Figure 1

LHFPL3-AS2 lncRNA is reduced in CD patients and its expression is negatively correlated with CD severity. (A,B) LHFPL3-AS2 mRNA is significantly reduced in bulk mucosal biopsies of CD cases vs. controls in two independent cohorts: the pediatric RISK (A) 213 CD, and 47 controls) and the adult SOURCE (B) 8 CD, and 12 controls) cohorts. (C) LHFPL3-AS2 is expressed in human ileum-derived organoid culture and is reduced upon treatment with 40 ng/ml IFNγ and 20 ng/ml TNFa. (D) LHFPL3-AS2 levels are further reduced in CD patients with deep ulcers (CD-DU, n = 71) in comparison to those without (CD-noDU, n = 78). LHFPL3-AS2 (TPM) values are shown. (E,F) LHFPL3-AS2 log2(TPM) significantly correlates with the calprotectin S100A8 gene as a continuous value in RISK ((E), n = 260) and SOURCE (F, n = 20). (G) Functional annotation enrichment analyses of 470 genes that were co-expressed with LHFPL3-AS2 in RISK using ToppGene/ToppCluster^{32, 33} and Cytoscape³⁴. GO: Biological Process (orange), GO: Cellular component (green), GO: Molecular function (blue). The full list of functional enrichment results and P values are in Supplementary Dataset S1. A two-sided t-test was calculated between groups and Pearson correlation was used for correlations. *P < 0.05, **P < 0.01, ***P < 0.001.