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Series GSE173808 Query DataSets for GSE173808
Status Public on May 05, 2021
Title The transcriptome of paired major and minor salivary gland tissue in patients with primary Sjögren's syndrome
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary While all salivary glands (SGs) can be involved in primary Sjögren’s syndrome (pSS), their respective role in pathogenesis remains unclear. To assess immunopathway activation in paired parotid and labial gland tissue from biopsy-positive and biopsy-negative pSS and non-SS sicca patients, paraffin-embedded, paired parotid and labial salivary gland tissue and peripheral blood mononuclear cells were obtained from 39 pSS and 20 non-SS sicca patients. The patients were subdivided based on fulfillment of ACR-EULAR criteria and histopathology and the samples were analyzed for differentially expressed genes (DEGs). The principal component analysis of SG gene expression could only separate biopsy-positive pSS from non-SS sicca patients. However, when comparing the transcriptome of biopsy-positive pSS and biopsy-negative non-SS sicca patients, 1235 and 624 DEGs (FDR<-1 or >1) were identified for parotid and labial glands, respectively. The number of DEGs between biopsy negative pSS and non-SS sicca patients was scarce. The overall, transcript expression levels correlated strongly between parotid and labial glands (R2=0.86, p‐value<0.0001). Gene signatures present in both glands of biopsy‐positive pSS patients included IFN‐α signaling, IL-12/IL-18 signaling, CD3/CD28 T-cell activation, CD40 signaling in B-cells, DN2 B-cells, and FcRL4+ B-cells. Signature scores varied considerably amongst pSS patients. In conclusion, the transcriptomes of paired major and minor SGs in pSS were overall comparable, although significant inter-individual heterogeneity in immunopathway activation existed. The SG transcriptome of biopsy-negative pSS was indistinguishable from non-SS sicca patients. The different patterns of SG immunopathway activation in pSS argue for personalized treatment approaches.
 
Overall design Differential expression analysis of a cohort of 39 patients with primary Sjogren's syndrome and 20 non-SS sicca patients.
 
Contributor(s) Verstappen GM, Gao L, Pringle S, Haacke EA, van der Vegt B, Liefers SC, Patel V, Hu Y, Mukherjee S, Carman J, Menard L, Spijkervet FK, Vissink A, Bootsma H, Kroese FG
Citation(s) 34295332
Submission date May 04, 2021
Last update date Jul 28, 2021
Contact name Yanhua Hu
E-mail(s) sarah.hu@bms.com
Organization name Bristol Myers Squibb
Street address 3551 Lawrenceville Princeton Rd
City West Windsor
State/province NJ
ZIP/Postal code 08648
Country USA
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (114)
GSM5278954 GRCh37ERCC-ensembl75-genes-N-20180723MN1-A01P1-Run1_S1_L001
GSM5278955 GRCh37ERCC-ensembl75-genes-N-20180723MN1-A02P1-Run1_S9_L001
GSM5278956 GRCh37ERCC-ensembl75-genes-N-20180723MN1-A03P1-Run1_S9_L001
Relations
BioProject PRJNA727106
SRA SRP318393

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE173808_Raw_gene_counts_matrix.csv.gz 7.5 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record
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