Fig 1.
CONSORT flowchart for the study.
Table 1.
Baseline demographics and disease characteristics of SSc patients (n = 31).
Fig 2.
Drop plots of changes in texture-based quantitative scores from baseline using HRCT.
(A) QLF and (B) QILD for the most severe lobe. (C) QLF and (D) QILD for the whole lung. Dashed lines of ±3% and ±2% are indicators of thresholds for changes in regional analysis in lobe and whole lung, respectively.
Fig 3.
Representative pairs of baseline and follow-up HRCT images.
(A) Better case: pulmonary fibrosis (PF) improved and ground glass opacity (GGO) worsened by the visual assessment in whole lung; (B) annotated HRCT of (A) with a CAD system: QLF and QILD in whole lung decreased, by 2.9% (3.9% to 1.0%) and 0.2% (19.9% to 19.7%), respectively. (C) Stable case; (D) annotated CAD of (C): QLF in the worst lobe (lower left) increased by 2% (64% to 66%). In whole lung, QLF and QILD increased, by 2.3% (39.5% to 41.8%) and 1.8% (72.4% to 74.2%), respectively. (E) Worse case: PF worsened and GGO improved; (F) annotated CAD of (E): QLF increased by 6.0% (28% to 34%) in the most severe lobe (lower right) and 1.8% (9.8% to 11.6%) in whole lung. QILD in whole lung was stable (41.3% to 40.5%).
Fig 4.
Intrinsic gene expression subset assignment and response status.
(A) Intrinsic gene analysis. 3,207 probes (2,532 unique genes) at FDR<1.1% were used to organize samples into three gene expression-based clusters (intrinsic subsets). Sample color legend: red–fibroproliferative, purple–inflammatory, green–normal-like. (B) Distribution of patients according to their baseline intrinsic subsets and their response status. (C) Comparison between inflammatory and non-inflammatory (fibroproliferative and normal-like) patients in terms of the percentage of improvers.
Fig 5.
Baseline and improver gene expression and pathway enrichment analysis.
(A) 1,062 genes were differentially expressed (p<0.05) between improvers and non-improvers at baseline. Sample color legend: blue–improvers, orange–non-improvers. (B) 14 pathways showing differential expression (FDR<10%) at baseline. (C) 454 genes displaying differential expression (p<0.05) between baseline and post-treatment in improvers. Sample color legend: blue–baseline samples, black–post-treatment samples. (D) 13 pathways were differentially expressed (FDR<10%) in improvers.
Fig 6.
HRCT trends across improvers and non-improvers.
(A) QGG trends. (B) QLF trends. (C) Baseline [QGG-QLF] marker vs. intrinsic subset. (D) Baseline [QGG-QLF] marker vs. response status.