Association Between Genetic Polymorphisms of lncRNA NEAT1 and Pulmonary Tuberculosis Risk, Clinical Manifestations in a Chinese Population

Figures & data

Table 1 The Demographic and Clinical Characteristics of PTB Patients and Healthy Controls

Characteristics	PTB Patients	Healthy Controls
Demographic characteristics
Age (years)	45.07±17.74	43.36±13.84
Sex (male/female)	313/166	208/268
Clinical characteristics^a
Fever (+/-)	85/389	NA
Drug resistance (+/-)	74/402	NA
DILI (+/-)	70/408	NA
Pulmonary infection (+/-)	104/374	NA
Hypoproteinemia (+/-)	34/444	NA
Leukopenia (+/-)	32/446	NA
Sputum smear (+/-)	301/129	NA

Note: ^aPart of the study subjects of data missing.

Abbreviations: PTB, pulmonary tuberculosis; DILI, drug-induced liver injury; NA, not applicable; +/−, with/without.

Table 2 Genotypes and Alleles Frequencies of NEAT1 Gene in PTB Patients and Healthy Controls

SNP	Analyze Model	PTB (N = 479) n (%)	Control (N = 476) n (%)	P value	OR (95% CI)
rs2239895	Genotype
	CC	13(2.71)	7(1.47)	0.214	0.554(0.219, 1.407)
	GC	120(25.05)	133(27.94)	0.370	1.141(0.855, 1.524)
	GG	346(72.23)	336(70.59)	Reference
	Allele
	C	146(15.24)	147(15.44)	0.903	0.992(0.768, 1.263)
	G	812(84.76)	805(84.56)	Reference
	Dominant model
	GG	346(72.23)	336(70.59)	0.574	1.041(0.903, 1.201)
	GC+CC	133(27.77)	140(29.41)	Reference
	Recessive model
	CC	13(2.71)	7(1.47)	0.180	0.698(0.383, 1.272)
	GC+GG	466(97.29)	469(98.53)	Reference
rs3741384	Genotype
	AA	12(2.51)	6(1.26)	0.193	0.518(0.192, 1.395)
	GA	117(24.43)	132(27.73)	0.294	1.168(0.874, 1.562)
	GG	350(73.06)	338(71.01)	Reference
	Allele
	A	141(14.72)	144(15.13)	0.802	0.984(0.867, 1.117)
	G	817(85.28)	808(84.87)	Reference
	Dominant model
	GG	350(73.06)	338(71.01)	0.478	1.053(0.912, 1.216)
	GA+AA	129(26.93)	138(28.99)	Reference
	Recessive model
	AA	12(2.51)	6(1.26)	0.157	0.665(0.345, 1.281)
	GA+GG	467(97.49)	470(98.74)	Reference
rs3825071	Genotype
	TT	12(2.51)	11(2.31)	0.821	0.909(0.395, 2.088)
	CT	129(26.93)	124(26.05)	0.743	0.953(0.714, 1.272)
	CC	338(70.56)	341(71.64)	Reference
	Allele
	T	153(15.97)	146(15.34)	0.703	0.976(0.861, 1.107)
	C	805(84.03)	806(84.67)	Reference
	Dominant model
	CC	338(70.56)	341(71.64)	0.714	1.027(0.891, 1.183)
	CT+TT	141(29.44)	135(28.36)	Reference
	Recessive model
	TT	12(2.51)	11(2.31)	0.845	0.959(0.623, 1.476)
	CT+CC	467(97.49)	465(97.69)	Reference
rs512715	Genotype
	CC	35(7.31)	27(5.67)	0.399	0.796(0.468, 1.353)
	GC	181(37.79)	194(40.76)	0.460	1.105(0.847, 1.442)
	GG	263(54.91)	255(53.57)	Reference
	Allele
	C	251(26.20)	248(26.05)	0.941	0.998(0.946, 1.053)
	G	707(73.80)	704(74.95)	Reference
	Dominant model
	GG	263(54.91)	255(53.57)	0.679	1.025(0.912, 1.152)
	GC+CC	216(45.09)	221(46.43)	Reference
	Recessive model
	CC	35(7.31)	27(5.67)	0.305	0.983(0.950, 1.016)
	GC+GG	444(92.69)	449(94.33)	Reference

Note: After Bonferroni correction, P value was still not statistically significant.

Table 3 The Associations Between NEAT1 Gene Polymorphisms and Several Clinical Features of PTB Patients

SNP	Allele	Clinical Features	Group	Genotype n (%)			P value^a	Allele n (%)		P value
	(M/m)			MM	Mm	mm		M	m
rs2239895	G/C	Fever	+	59	25	1	0.407	143	27	0.814
			–	283	94	12		660	118
		Drug resistance	+	56	17	1	0.624	129	19	0.359
			–	287	103	12		677	127
		DILI	+	53	16	1	0.667	122	18	0.390
			–	292	104	12		688	128
		Pulmonary infection	+	71	29	4	0.519	171	37	0.254
			–	274	91	9		639	109
		Hypoproteinemia	+	24	10	0	0.528	58	10	0.893
			–	321	110	13		752	136
		Leukopenia	+	24	8	0	0.615	56	8	0.523
			–	321	112	13		754	138
		Sputum smear	+	220	76	5	0.080	516	86	0.452
			–	94	28	7		216	42
rs3741384	G/A	Fever	+	60	24	1	0.489	144	26	0.831
			–	286	92	11		664	114
		Drug resistance	+	57	16	1	0.609	130	18	0.324
			–	290	101	11		681	123
		DILI	+	53	16	1	0.759	122	18	0.494
			–	296	101	11		693	123
		Pulmonary infection	+	74	26	4	0.600	174	34	0.463
			–	275	91	8		641	107
		Hypoproteinemia	+	24	10	0	0.519	58	10	0.992
			–	325	107	12		757	131
		Leukopenia	+	24	8	0	0.643	56	8	0.599
			–	325	109	12		759	133
		Sputum smear	+	223	73	5	0.081	519	83	0.421
			–	95	27	7		217	41
rs3825071	C/T	Fever	+	67	17	1	0.148	151	19	0.052
			–	266	112	11		644	134
		Drug resistance	+	48	24	2	0.520	120	28	0.305
			–	287	105	10		679	125
		DILI	+	44	23	3	0.252	111	29	0.100
			–	293	106	9		692	124
		Pulmonary infection	+	76	26	2	0.778	178	30	0.482
			–	261	103	10		625	123
		Hypoproteinemia	+	28	6	0	0.243	62	6	0.094
			–	309	123	12		741	147
		Leukopenia	+	24	7	1	0.786	55	9	0.661
			–	313	122	11		748	144
		Sputum smear	+	196	95	10	0.010	487	115	0.003
			–	103	24	2		230	28
rs512715	G/C	Fever	+	44	34	7	0.790	122	48	0.497
			–	217	144	28		578	200
		Drug resistance	+	45	26	3	0.374	116	32	0.172
			–	217	153	32		587	217
		DILI	+	40	25	5	0.926	105	35	0.737
			–	223	155	30		601	215
		Pulmonary infection	+	56	34	14	0.021	146	62	0.175
			–	207	146	21		560	188
		Hypoproteinemia	+	22	7	5	0.045	51	17	0.823
			–	241	173	30		655	233
		Leukopenia	+	19	11	2	0.874	49	15	0.609
			–	244	169	33		657	235
		Sputum smear	+	170	112	19	0.395	452	150	0.359
			–	70	46	13		186	72

Notes: Part of the study subjects of data missing. ^aP-value was corrected by Bonferroni correction (0.05/3), P < 0.0167 was considered as statistical significance.

Abbreviations: +/-, with/without; M, major alleles; m, minor alleles.

Table 4 Haplotype Analysis of NEAT1 Gene in PTB Patients and Controls

Haplotype	PTB [n(%)]	Control [n(%)]	P value	OR (95% CI)
rs2239895-rs3741384-rs3825071-rs512715
CACC	140(14.6)	142(14.9)	0.824	0.972(0.754, 1.252)
GGCC	81(8.5)	74(7.7)	0.566	1.101(0.792, 1.531)
GGCG	580(60.6)	584(61.4)	0.622	0.954(0.789, 1.152)
GGTG	126(13.1)	118(12.4)	0.640	1.066(0.814, 1.397)

Notes: Global χ² is 0.623, df=3 (frequency<0.03 in both control and case has been dropped). Fisher’s p value is 0.891.