Association of twelve polymorphisms in three onco-lncRNA genes with hepatocellular cancer risk and prognosis: A case-control study

Table 1 Association of lncRNA gene single nucleotide polymorphisms and risk of hepatocellular cancer (n)

Gene	Chr. Pos.	SNP1	Loc.	Genotype	Controls (%)	Cases (%)	P2 value	OR (95%CI)	PHWE value
HOTTIP	7p15.2	rs17501292	Exon	TT	732 (91.2)	453 (87.1)		1 (Ref.)	0.190
				TG	71 (8.8)	66 (12.7)	0.021	1.52 (1.06-2.17)
				GG	0 (0)	1 (0.2)	NA	NA
				TG + GG vs TT			0.017	1.54 (1.08-2.20)
				G vs T			0.012	1.55 (1.10-2.18)
		rs2067087	Exon	GG	174 (21.7)	88 (16.9)		1 (Ref.)	0.674
				GC	405 (50.6)	263 (50.7)	0.236	1.16 (0.90-1.49)
				CC	222 (27.7)	168 (32.4)	0.015	1.49 (1.08-2.08)
				CC vs GG + GC			0.035	1.35 (1.02-1.82)
				C vs G			0.017	1.20 (1.03-1.41)
		rs17427960	Intron	CC	172 (21.7)	85 (16.7)		1 (Ref.)	0.613
				CA	387 (48.8)	259 (50.9)	0.707	1.05 (0.81-1.35)
				AA	234 (29.5)	165 (32.4)	0.032	1.78 (1.03-2.00)
				AA vs CC + CA			0.028	1.39 (1.03-1.85)
				A vs C			0.049	1.18 (1.00-1.37)
MALAT1	22q13.2	rs4102217	Promoter	GG	608 (75.1)	362 (69.6)		1 (Ref.)	0.055
				GC	180 (22.2)	148 (28.5)	0.011	1.39 (1.08-1.79)
				CC	22 (2.7)	10 (1.9)	0.481	0.76 (0.36-1.63)
				GC + CC vs GG			0.028	1.32 (1.03-1.69)
				C vs G			0.097	1.20 (0.97-1.50)

¹The sort order was according to the SNP location in its genes from 5' starting to 3' ends.

²P value was calculated by adjusted by age and gender. NA: Not available; Chr. Pos.: Chromosomal position; Loc.: Localisation; P_HWE: P value for Hardy-Weinberg Equilibrium.

Table 2 Association of haplotype of lncRNA gene and hepatocellular cancer risk (n)

Haplotype	Control (%)	Case (%)	OR (95%CI)	P value
HOTTIP1
CGCA	33.54 (2.4)	407.00 (4.5)	1.91 (1.20-3.05)	0.006
CTGC	663.39 (47.3)	389.97 (43.4)	0.85 (0.71-1.01)	0.066
GTCA	604.75 (43.1)	401.77 (44.7)	1.08 (0.91-1.28)	0.406
CCAT22
AAG	623.60 (39.8)	434.27 (42.7)	1.13 (0.96-1.33)	0.136
AAT	937.40 (59.8)	577.73 (56.9)	0.89 (0.75-1.04)	0.136
MALAT13
CTCA	217.99 (13.8)	167.00 (16.3)	1.22 (0.08-1.52)	0.080
GCCA	934.81 (59.3)	599.74 (58.6)	0.97 (0.82-1.14)	0.718
GTCA	296.19 (18.8)	1720 (16.6)	0.86 (0.70-1.06)	0.160
GTGG	85.00 (5.4)	58.94 (5.8)	1.07 (0.76-1.51)	0.689

Haplotype for

¹HOTTIP rs3807598-rs17501292-rs2067087-rs17427960;

²CCAT2 rs3843549-rs138947056-rs6983267;

³MALAT1 rs4102217-rs591291-rs11227209-rs619586.

Table 3 The two-way interaction of HOTTIP rs17501292-MALAT1 rs619586 polymorphisms in the risk of hepatocellular cancer

Variables	MALAT1 rs619586
	AA	AG + GG
	HCC vs CON (n = 335 vs 572)
HOTTIP rs17501292
TT
Case/control	372/617	78/107
OR (95%CI)	1	1.21(0.88-1.66)
TG + GG
Case/control	61/55	6/15
OR (95%CI)	1.84 (1.25-2.71)	0.66 (0.26-1.73)
	Pinteraction = 0.028, OR (95%CI) = 0.30 (0.10-0.88)

HCC: Hepatocellular cancer; CON: Control.

Table 4 Univariate proportional hazard analysis stratified by host characteristics for the association of lncRNA polymorphisms and hepatocellular cancer n (%)

Gene	SNP	Stratified	Stratified factors	Genotype	HCC	Death	MST (M)	P value	Hazard ratio (95%CI)
HOTTIP	rs3807598				n = 136
		HBV	Positive	CC	30 (22.06)	12	90.0		1 (reference)
				CG	73 (53.68)	23	90.1b	0.391	0.74 (0.37-1.48)
				GG	33 (24.26)	11	64.1b	0.680	0.84 (0.37-1.91)
					n = 31
			Negative	CC	10 (32.26)	7	21.0		1 (reference)
				CG	13 (41.94)	4	41.8b	0.374	0.60 (0.16-1.97)
				GG	8 (25.80)	1	70.3b	0.049	0.12 (0.02-0.99)
					n = 285
MALAT1	rs591291				n = 286
		Gender	Male	CC	98 (34.27)	39	48.0		1 (reference)
				TC	146 (51.05)	56	56.0	0.865	0.97 (0.64-1.45)
				TT	42 (14.68)	19	47.0	0.678	1.12 (0.65-1.94)
					n = 64
			Female	CC	22 (34.38)	13	32.0		1 (reference)
				TC	37 (57.81)	9	56.0	0.022	0.37 (0.16-0.87)
				TT	5 (7.81)	0	NA	0.286	0.04 (0.00-16.09)
					n = 139
		HBV	Positive	CC	54 (38.85)	18	69.0		1 (reference)
				TC	69 (49.64)	21	92.1b	0.816	0.93 (0.49-1.74)
				TT	16 (11.51)	7	90.0	0.965	0.98 (0.41-2.35)
					n = 31
			Negative	CC	8 (25.81)	5	6.0		1 (reference)
				TC	16 (51.61)	4	27.0	0.042	0.25 (0.07-0.95)
				TT	7 (22.58)	3	21.0	0.215	0.40 (0.09-1.71)

HR: Hazard rate; MST: Median survival time (months); NA: Not available.

Table 5 Differences of lncRNA gene mRNA levels in different genotypes in hepatocellular cancer and non-cancer tissues

Variable	Non-cancer tissues				Cancer tissues
	n	ΔCt (Mean ± SD)	Normalized 2-ΔΔCt	P1 value	n	ΔCt (Mean ± SD)	Normalized 2-ΔΔCt	P1 value
The effect of HOTTIP rs17501292 genotypes to HOTTIP mRNA expression
TT	10	12.32 ± 4.06	1 (0.60, 16.68)	Ref.	25	11.84 ± 3.87	1.39 (0.10, 20.39)	Ref.
TG	1	NA	NA	NA	2	15.30 ± 1.65	NA	0.735
GG	0	NA	NA	NA	0	NA	NA	NA
The effect of HOTTIP rs2067087 genotypes to HOTTIP mRNA expression
GG	2	8.64 ± 2.06	1 (0.24, 4.17)	Ref.	5	11.66 ± 1.43	1 (0.37, 2.69)	Ref.
GC	5	12.25 ± 4.17	0.13 (0.01, 1.23)	0.253	13	11.85 ± 3.53	0.88 (0.08, 10.13)	0.101
CC	4	13.70 ± 3.86	0.03 (0.00, 0.86)	0.453	8	12.23 ± 5.42	0.67 (0.02, 28.84)	0.444
The effect of HOTTIP rs17427960 genotypes to HOTTIP mRNA expression
CC	2	8.64 ± 2.06	1 (0.24, 4.17)	Ref.	6	12.47 ± 2.34	1 (0.20, 5.06)	Ref.
CA	5	11.55 ± 3.21	0.13 (0.01, 1.15)	0.254	13	11.88 ± 3.72	2.13 (0.04, 125.37)	0.063
AA	3	13.56 ± 4.71	0.03 (0.00, 0.86)	0.465	6	11.38 ± 5.88	1.51 (0.11, 19.84)	0.348
The effect of MALAT1 rs4102217 genotypes to MALAT1 mRNA expression
GG	52	-2.25 ± 4.40	1 (0.05, 21.11)	Ref.	51	-0.98 ± 4.88	1 (0.03, 29.45)	Ref.
GC	16	-3.76 ± 3.60	2.85 (0.23, 34.54)	0.404	16	-2.79 ± 4.55	3.51 (0.15, 82.14)	0.742
CC	NA	NA	NA	NA	1	NA	NA	NA

¹The statistical analysis for the effect of genotype to phenotype was used two-independent sample t-test, and for the combination of genotype to phenotype was used ANOVA analysis. NA: Not available.