MicroRNA signatures in chemotherapy resistant esophageal cancer cell lines

Table 1 Dysregulated microRNAs in resistant cells: Microarray results

	EAC			ESCC
	miRNA	Stepup P-value	Fold-change	miRNA	Stepup P-value	Fold-change
Dysregulated microRNAs in cisplatin-resistant variants	miR-181a-5p	0.00141	-1.78	miR-320a	0.002	-1.75
	miR-125a-5p	0.00169	-2.23	miR-320b	0.002	-1.76
	let-7e-5p	0.00170	-2.21	miR-320c	0.002	-1.66
	miR-181b-5p	0.00170	-1.68	miR-744-5p	0.023	-1.90
	miR-200b-3p	0.00170	-5.38	miR-99b-5p	0.023	-1.70
	miR-31-5p	0.00188	-1.57	miR-92a-3p	0.030	-1.53
	miR-200b-5p	0.00278	-5.11	miR-25-5p	0.041	-2.52
	miR-455-3p	0.00510	-2.78	miR-339-5p	0.047	-1.60
	miR-191-5p	0.00934	1.30	miR-18a-3p	0.056	-2.42
	miR-638	0.00934	1.74	miR-193b-3p	0.062	-1.73
	miR-92b-5p	0.01344	1.79	miR-130a-3p	0.077	2.28
	miR-23a-3p	0.01799	-2.31
	miR-200a-3p	0.03240	-5.05
	miR-296-3p	0.04236	1.66
	let-7a-5p	0.04236	-1.87
	miR-203a	0.04236	-2.84
	miR-663a	0.04480	2.40
	miR-532-5p	0.04913	-2.44
Dysregulated microRNAs in 5-FU-resistant variants	miR-31-5p	0.00031	1.84	miR-550 a-5p	0.001	3.23
	miR-192-5p	0.00151	-2.57	miR-935	0.008	-3.69
	miR-194-5p	0.00151	-2.55	miR-550 a-3p	0.037	2.65
	miR-378 a-3p	0.00277	-3.17	miR-99b-5p	0.045	-1.70
	miR-222-3p	0.00277	2.06	miR-18a-3p	0.047	-2.71
	miR-210-3p	0.00289	-2.90	miR-1226-3p	0.072	-2.45
	miR-18a-3p	0.00456	-1.84	miR-1292-5p	0.072	1.77
	miR-21-3p	0.00556	2.53	miR-125a-5p	0.127	-1.92
	miR-1268a	0.00880	2.95	miR-410-3p	0.233	-1.46
	miR-25-5p	0.01189	2.21	miR-331-3p	0.240	-2.21
	miR-27b-3p	0.01797	-2.12	miR-663a	0.240	-2.61
	miR-17-5p	0.01928	-1.35	miR-196b-5p	0.251	-2.58
	miR-193b-3p	0.01961	3.78
	miR-17-3p	0.03118	-3.03
	miR-455-5p	0.03143	-1.40
	miR-1275	0.03143	3.29
	miR-203a	0.03456	-2.85
	miR-663a	0.04074	2.39

Summary of miRNA microarray results for the different chemotherapy resistant cell lines, including dysregulated miRNAs, stepup P-value and fold changes in expression, compared to sensitive controls. FU: 5-FU resistant cells; EAC: Esophageal adenocarcinoma cells; ESCC: Esophageal squamous cell carcinoma cells.

Table 2 Dysregulated microRNAs in resistant cells: quantitative real-time polymerase chain reaction validation

	Cisplatin resistant EAC	Cisplatin resistant ESCC	5-FU resistant EAC	5-FU resistant ESCC
Significantly dysregulated miRNAs in resistant variants	miR-455-3p (-3.06)	miR-130a-3p (1.70)	miR-378a-3p (-3.58)	miR-935 (-2.29)
	miR-200b-3p (-2.46)		miR-192-5p (-2.32)	miR-550a-3p (2.21)
	let-7e-5p (-2.44)		miR-210-3p (-2.19)	miR-125a-5p (-2.20)
	miR-181b-5p (-1.88)		miR-194-5p (-2.01)	miR-1226-3p (-2.12)
	miR-125a-5p (-1.79)		miR-222-3p (1.85)	miR-99b-5p (-1.88)
	miR-181a-5p (-1.63)		miR-17-3p (-1.83)	miR-18a-3p (-1.75)
	miR-200b-5p (-1.63)		miR-193b-3p (1.54)
	miR-31-5p (-1.58)		miR-31-5p (1.40)
	miR-200a-3p (-1.57)		miR-27b-3p (1.36)
	miR-638 (1.55)
	miR-191-5p (1.42)

Final quantitative real-time polymerase chain reaction validation results for the different chemotherapy resistant cell lines, including dysregulated miRNAs and fold changes in expression compared to chemotherapy sensitive controls. All listed miRNAs were significantly dysregulated compared to controls. FU: 5-FU resistant cells; EAC: Esophageal adenocarcinoma cells; ESCC: Esophageal squamous cell carcinoma cells.

Table 3 Target gene expression of potential target genes

	MicroRNA		Target
	Dysregulated miRNA	Up-/down regulation	mRNA target	Up-/down regulation	X-fold (P-value)
5-FU resistant EAC	miR-192-5p	↓	TYMS	↑	+2.30 (< 0.001)
	miR-378a-3p	↓	CBL-B	↑	+1.93 (0.003)
	miR-192-5p	↓	ABCC3	↑	+1.30 (0.008)
	miR-27b-3p	↑	KRAS	↓	-1.24 (0.036)
	miR-193b-3p	↑	KRAS	↓	-1.24 (0.036)
5-FU resistant ESCC	miR-18a-3p	↓	KRAS	↑	+1.60 (0.036)
	miR-125a-5p	↓	ERBB2	↑	+1.40 (0.026)

Summary of gene expression analysis for potential target genes, regulated in a direction consistent with negative posttranscriptional control of target gene expression via the respective miRNA (presented in the first column). ↓: Downregulation of the miRNA or mRNA. ↑: Upregulation of the miRNA or mRNA. Fold changes for target gene expression are provided with P-values in brackets. FU: 5-FU resistant cells; EAC: Esophageal adenocarcinoma cells; ESCC: Esophageal squamous cell carcinoma cells.