Background/Purpose:  While a hallmark of systemic sclerosis (SSc) is skin fibrosis, internal organ involvement is the primary cause of mortality. Pulmonary Arterial Hypertension (PAH), Interstitial Lung Disease (ILD) and gastrointestinal dysfunction are common in these patients. Here we tested the hypothesis, generated from meta-analysis of ten different SSc datasets, that any single SSc patient would have the same molecular signatures across multiple organ systems, consistent with the systemic nature of the disease. Asking the question, “if a patient shows an inflammatory signature in skin, do they show that same signature in esophagus, fundus, duodenum, lung or blood?” To test this, we performed RNA-seq on biopsy samples for up to four different tissues from each patient.

Methods: All patients met 2013 ACR/EULAR criteria for SSc. Biopsy samples were collected from skin, esophagus, fundus, duodenum, lung and blood from 12 SSc patients. Additional tissues, from our current cohort and other SSc patients, are continuing to be collected. Lung biopsies lacked at least two paired tissues and so were excluded from current analyses. Only patients from whom at least skin, esophagus and fundus were collected were analyzed, resulting in 9/12 patients used for the analysis. 4/9 patients also had duodenum analyzed. RNA was sequenced by 75bp paired-end RNA-seq at >80 million reads per sample and aligned to the reference genome. Bioinformatic analyses were performed to determine if intrinsic gene expression subset signatures found in one tissue, were found in other tissues of the same patient.

Results: Tissue of origin showed the most robust signal with each tissue having distinct, tissue-specific gene expression signatures. Batch biases from library preparation were not significant (p = 0.979). Analysis of skin and esophagus from the same patient was able to recapitulate the previously defined inflammatory intrinsic gene expression subset. The fibroproliferative subset was most clearly observed in skin (n = 4/9 patients). Furthermore, for the first time, the inflammatory subset was found in the fundus (n = 5/9) and duodenum (n = 2/4) of SSc patients. 5/9 patients showed concordant intrinsic assignment across three tissues, one of whom showed concordance across all four tissues, possibly because all four tissues were collected on the same date.

Conclusion: This is the first molecular analysis of biopsies from multiple organs within an individual SSc patient. Our data suggests that molecular subsets in SSc are reproducible across organs within the same patient. We cannot rule out the possibility that pathogenic mechanisms of disease activity and progression are discordant in time in each organ, consistent with clinical observation. Further analysis of the skin, esophagus, fundus and duodenum coupled with lung and blood will provide additional insights into the progression of this systemic disease.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/multi-organ-rna-sequencing-of-systemic-sclerosis-ssc-patients-shows-reproducible-gene-expression-profiles-across-organ-systems/