title: High Rhodotorula sequences in skin transcriptome of patients with diffuse systemic sclerosis.
abstract: Previous studies have suggested a role for pathogens as a trigger of systemic sclerosis (SSc), although neither a pathogen nor a mechanism of pathogenesis is known. Here we show enrichment of Rhodotorula sequences in the skin of patients with early, diffuse SSc compared with that in normal controls. RNA-seq was performed on four SSc patients and four controls, to a depth of 200 million reads per patient. Data were analyzed to quantify the nonhuman sequence reads in each sample. We found little difference between bacterial microbiome and viral read counts, but found a significant difference between the read counts for a mycobiome component, R. glutinis. Normal samples contained almost no detected R. glutinis or other Rhodotorula sequence reads (mean score 0.021 for R. glutinis, 0.024 for all Rhodotorula). In contrast, SSc samples had a mean score of 5.039 for R. glutinis (5.232 for Rhodotorula). We were able to assemble the D1-D2 hypervariable region of the 28S ribosomal RNA (rRNA) of R. glutinis from each of the SSc samples. Taken together, these results suggest that R. glutinis may be present in the skin of early SSc patients at higher levels than in normal skin, raising the possibility that it may be triggering the inflammatory response found in SSc.
authors.affiliation: Department of Dermatology, University of California, San Francisco, San Francisco, California, USA. Electronic address: arrons@derm.ucsf.edu.
authors.forename: Sarah T
authors.initials: ST
authors.lastname: Arron
authors.affiliation: Department of Dermatology, University of California, San Francisco, San Francisco, California, USA.
authors.forename: Michelle T
authors.initials: MT
authors.lastname: Dimon
authors.affiliation: Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.
authors.forename: Zhenghui
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Johnson
authors.affiliation: Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.
authors.forename: Tammara A
authors.initials: TA
authors.lastname: Wood
authors.affiliation: Department of Dermatology, University of California, San Francisco, San Francisco, California, USA.
authors.forename: Luzviminda
authors.initials: L
authors.lastname: Feeney
authors.affiliation: Department of Dermatology, University of California, San Francisco, San Francisco, California, USA.
authors.forename: Jorge G
authors.initials: JG
authors.lastname: Angeles
authors.affiliation: Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Lafyatis
authors.affiliation: Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA. Electronic address: michael.L.whitfield@dartmouth.edu.
authors.forename: Michael L
authors.initials: ML
authors.lastname: Whitfield
mesh_terms: D000368:Aged; D005260:Female; D006801:Humans; D008297:Male; D056186:Metagenomics; D008875:Middle Aged; D012339:RNA, Ribosomal, 28S / Q000235:genetics; D012248:Rhodotorula / Q000235:genetics / Q000302:isolation & purification*; D045743:Scleroderma, Diffuse / Q000382:microbiology*; D012867:Skin / Q000382:microbiology*; D059467:Transcriptome
chemical_list: D012339:RNA, Ribosomal, 28S