Browsing by Author "Almeida, Isabel"
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- Automatic Quantification of Interstitial Lung Disease From Chest Computed Tomography in Systemic SclerosisPublication . Carvalho, Alysson Roncally S.; Guimarães, Alan R.; Sztajnbok, Flávio R.; Rodrigues, Rosana Souza; Silva, Bruno Rangel Antunes; Lopes, Agnaldo José; Zin, Walter Araujo; Almeida, Isabel; França, ManuelaBackground: Interstitial lung disease (ILD) is a common complication in patients with systemic sclerosis (SSc), and its diagnosis contributes to early treatment decisions. Purposes: To quantify ILD associated with SSc (SSc-ILD) from chest CT images using an automatic quantification method based on the computation of the weight of interstitial lung opacities. Methods: Ninety-four patients with SSc underwent CT, forced vital capacity (FVC), and carbon monoxide diffusion capacity (DLCO) tests. Seventy-three healthy individuals without radiological evidence of lung disease served as controls. After lung and airway segmentation, the ratio between the weight of interstitial opacities [densities between -500 and +50 Hounsfield units (HU)] and the total lung weight (densities between -1,000 and +50 HU) was used as an ILD indicator (ILD[%] = 100 × [LW(-500 to +50HU)/LW(-1, 000 to +50HU)]). The cutoff of normality between controls and SSc was determined with a receiver operator characteristic curve. The severity of pulmonary involvement in SSc patients was also assessed by calculating Z scores of ILD relative to the average interstitial opacities in controls. Accordingly, SSc-ILD was classified as SSc Limited-ILD (Z score < 3) and SSc Extensive-ILD (Z score ≥ 3 or FVC < 70%). Results: Seventy-eight (83%) SSc patients were classified as presenting SSc-ILD (optimal ILD threshold of 23.4%, 0.83 sensitivity, 0.92 specificity, and 0.94 area under the receiver operator characteristic curve, 95% CI from 0.89 to 0.96, 0.93 positive predictive value, and 0.81 negative predictive value, p < 0.001) and exhibited radiological attenuations compatible with interstitial pneumonia dispersed in the lung parenchyma. Thirty-six (38%) patients were classified as SSc Extensive-ILD (ILD threshold ≥ 29.6% equivalent to a Z score ≥ 3) and 42 (45%) as SSc Limited-ILD. Eighteen (50%) patients with SSc Extensive-ILD presented FVC < 70%, being only five patients classified exclusively based on FVC. SSc Extensive-ILD also presented lower DLCO (57.9 ± 17.9% vs. 73.7 ± 19.8%; p < 0.001) and total lung volume (2,916 ± 674 vs. 4,286 ± 1,136, p < 0.001) compared with SSc Limited-ILD. Conclusion: The proposed method seems to provide an alternative to identify and quantify the extension of ILD in patients with SSc, mitigating the subjectivity of semiquantitative analyzes based on visual scores.
- Genome-wide whole blood transcriptome profiling in a large European cohort of systemic sclerosis patientsPublication . Beretta, Lorenzo; Barturen, Guillermo; Vigone, Barbara; Bellocchi, Chiara; Hunzelmann, Nicolas; De Langhe, Ellen; Cervera, Ricard; Gerosa, Maria; Kovács, László; Ortega Castro, Rafaela; Almeida, Isabel; Cornec, Divi; Chizzolini, Carlo; Pers, Jacques-Olivier; Makowska, Zuzanna; Lesche, Ralf; Kerick, Martin; Alarcón-Riquelme, Marta Eugenia; Martin, JavierObjectives: The analysis of annotated transcripts from genome-wide expression studies may help to understand the pathogenesis of complex diseases, such as systemic sclerosis (SSc). We performed a whole blood (WB) transcriptome analysis on RNA collected in the context of the European PRECISESADS project, aiming at characterising the pathways that differentiate SSc from controls and that are reproducible in geographically diverse populations. Methods: Samples from 162 patients and 252 controls were collected in RNA stabilisers. Cases and controls were divided into a discovery (n=79+163; Southern Europe) and validation cohort (n=83+89; Central-Western Europe). RNA sequencing was performed by an Illumina assay. Functional annotations of Reactome pathways were performed with the Functional Analysis of Individual Microarray Expression (FAIME) algorithm. In parallel, immunophenotyping of 28 circulating cell populations was performed. We tested the presence of differentially expressed genes/pathways and the correlation between absolute cell counts and RNA transcripts/FAIME scores in regression models. Results significant in both populations were considered as replicated. Results: Overall, 15 224 genes and 1277 functional pathways were available; of these, 99 and 225 were significant in both sets. Among replicated pathways, we found a deregulation in type-I interferon, Toll-like receptor cascade, tumour suppressor p53 protein function, platelet degranulation and activation. RNA transcripts or FAIME scores were jointly correlated with cell subtypes with strong geographical differences; neutrophils were the major determinant of gene expression in SSc-WB samples. Conclusions: We discovered a set of differentially expressed genes/pathways validated in two independent sets of patients with SSc, highlighting a number of deregulated processes that have relevance for the pathogenesis of autoimmunity and SSc.