ESA-SRB-AOTA 2019

Expression and function of the endometriosis risk gene Long Intergenic Non-Coding RNA 339 (#718)

Sarah J Holdsworth-Carson 1 , Jacqueline Donoghue 1 , Katie-Rose Campbell 1 , Molly L Churchill 1 , Leonie Cann 1 , Jessica Chung 2 , Clare Sloggett 2 , Martin Healey 1 , Raden Kendarsari 3 , Jenny N Fung 3 , Sally Mortlock 3 , Grant Montgomery 3 , Jane E Girling 4 , Peter AW Rogers 1
  1. Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
  2. Melbourne Bioinformatics, University of Melbourne, Parkville, VIC, Australia
  3. Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
  4. Department of Anatomy, University of Otago, Dunedin, New Zealand

INTRODUCTION: Meta-analyses of endometriosis GWAS have identified significant associations for single nucleotide polymorphisms (SNP) on chromosome 1.  A common mechanism by which SNPs influence disease is by regulating transcription or expression quantitative trait loci (eQTL).  The strongest eQTL is for ‘long intergenic non-coding RNA 339’ (LINC00339) where the risk allele decreases LINC00339 expression in blood and endometrium.  The aim of this study was to examine the expression and function of LINC00339 in ectopic and eutopic endometrium.

 

METHODS: The expression of LINC00339 was examined in endometrium and stromal and epithelial cultures by RNA-seq (n=184) and qRT-PCR (n=6-13).  LINC00339 in situ hybridization was performed on n=8 cases (lesion and endometrium) and n=8 controls (endometrium).  LINC00339 was overexpressed in 3 endometrial stromal cell lines and differential gene expression and pathway analysis was performed following RNA-seq and Ingenuity Pathway Analysis.

 

RESULTS:  The most abundant LINC00339 transcript was ENST00000416769, associated with LINC00339 variants 2, 5 and 6 and validated by RT-PCR in endometrial stromal lines (n=13).  LINC00339 variants were not differentially expressed between cultures of stromal versus epithelial cells (n=6).  LINC00339 in situ hybridization demonstrated nuclear localization.  Interestingly, in lesions, LINC00339 was only expressed in disease foci, not in surrounding tissues.  Examination of gene expression following LINC00339 overexpression identified 290 significantly deferentially expressed genes (adj. p-values <0.05) (top 5 genes IL33, FENDRR, PRKCA, NACC2 and RHEBL1); Ingenuity Pathway Analysis revealed that the top functional biological pathways included Interferon Signaling, Role of Pattern Recognition Receptors and Hepatic Fibrosis.

 

CONCLUSIONS:  LINC00339 was expressed equally in stroma and epithelium of eutopic and ectopic endometrium but was absent in the tissues surrounding foci of endometriosis.  Functional characterisation of LINC00339 suggests the endometriosis-risk gene has a role in immune function and inflammation; features well established in the aetiology of endometriosis.