Three Distinct Transcriptional Profiles of Monocytes Associate with Disease Activity in Scleroderma Patients

Abstract

Objective Patients with diffuse cutaneous systemic sclerosis (dcSSc) display a complex clinical phenotype. Transcriptional profiling of whole blood or tissue from patients are affected by changes in cellular composition that drive gene expression and an inability to detect minority cell populations. We undertook this study to focus on the 2 main subtypes of circulating monocytes, classical monocytes (CMs) and nonclassical monocytes (NCMs) as a biomarker of SSc disease severity. Methods SSc patients were recruited from the Prospective Registry for Early Systemic Sclerosis. Clinical data were collected, as well as peripheral blood for isolation of CMs and NCMs. Age‐, sex‐, and race‐matched healthy volunteers were recruited as controls. Bulk macrophages were isolated from the skin in a separate cohort. All samples were assayed by RNA sequencing (RNA‐seq). Results We used an unbiased approach to cluster patients into 3 groups (groups A–C) based on the transcriptional signatures of CMs relative to controls. Each group maintained their characteristic transcriptional signature in NCMs. Genes up‐regulated in group C demonstrated the highest expression compared to the other groups in SSc skin macrophages, relative to controls. Patients from groups B and C exhibited worse lung function than group A, although there was no difference in SSc skin disease at baseline, relative to controls. We validated our approach by applying our group classifications to published bulk monocyte RNA‐seq data from SSc patients, and we found that patients without skin disease were most likely to be classified as group A. Conclusion We are the first to show that transcriptional signatures of CMs and NCMs can be used to unbiasedly stratify SSc patients and correlate with disease activity outcome measures.

Distinct genome-wide DNA methylation and gene expression signatures in classical monocytes from African American patients with systemic sclerosis

“…However, when we focus on classical monocytes, our results are consistent in significance and directionality of effect to those reported by Makinde and colleagues for HPSE, CYTH4, KLF6, KYNU, C6orf62, and TUBB4B [38],…”

“…This study has virtually no power to detect the DNA methylation differences herein reported, but is powered to detect a reasonable fraction of the differentially expressed transcripts between cases and controls. Nevertheless, with 16 total SSc cases, it is comparable to sample sizes from previous studies that assessed genome-wide DNA methylation and gene expression primarily in European Americans [16,38,90,91]. Also, our results are consistent with the heightened monocyte activation previously reported in African American patients with SSc [30,31].…”

“…This includes the only analysis of classical monocytes to date [38], and contrasts with the weaker upregulation of inflammatory and immune genes we observed in classical monocytes from African American SSc patients. Multiple DEGs found in our analysis have been previously reported as differentially expressed in different blood cells from patients with SSc, including the endoplasmic reticulum transmembrane channel-like TMC8 [76], the collagen COL9A2 [67], the Kruppel-like transcription factor KLF6 [38,62,76], the zinc finger ZNF654 [76], the insulin-Induced INSIG2 [76], the transcription regulator SMARCA4 [76],…”

“…the kynureninase KYNU [38,63,64,69], the telomere regulator POT1 [76], and the hydrolase ABHD5 [64,69].…”

“…S6 and S7). Interestingly, in their transcriptional analysis of classical monocytes in SSc patients, Makinde et al [38] which included participants of different self-reported racial groups, note the substantial variability in the transcriptional profiles of the patients, with several patients, especially those on current immunosuppressive therapies, more closely resembling controls. This observation is consistent with our results where African American patients, who tend to have more severe disease and be on immunosuppressants, show modest differences in gene expression relative to controls.…”