Genetic Variability in Patients with HCV-Related Hepatocellular Carcinoma

Figures & data

Table 1 Demographic and Clinical Characteristics in the Cases and Controls

	Cases	Controls	P
Patients	17	13
Median age (range)	71 (66–79)	60 (42–71)	<0.00001
Males (%)	10 (58.8)	6 (46.2)	0.490644
ALT/mL × normal value (media ± SD)	1.51± 0.99	3.02±1.58	0.166052
AST/mL × normal value (media ± SD)	1.59± 0.97	1.87±1.07	0.712249
Total bilirubin mg/dL (media ± SD)	1.64±1.17	0.99±0.50	0.108374
Median HCV-RNA UI/ML (range)	3.4 X 10^5 (1.3 x 10^3–6.9×10^6)	2.5 X 10^5 (4.5 X 10^5–2.8×10^7)	0.032062
N° (%) of patients with
HCV genotype 1b	14 (82.4)	11 (84.6)	0.869125
HCV genotype 2a	0	2 (15.4)	0.0941
HCV genotype 2c	3 (17.6)	0	0.1104

Figure 1 Continued.

Figure 1 Continued.

Figure 1 (A) Phylogenetic analysis of the NS3 HCV region in the cancer (circle), non-cancer (quadrate) and serum (triangle) samples of the Cases. (B) Phylogenetic analysis of the CORE HCV region in the cancer (circle), non-cancer (quadrate) and serum (triangle) samples of the Cases. (C) Phylogenetic analysis of the NS5A HCV region in the cancer (circle), non-cancer (quadrate) and serum (triangle) samples of the Cases.

Table 2 Number of aa Substitutions in Core, NS3 and NS5A Regions for the Cases and Controls

	Compartments	NS3		NS5A		Core
		Samples	Median (IQR)	Samples	Median (IQR)	Samples	Median (IQR)
Cases	Cancer tissue	16	9 (9.5)	10	6 (3.5)	15	3 (3)
	Non-cancer tissue	16	7.5 (12.75)	10	5.5 (4.5)	13	3 (4)
	Serum	13	8 (24)	10	6 (4)	11	3 (3)
Controls	Liver tissue	11	5 (4)	9	5 (2.5)	11	3 (3)

Table 3 Prevalence of Patients with More Frequent* Amino Acid Substitutions at Different Positions of the Core Region

Core Region			ρ
Position	Cases (16)	Controls (11)
70	4 (25%)	4 (36.4%)	0.5252
75	7 (43.8%)	5 (45.5%)	0.9302
91	4 (25%)	1 (9.1%)	0.2957
110	4 (25%)	3 (27.3%)	0.8947

Note: *Amino acid substitutions present in at least 25% of the subjects.

Table 4 Prevalence of Patients with More Frequent* Amino Acid Substitutions at Different Positions of the NS3 Region

NS3 Region			ρ
Position	Cases (16 Patients)	Controls (11 Patients)
7	4 (25%)	5 (45.5%)	0.2679
48	6 (37.5%)	7 (63.6%)	0.1817
61	7 (43.8%)	4 (36.4%)	0.7011
65	4 (25%)	1 (9.1%)	0.2957
71	6 (37.5%)	2 (18.2%)	0.2801
72	4 (25%)	4 (36.4%)	0.5252
86	4 (25%)	3 (27.3%)	0.8947
87	5 (31.3%)	3 (27.3%)	0.8240
103	8 (50%)	1 (9.1%)	0.0267
122	8 (50%)	1 (9.1%)	0.0267
132	4 (25%)	5 (45.5%)	0.2679
170	5 (31.3%)	4 (36.4%)	0.7818
30	6 (37.5%)	0	0.06
32	7 (43.8%)	0	0.035
41	4 (25%)	0	0.21
44	7 (43.8%)	0	0.035
52	5 (31.3%)	0	0.12
54	4 (25%)	0	0.21
57	6 (37.5%)	0	0.06
79	9 (56.3%)	0	0.008
80	4 (25%)	0	0.21
107	4 (25%)	0	0.21
112	6 (37.5%)	0	0.06
117	6 (37.5%)	0	0.06
121	8 (50%)	0	0.018
130	5 (31.3%)	0	0.12

Note: *Amino acid substitutions present in at least 25% of the subjects.

Table 5 Prevalence of Patients with More Frequent* Amino Acid Substitutions at Different Positions of the NS5A Region

NS5A Region			ρ
Position	Cases (10)	Controls (9)
34	3(30%)	1(11.1%)	0.3133
37	9(90%)	5(55.6%)	0.0887
54	8(80%)	3(33.3%)	0.0397
75	5(50%)	2(22.2%)	0.2101
78	4(40%)	2(22.2%)	0.4052
79	3(30%)	1(11.1%)	0.3133
101	3(30%)	0	0.25
120	4(40%)	0	0.11
126	3(30%)	0	0.25

Note: *Amino acid substitutions present in at least 25% of the subjects.

Table 6 Positions of Amino Acid (aa) Substitutions in NS3, NS5A and Core Region, Amino Acid Substitutions Identified and the Compartments in Which These Were Found

	Positions	Amino Acid Substitutions	Compartiments
NS3	7	S7A	C, NC, S, T
	30	D30E	C, NC, S,
	32	E32K	C, NC, S
	41	Q41H	C, NC, S
	44	L44R	C, NC, S
	48	V48I	C, NC, S, T
	52	C52R	C, NC, S
	54	T54I	C, S
	57	H57Q	C, NC, S
	61	S61T	C, NC, S, T
	65	A65P	C, NC, S, T
	71	I71V	C, NC, S, T
	72	T72I	C, NC, S, T
	79	D79N	C, NC, S
	80	Q80E	C, NC, S
	86	Q86P	C, NC, S, T
	87	A87G	C, NC, S, T
	103	D103N	C, NC, S, T
	107	V107A	C, NC, S
	112	D112N	C, NC, S
	117	R117P	C. NC, S
	121	D121N	C, NC, S
	122	S122G	C, NC, S, T
	130	R130K	C, NC, S
	132	V132I	C, NC, S, T
	168	D168E	NC, S
	170	V170I	C, NC, S, T
NS5A	31	L31M	T
	34	V34I	C, NC, S, T
	37	F37L	C, NC, S, T
	54	Q54H	C, NC, S, T
	75	V75A	C, NC, S, T
	78	K78R	C, NC, S, T
	79	T79A	C, NC, S
	93	Y93H	C, NC, S, T
	101	S101C	NC, S
	120	E120K	C, NC, S,
	126	D126N	C, S
CORE	70	Q70R	C, NC, S, T
	75	A75T	C, NC, S, T
	91	M91L	C, NC, S, T
	110	T110N	C, NC, S, T

Notes: C, cancer; NC, non-cancer; S, serum; T, hepatic tissue.