Clinical profiles of the enrolled patients
Thirty-two patients with primary iron overload from the CR-GMLD were recruited to screen for genetic variants in known HH-related genes and novel iron homeostasis-related genes. All the probands with primary iron overload were validated by liver biopsy and/or MRI examinations. Demographic characteristics of patients with non-HFE HH are shown in Table 1.
Table 1
Demographic characteristics of patients in non-HFE HH cases
Factor
|
Total (32)
|
Gender
|
-
|
Male
|
23
|
Female
|
9
|
Age(y)
|
45.07 ± 15.94 (18–79)
|
SF(ng/ml)
|
2631.0 (1115.95, 6371.25)
|
TS(%)
|
92.30 (81.30,96.10)
|
ALT(U/L)
|
72.0 (30.0,104.0)
|
AST(U/L)
|
62.8 (34.6,103.0)
|
GGT(U/L)
|
42 (27.00,72.0)
|
TBIL(umol/L)
|
37.88 ± 43.86
|
ALB(g/L)
|
40.30 ± 8.33
|
Cirrhosis
|
11
|
Skin pigmentation
|
13
|
Arthropathy
|
2
|
Cardiac involvement
|
5
|
Diabetes
|
11
|
Hypogonadism
|
9
|
SF = serum ferritin, TS = transferrin saturation, ALT = alanine transaminase, AST = aspartate aminotransferase, GGT = γ-glutamyltransferase, TBIL = total bilirubin, ALB = albumin |
Gene variants distribution
We found that genetic variants forms of Chinese patients with primary iron overload are mainly non-HFE-related combined heterozygous variants. 1 case (3.13%) carried combined heterozygous HFE p.C282Y/71X pathogenic variants. 8 cases (25%) carried HJV pathogenic variants, among which 4 cases carried homozygous pathogenic variants in HJV gene, including p. Q6H, p. F103L, p. Q312X and p. C321X. 7 (21.88%) cases with SLC40A1 pathogenic variants, 8 (25%) cases with SUGP2 likely pathogenic variants, 5 (15.63%) cases with DENND3 likely pathogenic variants. None of damaging or probably damaging variants for HAMP and TFR2 was identified in any cases. The significance and pathogenicity of novel variants in HH-related genes are shown in Table 2.
Table 2
The significance and pathogenicity of novel variants in HH-related genes
Gene
|
Nucleotide change
|
Amino acid alteration
|
MAF
|
Polyphen-2 HDIV
|
SIFT
|
Mutation Taster
|
Prediction
|
Score
|
Prediction
|
Score
|
Prediction
|
Score
|
HFE
|
c.62A > G
|
p. Q21R
|
-
|
Probably damaging
|
0.651
|
Tolerable
|
0.888
|
Polymorphism
|
1.000
|
HFE
|
c.1006 + 8G > A
|
NA
|
-
|
NA
|
NA
|
NA
|
NA
|
Polymorphism
|
1.000
|
HFE
|
c.902C > T
|
p. P301L
|
-
|
Benign
|
0.037
|
Tolerable
|
1
|
Polymorphism
|
1.000
|
HFE
|
c.340 + 4T > C
|
NA
|
0.4267
|
NA
|
NA
|
NA
|
NA
|
Polymorphism
|
1.000
|
TFR2
|
c.1097G > A
|
p. R336H
|
0.0004
|
Benign
|
0.003
|
Tolerable
|
0.052
|
Polymorphism
|
1.000
|
SLC40A1
|
c.1531G > A
|
p. V511I
|
-
|
Probably damaging
|
0.984
|
Damaging
|
0
|
Disease causing
|
1.000
|
MAF = minor allele frequency, data from the 1000 Genomes Project. |
Among these 31 non-HFE HH cases, 4 cases harbored homozygous variants, 2 cases harbored homozygous + heterozygous variants, 19 cases harbored heterozygous or combined heterozygous variants, and 6 cases harbored no damaging variants. Genetic characteristics of patients with HH are shown in Table 3.
Table 3
Genetic characteristics of 32 patients in HH cases
NO.
|
Age
|
Gender
|
SF (ng/ml)
|
TS (%)
|
Iron deposition on liver biopsy
|
Iron overload on MRI
|
Known HH-related genes
|
Iron homeostasis -related genes
|
1
|
26
|
M
|
7004
|
92.0
|
predominant in hepatocytes
|
Liver
|
HJV p.Q6H/C321X/I281T
|
-
|
2
|
28
|
M
|
6269
|
95.4
|
predominant in hepatocytes
|
Liver, pancreas
|
HJV p.Q6H/C321X/I281T
|
-
|
3
|
22
|
F
|
2995
|
89.1
|
predominant in hepatocytes
|
Liver, pancreas
|
HJV p. Q312X (homo)
|
-
|
4
|
18
|
M
|
6678
|
100
|
predominant in hepatocytes
|
ND
|
HJV p.Q6H/C321X/H104R
|
-
|
5
|
57
|
M
|
4001
|
93.0
|
predominant in hepatocytes
|
Liver
|
HJV p.Q6H/C321X/V274M
|
-
|
6
|
36
|
F
|
2000
|
96.0
|
predominant in hepatocytes
|
Liver
|
HJV p. F103L (homo)
|
-
|
7
|
30
|
M
|
11555
|
98.0
|
ND
|
Liver, spleen, pancreas
|
HJV p. Q6H(homo)/ C321X (homo)
|
-
|
8
|
24
|
M
|
6037
|
94.3
|
ND
|
Liver, pancreas
|
HJV p. Q6H(homo)/C321X (homo)
|
-
|
9
|
57
|
F
|
5886.1
|
71.1
|
Hepatocytes and reticuloendothelial cells
|
Liver, spleen, pancreas
|
SLC40A1 p. N144D
|
-
|
10
|
66
|
F
|
1446.2
|
92.7
|
ND
|
Liver, spleen, pancreas
|
SLC40A1 p. Y333H
|
SUGP2 p. R639Q
|
11
|
48
|
M
|
2267-
|
91.8
|
ND
|
Liver, spleen, pancreas
|
SLC40A1 p. V511I
|
-
|
12
|
58
|
M
|
5949
|
28.4
|
predominant in hepatocytes
|
Liver, spleen
|
SLC40A1 p. v162del
|
-
|
13
|
49
|
M
|
7445
|
97.0
|
predominant in hepatocytes
|
Liver, spleen
|
SLC40A1 p. Y333H
|
-
|
14
|
60
|
M
|
15000
|
94.0
|
predominant in hepatocytes
|
Liver, spleen, pancreas
|
SLC40A1 p. Y333H
|
-
|
15
|
79
|
M
|
493.8
|
97.1-
|
ND
|
Liver, pancreas
|
-
|
SUGP2 p. R639Q
|
16
|
63
|
M
|
3868
|
97.7
|
predominant in hepatocytes
|
Liver, spleen
|
-
|
SUGP2 p. R639Q
|
17
|
67
|
M
|
1102
|
92.3
|
predominant in hepatocytes
|
Liver, spleen
|
-
|
DENND3 p. L708V(homo)
SUGP2 p. R639Q
|
18
|
28
|
M
|
738
|
46.4
|
predominant in hepatocytes
|
ND
|
-
|
DENND3 p. L708V
|
19
|
38
|
F
|
843
|
96.2
|
predominant in hepatocytes
|
ND
|
-
|
DENND3 p. L708V
|
20
|
53
|
F
|
1402
|
49.0
|
predominant in hepatocytes
|
Liver, spleen
|
-
|
SUGP2 p. R639Q
|
21
|
46
|
M
|
2000
|
85.0
|
ND
|
Liver, spleen
|
-
|
SUGP2 p. R639Q
|
22
|
45
|
M
|
685
|
-
|
predominant in hepatocytes
|
ND
|
-
|
DENND3 p. L708V
|
23
|
33
|
M
|
626
|
68.0
|
Hepatocytes and reticuloendothelial cells
|
ND
|
-
|
SUGP2 p. R639Q
|
24
|
31
|
M
|
6000
|
81.0
|
ND
|
Liver
|
-
|
DENND3 p. L708V
|
25
|
66
|
F
|
12703-
|
91.7
|
predominant in hepatocytes
|
Liver, spleen, pancreas
|
-
|
-
|
26
|
50
|
F
|
9272
|
81.6
|
predominant in hepatocytes
|
Liver, spleen, pancreas
|
-
|
-
|
27
|
53
|
M
|
1121
|
37.6
|
predominant in reticuloendothelial cells
|
Liver, spleen
|
-
|
-
|
28
|
53
|
M
|
773
|
96.8
|
predominant in hepatocytes
|
Liver
|
-
|
-
|
29
|
31
|
M
|
1220
|
92.4
|
ND
|
Liver, spleen, pancreas
|
-
|
-
|
30
|
37
|
M
|
1316
|
85.0
|
ND
|
Liver, spleen
|
-
|
-
|
31
|
48
|
F
|
7078
|
99.7
|
predominant in hepatocytes
|
Liver, spleen
|
SLC40A1 IVS3 + 10delGTT
|
SUGP2 p. R639Q(homo)
|
32
|
28
|
M
|
2153
|
91.7
|
predominant in hepatocytes
|
Liver
|
HFE p.C282Y/R71X
|
-
|
HH = Hereditary hemochromatosis, ND = not done |
Grouping of non- HFE HH
Patients with non-HFE related HH were divided into four groups in the study, HJV HH (Type 2A HH), SLC40A1 HH (Type 4B HH), SUGP2 or DENND3 variants HH and No pathogenic or likely pathogenic variants HH groups, based on the pathogenic variants identified in these cases. Demographic and laboratory characteristics of the four groups of HH cases are shown in Table 4.
Table 4
Demographic and laboratory characteristics of patients in different groups with HH
Characteristic
|
HJV (n = 8)
|
SLC40A1 (n = 6)
|
SUGP2 or DENND3 (n = 10)
|
HH without P or LP variants* (n = 6)
|
p
|
Male, n (%)
|
6 (75)
|
4 (66.7)
|
8 (80)
|
4 (66.7)
|
0.897
|
Age, y
|
30.13 ± 12.12
|
56.33 ± 6.83
|
48.30 ± 16.99
|
48.33 ± 12.55
|
0.007
|
SF, ng/ml
|
6153(3246.5,6922.5)
|
5917.6(2061.8,9333.8)
|
972 (670.3,2467.1)
|
1267(1033.8,10129.7)
|
0.010
|
TS, %
|
94.85(92.25,97.5)
|
92.25(60.43,95.75)
|
85.0(58.5,96.7)
|
88.35(70.6,93.5)
|
0.210
|
ALT, U/L
|
99.5(67.3,12)
|
78.5(39.5,141.3)
|
31(22.5,44.5)
|
72(18.5,121.5)
|
0.161
|
AST, U/L
|
92(64.4,121.0)
|
60.4(37.6,111.8)
|
33.4(22.9,48.5)
|
72(20.7,124.3)
|
0.051
|
GGT, U/L
|
48(34.3,75)
|
38(19.8,278.3)
|
29.9(26.5,58.5)
|
56(22.5,403)
|
0.622
|
TBIL, µmol/L
|
17.56 ± 8.85
|
18.79 ± 10.72
|
64.14 ± 62.59
|
51.25 ± 48.90
|
0.094
|
ALB, g/L
|
43.98 ± 10.12
|
38.88 ± 3.87
|
39.14 ± 9.42
|
37.96 ± 7.58
|
0.540
|
HH without P or LP variants*= HH without pathogenic or likely pathogenic variants, SF = serum ferritin, TS = transferrin saturation, ALT = alanine transaminase, AST = aspartate aminotransferase, GGT = γ-glutamyltransferase, TBIL = total bilirubin, ALB = albumin |
Among the 31 cases with non-HFE related HH, 2 cases (the first is SLC40A1 p. Y333H + SUGP2 p. R639Q, the second is SLC40A1 IVS3 + 10delGTT + SUGP2 p. R639Q(homo)) carried two different pathogenic or likely pathogenic variants. The first was grouped into the SLC40A1 HH due to the definite pathogenicity of SLC40A1 p. Y333H. Previous functional studies showed that the SLC40A1 p. Y333H variant was associated with gain-of-function of ferroportin and caused iron overload and organ damage []. The second carried two likely pathogenic variants. This patient was a 48-year-old female with SF 7078 ng/ml and TS 99.7%. Liver biopsy suggested that iron deposition was predominant in hepatocytes, MRI suggested iron overload in liver and spleen, and gene test suggested SLC40A1 IVS3 + 10delGTT + SUGP2 p. R639Q(homo) combined likely pathogenic variants. We excluded this patient due to difficulty in grouping. Therefore, we finally analyzed the remaining 30 cases.
Genotype and phenotype associations in different types of non- HFE HH
HJV HH (Type 2A HH)
There were more males than females in HJV HH, the ratio of males and females was 3:1. Mean age at diagnosis of this group of patients was the lowest (30 years) in the four types. Totally, 62.5% of the patients had hypogonadism, half of them developed skin pigmentation, 37.5% had both cardiac involvement and diabetes. Only one case developed arthropathy. None of patients in HJV HH developed cirrhosis.
ALT and AST (median 99.5 and 92 U/L) levels increased in this group. GGT (median 48 U/L), TBIL (mean 17.6 µmol/L) and ALB (mean 44.0 g/L) levels were normal. The median SF (6153 ng/ml) and TS (median 95%) levels were highest in four types.
SLC40A1 HH (Type 4B HH)
There were more males than females in SLC40A1 HH, the ratio of males and females was 2:1. Mean age at diagnosis of this group of patients was the highest (56 years) in the four types. Totally, 83.3% of the patients had both cirrhosis and diabetes, 66.6% had skin pigmentation, half of them had hypogonadism. Only one case had arthropathy. None of patients in SLC40A1 HH developed cardiac diseases.
ALT and AST (median 78.5 and 60.4 U/L) levels increased in this group. GGT (median 38 U/L), TBIL (mean 18.9 µmol/L), and ALB (mean 38.9 g/L) levels were normal. The median SF level was 5918 ng/ml. The median TS was 92%.
SUGP2 or DENND3 variants HH
There were more males than females in SUGP2 or DENND3 HH, the ratio of males and females was 4:1. Mean age at diagnosis of this group of patients was 48 years. Totally, 40% of the patients had cirrhosis, 20% had skin pigmentation, 10% had both diabetes and hypogonadism. None of patients in SUGP2 or DENND3 HH developed arthropathy and cardiac diseases.
ALT (median 31 U/L), AST (median 33.4 U/L), GGT (median 29.9 U/L), and ALB (mean 39.1 g/L) levels were normal in this group. TBIL (mean 64.1 µmol/L) levels were higher than other groups. The median SF level was 972 ng/ml. The median TS level was 85%.
HH without pathogenic or likely pathogenic variants
There were more males than females in HH without pathogenic or likely pathogenic variants, the ratio of males and females was 2:1. Mean age at diagnosis of this group of patients was 48 years. Totally, 50% of the patients had skin pigmentation, 33.3% had cirrhosis, 33.3% had both cardiac diseases and diabetes. None of patients developed arthropathy and hypogonadism.
ALT and AST (median 72 and 72 U/L), TBIL (mean 51.3 µmol/L) levels increased in this group. GGT (median 56 U/L) and ALB (mean 38.0 g/L) levels were normal. The median SF level was 1267 ng/ml. The median TS level was 88%.
There were more males than females in all groups (Fig. 1A). The age at diagnosis was statistically different between HJV HH and SLC40A1 HH groups (p = 0.001), between HJV HH and SUGP2 or DENND3 HH groups(p = 0.008), between HJV HH and HH without pathogenic or likely pathogenic variants groups(p = 0.018), while the comparison between other groups was not statistically significant (Fig. 1B). The incidence of cirrhosis (p = 0.011), cardiac involvement (p = 0.042), diabetes(p = 0.035) and hypogonadism (p = 0.020) was statistically significant in the four groups. However, due to the limited sample size, the pairwise comparison showed no significant difference (Fig. 2). HH without P or LP variants*= HH without pathogenic or likely pathogenic variants
TBIL levels were significantly higher in SUGP2 or DENND3 HH when compared to HJV HH groups(p = 0.032). there was no significant difference about other liver function indices in the four groups. SF levels increased greatly in all the four groups. There were statistical differences between HJV HH and SUGP2 or DENND3 HH groups (p = 0.002), between SLC40A1 HH and SUGP2 or DENND3 HH groups (p = 0.01), while the comparison between other groups was not statistically significant. TS increased greatly in all HH groups, with a median TS of 92% in all cases.