Mucosal gene transcription of ulcerative colitis in endoscopic remission

Figures & data

Table 1. Baseline characteristics in ulcerative colitis in clinical remission, active and in normal controls.

	Normal controls	UC Remission	UC Active
qPCR (SYBR-green)
Number	10	9	4
Gender (M/F)	7/3	3/6	2/2
Age (mean)	56.9	42.6	27.2
Biopsy location	1/9/0*	3/4/2*	2/1/1*
Average endoscopic score	0	0	2.25
qPCR (hydrolysis probe)
Number	24	44
Gender (M/F)	16/8	19/25
Age (mean)	54.5	40.5
Biopsy location	2/21/1*	23/15/6*
Average endoscopic score	0	0.25

*Rectum/Sigmoid colon/Unknown.

Figure 1. Volcano plot demonstrating differentially regulated genes between clinical remission and normal controls when adjusted for age, gender, endoscopic score and Geboes score. *TBX21 is analyzed with a nonparametric method (Mann–Whitney U-test). Genes analyzed with hydrolysis probe. All named genes are significant (<.05) and genes on the left-side are down-regulated, conversely, genes on the right-side are up-regulated.

Figure 2. Volcano plot demonstrating differentially regulated genes when comparing Ulcerative colitis in clinical remission to normal controls. Genes are analyzed with SYBR-green and are adjusted for age and gender. Genes on the left-side are down-regulated and genes on the right-side are up-regulated.

Figure 3. Volcano plot demonstrating differentially regulated genes when comparing active Ulcerative colitis to normal controls. Genes are analyzed with SYBR-green and are adjusted for age and gender. Genes on the left-side are down-regulated and genes on the right-side are up-regulated.

Table 2. All tested genes by the analysis method.

Method	Cytokines	Transcription factors	Receptors	Reference genes	Others
qPCR hydrolysis probe	IFN, TNF, TGFB1, IL1B, IL4, IL6, IL8, IL10, IL13, IL17a/f IL18, IL21, IL22, IL23, IL33,	TBX, GATA3, RORC, FOXP3, SPI1,	TLR4, IL1RL1	ACTB
PCR-array – SYBR-green	TNFSF15, IL22, IL13, IL10, IL9,	SMAD7, CHUK, STAT1, SPI1, STAT3, SMAD3,	IL1R2, IL9R, IL13RA2, TRAF1,TNFRSF6B TNFRSF25	PPIA, RPLP0, HPRT1	OCLN, TFF3, ADAM17, PTK2, CASP8, CCR2, DEFB1, BCL2, CLDN2

Table 3. Hydrolysis probes results are adjusted for age, gender, endoscopic subscore and Geboes score. SYBR-green results are adjusted for age and gender.

Gene	Remission vs. Normal	p-value	Mayo 0 vs. 1	p-value
Hydrolysis probe
IL1b	1.6↑	<.001		Ns
TNF	0.9↑	.011		Ns
IL33	0.7↑	.019	0.8↑	.012
TGFb	0.5↓	.038	0.9↑	.000
TBX21	2.8↓	<.001	3.4↑	.000
IL6		Ns	1.2↑	.033
IL10		Ns	0.9↑	.010
TLR4		Ns	0.8↑	.001
IL1RL1		Ns	1.2↑	.000
SPI1		Ns	1.0↑	.004
FOXP3		Ns	1.6↑	.001
GATA3		Ns	1.4↑	.000
RORC		Ns	0.7↑	.039
SYBR-green	Remission vs. Normal	p-value	Active vs. Normal	p-value
Adam17		Ns	49↑	.011
CASP8		Ns	2.2↑	.001
TRAF1	2.2↑	.006	8,2↑	.001
CHUK		Ns	1.9↓	.043
CLDN2	2.12↑	.039	4.3↑	.005
DEFB1		Ns	2.8↑	.011
IL13RA2	1.32↑	.023	2.6↑	.001
STAT1	1.42↑	.049	2.3↑	.002
STAT3	1.49↑	.024	1.9↑	.006
TFF3		Ns	29↑	.001

Up-regulated genes are labelled ↑ while down-regulated genes are labelled ↓. For further details see text (Section Results) and Figures 1–3.

Figure 4. Volcano plot demonstrating differently translated genes between mayo endoscopic score 0 and 1. Analyzed with hydrolysis probe. Several transcription factors for T-cell development are up-regulated.