Longitudinal global transcriptomic profiling of preclinical systemic sclerosis reveals molecular changes associated with disease progression

Objective: To investigate peripheral blood cell (PBCs) global gene expression profile of SSc at its preclinical stage (PreSSc) and to characterize the molecular changes associated with progression to a definite disease over time. Material and methods: Clinical data and PBCs of 33 participants with PreSSc and 16 healthy controls (HCs) were collected at baseline and follow-up (mean 4.2 years). Global gene expression profiling was conducted by RNA sequencing and a modular analysis was performed. Results: Comparison of baseline PreSSc to HCs revealed 2889 differentially expressed genes. Interferon signalling was the only activated pathway among top over-represented pathways. Moreover, 10 modules were significantly decreased in PreSSc samples (related to lymphoid lineage, cytotoxic/NK cell, and erythropoiesis) in comparison to HCs. At follow-up, 14 subjects (42.4%) presented signs of progression (evolving PreSSc) and 19 remained in stable preclinical stage (stable PreSSc). Progression was not associated with baseline clinical features or baseline PBC transcript modules. At follow-up stable PreSSc normalized their down-regulated cytotoxic/NK cell and protein synthesis modules while evolving PreSSc kept a down-regulation of cytotoxic/NK cell and protein synthesis modules. Transcript level changes of follow-up vs baseline in stable PreSSc vs evolving PreSSc showed 549 differentially expressed transcripts (336 up and 213 down) with upregulation of the EIF2 Signalling pathway. Conclusions: Participants with PreSSc had a distinct gene expression profile indicating that molecular differences at a transcriptomic level are al_x0002_ready present in the preclinical stages of SSc. Furthermore, a reduced NK signature in PBCs was related to SSc progression over time. Overall design: Whole blood global gene expression profiling was performed in baseline samples of patients with preclinical stages of systemic sclerosis and in their samples obtained on follow-up visit (mean 4.2 years after baseline visit), as well as in matched healthy control samples. Patients who kept preclinical features on follow-up visit, were labelled as 'stable PreSSc' while those progressing to definite SSc were labelled as 'evolving PreSSc'. Samples that have the same Pair number come from the same patient (one from baseline and one from follow-up). Healthy controls do not have follow-up samples