Table 1.
Known lncRNAs dysregulated in IBD
| LncRNA | Disease/population | Sample source | Assay method | Fold change1/P value | Comments | Ref. |
|---|---|---|---|---|---|---|
| DQ7862432 | aCD/11 iCD/8 CO/9 | PBMCs (blood) | qRT-PCR | aCD vs. iCD: P = 0.012aCD vs. CO: P = 0.002 | • Regulates the function of Treg through CREB and Foxp3—relates to the severity of CD | 25 |
| CDKN2B-AS1 (ANRIL) | CD/13 UC/20 CO/12 | Colonic tissue | Microarray qRT-PCR | UC: −8.31 P < 0.05CD: −2.97 P < 0.05 | • Haberman et al. (2018): Transcriptional regulatory role in intestinal epithelia (FC: −7.4) • Pothoulakis et al. (2017): Associate with lipid metabolism process and with cell–cell interactions (FC: −12 in UC and −4.9 CD) |
33, 36 |
| IFNG-AS1 | aUC/8 iUC/4 CO/7 | Colonic tissue | Microarray qRT-PCR | 5.27P = 7.07E−06 | • An independent validation cohort of 16 control and 15 UC patients was used • Enhancer of inflammation by regulating IFNG inflammatory responses in CD4 T cells |
38 |
| H19 | UC/12 CO/PANT | Colonic tissue | qRT-PCR | 4.45P < 0.05 | • H19 upregulation causes miR-675-5p increased expression and vitamin D receptor and tight junction proteins decreased expression—destruction of intestinal epithelial barrier function | 47 |
| BC0129002 | aUC/16 iUC/15 CO/15 | Sigmoid colonic tissue | Microarray qRT-PCR | P < 0.001 | • Regulates intestinal epithelial cell apoptosis • Out of six top lncRNAs in this study, four were not found on the current built of the human reference genome (GRCh38) |
13 |
| BC062296 (B3GALT5-AS1) | aUC/16 iUC/15 CO/15 | Sigmoid colonic tissue | Microarray qRT-PCR | P < 0.05 | • Downregulated in the UC • No function is suggested for this lncRNA • Out of six top lncRNAs in this study, four were not found on the current built of the human reference genome (GRCh38) |
13 |
| GUSBP2 | CD/12 CO/12 | Plasma (blood) | Microarray qRT-PCR | 626.49P < 0.05 | • Among the lncRNAs 15 were antisense, 81 were enhancer and 161 were lincRNAs | 50 |
| AF113016 (MALAT1) | CD/12 CO/12 | Plasma (blood) | Microarray qRT-PCR | −481.03P < 0.05 | • Among the lncRNAs 15 were antisense, 81 were enhancer and 161 were lincRNAs | 50 |
| CCAT1 (CASC19) | UC/8 iUC/4 CO/7 | NCM460 cells Colonic tissue | Microarray | NCM460-NTR1: 2.3 P = 0.001UC: 11.9P = 0.0004 | • Human colonic epithelial cells (NCM460) where NTR1 is overexpressed was stimulated by neurotensin • Cohort of IBD patients and normal controls were from Padua et al. (2016) • Cross-compression of the lncRNA from in vitro and in vivo studies revealed CCAT1 and UCA1 were the two with highest significant overexpression |
57 |
| UCA1 | aUC/8 iUC/4 CO/7 | NCM460 cells Colonic tissue | Microarray | NCM460-NTR1: 2.9 P = 0.002UC: 2.3P = 0.002 | 57 | |
| HNF4A-AS1 | CD/111 CO/30 | Ileal biopsy | RNA-seq qRT-PCR | –6.1P < 0.05 | • An independent validation cohort of 8 control and 28 CD patients was used • Association with an epithelial metabolic signature • Unique to ileal cohort • 314 downregulated coexpressed genes |
33 |
| RP11-44K6.2 | CD/111 CO/30 | Ileal biopsy | RNA-seq qRT-PCR | 5.3P < 0.05 | • An independent validation cohort of 8 control and 28 CD patients was used • Also in adult colon • Mirza et al. (2015): in CD FC: 3.83 |
33 |
| LINC01272 (SMIM25) | CD/84 UC/84 CO/84 | Plasma (blood) Colonic tissue | qRT-PCR | P < 0.001 | • LINC01272 expression in CD tissue and plasma (R2 = 0.7133; P < 0.0001) • LINC01272 expression in UC tissue and plasma (R2 = 0.5326, P < 0.0001) • Haberman study: Also in adult colon (FC: 9.4), association with myeloid proinflammatory signature and immune activation functions • 187 upregulated coexpressed genes • Mirza et al. (2015): in CD FC: 3.35 |
70 |
| KIF9-AS1 | CD/84 UC/84 CO/84 | Plasma (blood) Colonic tissue | qRT-PCR | P < 0.001 | • KIF9-AS1 expression in CD tissue and plasma (R2 = 0.3788, P = 0.0002) • KIF9-AS1 expression in UC tissue and plasma (R2 = 0.3466, P = 0.0012) |
70 |
| DIO3OS | CD/84 UC/84 CO/84 | Plasma (blood) Colonic tissue | qRT-PCR | P < 0.001 | • DIO3OS expression in CD tissue and plasma (R2 = 0.2524, P = 0.0141) • DIO3OS expression in UC tissue and plasma (R2 = 0.2707, P = 0.0083) • Chen, Liu et al. (2016) study: Upregulated, FC: not mentioned • Other studies: downregulated, for example, Mirza et al. (2015): in CD FC: −3.01 |
70 |
| GAS5 | UC/16 CD/3 | PBMC (blood) HeLa and LoVo cells | qRT-PCR | Over all: P = 0.033 | • Patients treated with prednisone 1–2 mg/kg per day for 30 days • Resistance to glucocorticoid (GC) treatment • Candidate marker of GC resistance and consequently progression of the disease |
72 |
UC ulcerative colitis, CD Crohn’s disease, CO control, a active, i inactive, PBMC peripheral blood mononuclear cell, PANT paired adjacent normal tissues, NA not available
Note: Some lncRNAs have either dual annotation or their annotation is changed in the current built of the human reference genome (GRCh38)
aFold change values mainly relative to normal controls, otherwise stated
bChanged annotation based on the current built of the human reference genome (GRCh38), now protein-coding genes