaluate the role of radiographic patterns in mortality. Methods A longitudinal multicentric study was conducted in RA-ILD patients from 2005 to 2015 and followed-up until October 2018 in Madrid. Patients were included in the Neumologia-Reumatología y Enfermedades Autoinmunes Registry, from diagnosis of ILD. The main outcome was all-cause mortality. The radiographic pattern at baseline [usual interstitial pneumonia (UIP), nonspecific interstitial pneumonia (NSIP), or others] was the independent variable. Covariables included sociodemographic and clinical data. Survival techniques were used to estimate MR, expressed per 1000 persons-year with their 95% confidence intervals [CI]. Cox multiple regression model was run to examine the influence of radiographic patterns on survival. SMR [CI] was calculated comparing MR obtained with MR expected in the general population of Madrid by indirect age-gender standardization. Results 47 patients were included with a follow-up 242 patients-year. There were 16 (34%) deaths, and most frequent causes were acute ILD exacerbation and pneumonia. MR was 64.3 [39.4–104.9], and 50% of the patients died at 8.3 years from ILD diagnosis. After adjusting for confounders, (UIP compared to NSIP was associated with higher mortality risk. The overall SMR was 2.57 [1.4–4.17]. Women of 60–75 years of age were the group with the highest SMR. Conclusions RA-ILD is associated with an excess of mortality compared to general population. Our results support that UIP increases the risk of mortality in RA-ILD, regardless other factors.


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