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Erschienen in: BMC Ophthalmology 1/2017

Open Access 01.12.2017 | Research article

Next-generation sequencing for D47N mutation in Cx50 analysis associated with autosomal dominant congenital cataract in a six-generation Chinese family

verfasst von: Chao Shen, Jingbing Wang, Xiaotang Wu, Fuchao Wang, Yang Liu, Xiaoying Guo, Lina Zhang, Yanfei Cao, Xiuhua Cao, Hongxing Ma

Erschienen in: BMC Ophthalmology | Ausgabe 1/2017

Abstract

Background

Congenital cataract is the most frequent cause of blindness during infancy or early childhood. To date, more than 40 loci associated with congenital cataract have been identified, including at least 26 genes on different chromosomes associated with inherited cataract. This present study aimed to identify the genetic mutation in a six-generation Chinese family affected with congenital cataract.

Methods

A detailed six-generation Chinese cataract family history and clinical data of the family members were recorded. A total of 27 family members, including 14 affected and 13 unaffected individuals were recruited. Whole exome sequencing was performed to determine the disease-causing mutation. Sanger sequencing was used to confirm the results.

Results

A known missense mutation, c. 139G > A (p. D47N), in Cx50 was identified. This mutation co-segregated with all affected individuals and was not observed in the unaffected family members or in 100 unrelated controls. The homology modeling showed that the structure of the mutant protein was different with that wild-type Cx50.

Conclusions

The missense mutation c.139G > A in GJA8 gene is associated with autosomal dominant congenital cataract in a six-generation Chinese family. The result of this present study provides further evidence that the p. D47N mutation in CX50 is a hot-spot mutation.
Abkürzungen
CRYAA
Crystallin Alpha A
CRYAB
Crystallin Alpha B
CRYBA1
Crystallin Beta A1
CRYBA3
Crystallin Beta A3
CRYBA4
Crystallin Beta A4
CRYBB1
Crystallin Beta B1
CRYBB2
Crystallin Beta B2
CRYBB3
Crystallin Beta B3
CRYGA
Crystallin Gamma A
CRYGC
Crystallin Gamma C
CRYGD
Crystallin Gamma D
CRYGS
Crystallin Gamma S
Cx43
Connexin43
Cx46
Connexin46
Cx50
Connexin50
GJA1
Gap Junction Protein Alpha 1
GJA3
Gap Junction Protein Alpha 3
GJA8
Gap Junction Protein Alpha 8

Background

Congenital cataract is the most frequent cause of blindness during infancy or early childhood, with an occurrence of 1–15/10,000 live births worldwide [1, 2]. It explains for 10%–30% of childhood blindness [3]. Congenital cataract is characterized by the presence of an opacification of the lens at birth or during babyhood. On the basis of morphology, congenital cataract can be classified into several subtypes, including nuclear, sutural, polar, cortical cataract, etc. [4]. Congenital cataract pathogenesis involves several distinct reasons including gene defects, chromosomal abnormalities, metabolic disorders, and infections during embryogenesis. Approximately half of congenital cataracts are inherited [3]. Though autosomal recessive and X-linked inheritances have been reported, inheritance is mainly autosomal dominant [5]. Up to date, over 40 loci associated with congenital cataract have been confirmed, including no less than 26 genes on different chromosomes related to congenital cataract [6, 7]. Among these mutant genes, the connexin genes and crystallin genes are the most widespread. Briefly, half of the mutations were discovered in the crystalline genes, such as alpha crystallins, beta crystallins and gamma crytallins, and approximately 25% involve mutations in membrane transport genes, such as connexin proteins (Cx43, Cx46, and Cx50) [514].
In current study, we utilized next-generation sequencing of whole exome to investigate genetic defects in a Chinese pedigree with congenital cataract.

Methods

Subject recruitment and DNA sampling

A six-generation Chinese cataract family was examined at the General Hospital of Daqing Oil Field, Heilongjiang province, China. Pedigree medical history was taken directly by interviewing the family members. A total of 27 family members, including 14 affected (III12, IV11, IV28, IV30, IV39, IV72, IV73, V9, V11, V27, V28, VI3, VI9, and VI15) and 13 unaffected individuals (IV40, IV68, IV69, IV70, IV71, IV74, V10, V14, V19, V42, V57, V62, VI13) were recruited (Fig. 1). Ethical approval for current research was obtained from the ethics committee of General Hospital of Daqing Oil Field and the study was conducted according to the Declaration of Helsinki of the World Medical Association. All members recruited in this study underwent ophthalmologic examinations, including slit lamp ophthalmoscopy, biometry, visual acuity, and fundus examination. In addition, 100 unrelated healthy subjects without cataracts were also recruited from General Hospital of Daqing Oil Field.
DNA samples were extracted using the QIAamp DNA Blood Midi Kit (Qiagen, Hilden, Germany) from peripheral blood.

Exome sequencing

Ten patients (III12, IV11, IV28, IV30, IV73, V9, V27, VI3, VI9 and VI15) and one unaffected member of the family (IV40) were selected for exome sequencing. The whole exome-enriched library was built using NimbleGen SeqCap EZ Exome 64 Mb solution-based SeqCap EZ capture reagents, and solution hybridization exome capture was conducted in according with the manufacturer’s protocol. Exome sequencing was taken by using an Illumina HiSeq2000 sequencer.

Short-read alignment, variant calling and annotation

Low quality reads and PCR duplicates with >5 unknown bases were eliminated [15], for insertion/deletion (indel) and single nucleotide polymorphism (SNP), respectively. Aligning between read and the National Center for Biotechnology Information human reference genome (hg 19) were performed by sequencing reads were aligned to using Burrows-Wheeler Aligner (BWA) [15] and Short Oligonucleotide Analysis Package (SOAP3) tools [16]. Indels were validated according to the alignment result with the Genome Analysis Toolkit (GATK), and SNP calling was performed with Short Oligonucleotide Analysis Package (SOAPsnp). Variants were annotated using ANNOVAR tool.

Validation of mutation by Sanger sequencing

Sanger sequencing was used to validate the variants identified by exome sequencing. Specific primers were designed by Primer Premier 3.0 software for the target region. Genomic DNA from participants and 100 normal controls was analyzed.
Genomic DNA samples were amplified with the forward primer (5′- GCAGATCATCTTCGTCTCCA-3′) and the reverse primer(5′- GGCCACAGACAACATGAACA-3′). The following program was used: 95 °C for 3 min (1 cycle); 95 °C for 30 s, 60 °C for 30 s, 72 °C for 30 s (30 cycles); 72 °C for 10 min (1 cycle).

Bioinformatics analysis

The effects of wild-type amino acid sequences with the p. D47N mutant of Cx50 on the secondary structure were performed using Antheprot 2000 software (version 6.6.5, IBCP, Lypn, France). The solved structure of gap junction protein beta 2(Cx26) was taken as template (Protein Data Bank No.2ZW3). The model structure of homomeric wild-type and the mutant of GJA8 were modelled by Swiss-Model Server [17]. In addition, the possible functional effect of the amino acid change was predicted by PolyPhen-2 and SIFT.

Results

Clinical evaluations

Among 171 members in this six-generation Chinese family, affected individuals account for 23.39% (Fig. 1). All affect individuals in the pedigree had bilateral cataracts. Autosomal dominant inheritance mode of the congenital cataract was ascertained by the presence of affected individuals in each generation of the family, and male-to-male transmission. The proband’s son (VI 9) had been diagnosed with cataracts when he was 15 months old. Slit-lamp examination of his left eye showed perinuclear cataract.

Identification of Cx50 mutation

Whole exome sequencing was performed on genomic DNA from nine patients of congenital cataract family (III12, IV11, IV28, IV30, IV73, V9, V27, VI3, VI9 and VI15) and one unaffected individual (IV40) though next-generation sequencing technology. As demonstrated in Table 1, we obtained at least 64.06 million reads that mapped to targeted exome regions; more than 99.49% of the target region was covered. The mean depth of the target exome region was 180.98×, 191.56×, 191.23×, 155.43×, 184.67×, 197.75×, 203.48×, 160.48×, 167.92×, 155.12× and 187.92×, respectively. The raw Indel/SNP sequencing data are shown in Table 2. To help identify candidate mutations, untranslated regions, variants falling within intergenic, synonymous substitutions, intronic were excluded. Then the remaining variants were filtered out in at least four public genetic variant databases, including 1000 Genomes, dbSNP, HapMap and YH. Variants with an allele frequency > 0.5% were rejected. Variants shared by 10 patients and absent from 1 unaffected individual were analyzed.
Table 1
Coverage statistics with next-generation sequencing in ten patients with autosomal dominant congenital cataract and one unaffected member of family
Sample
III12
IV11
IV28
IV30
IV73
V9
V27
VI3
VI9
VI15
IV40
Total base mapped (G)
11.6
12.31
12.15
9.72
11.92
12.35
13.16
9.65
10.37
11.51
11.84
Region of target kit
64,558,893
64,326,610
64,326,610
64,326,610
64,558,893
64,558,893
64,558,893
64,326,610
64,326,610
64,326,610
64,326,610
Region of covered on target
64,226,731
64,090,887
64,126,819
64,109,790
64,332,815
64,368,416
64,322,956
64,060,274
64,112,774
64,117,790
64,141,226
Coverage of target region (%)
99.49
99.63
99.69
99.66
99.65
99.7
99.63
99.59
99.67
99.68
99.71
Effective bases on target (G)
11.68
12.32
12.3
10
11.92
12.77
13.14
10.32
10.8
9.98
12.09
Average sequencing depth on target region
180.98
191.56
191.23
155.43
184.67
197.75
203.48
160.48
167.92
155.12
187.92
Target coverage with at least 5× (%)
98.72
98.93
99.02
98.93
98.98
99.11
99.01
98.78
98.96
98.92
99.05
Target coverage with at least 10× (%)
98.07
98.32
98.42
98.19
98.37
98.54
98.47
98.09
98.32
98.24
98.45
Target coverage with at least 20× (%)
96.99
97.25
97.31
96.57
97.21
97.42
97.54
96.83
97.17
96.92
97.42
Flank region coverage with at least 5× (%)
22.26
18.67
18.83
18
18.1
17.42
17.67
17.1
16.92
17.07
16.61
Flank region coverage with at least 10× (%)
17.82
14.06
13.87
13.12
13.48
12.06
12.01
13.14
13.22
11.6
11.37
Flank region coverage with at least 20× (%)
15.16
11.79
11.58
10.7
11.18
9.94
9.88
10.88
11.02
9.34
9.34
Exome coverage with at least 5× (%)
98.1
98.3
98.4
98.3
98.4
98.6
98.4
98
98.3
98.3
98.4
Exome coverage with at least 5× (%)
97.2
97.4
97.6
97.4
97.6
97.8
97.6
97
97.4
97.3
97.5
Exome coverage with at least 5× (%)
95.9
96.2
96.4
95.9
96.4
96.6
96.5
95.6
96.1
95.9
96.3
Table 2
Variations identified by whole exome sequencing
Mutation type
III12
IV11
IV28
IV30
IV73
V9
V27
VI3
VI9
VI15
IV40
Indel analysis
 Total
15,930
15,690
15,489
13,623
15,448
15,678
18,613
14,028
14,873
14,520
15,657
 1000genome and dbsnp
6813
6707
6678
6153
6663
6561
8340
6123
6324
6375
6586
 1000genome specific
151
134
128
132
131
143
170
154
129
128
122
 dbSNP specific
4846
4570
4462
3853
4544
4448
5594
4036
4406
4324
4559
 dbSNP rate
73.19%
71.87%
71.92%
73.45%
72.55%
70.22%
74.86%
72.42%
72.14%
73.68%
71.18%
 Novel
4120
4279
4221
3485
4110
4526
4509
3715
4014
3693
4390
 Homozygous
4857
4935
4803
4405
4612
4448
3181
4304
4534
4601
4686
 Heterozygous
11,073
10,755
10,686
9218
10,836
11,230
15,432
9724
10,339
9919
10,971
 Frameshift
374
413
394
394
406
458
423
392
417
387
397
 Non-frameshift Insertion
158
180
189
153
181
208
195
173
189
164
169
 Non-frameshift Deletion
61
62
63
67
66
81
83
68
66
72
60
 Non-frameshift codon substitution plus Insertion
61
77
61
58
73
80
88
70
75
55
84
 Non-frameshift codon substitution plus Deletion
28
28
35
25
33
34
30
38
25
23
26
 Stopgain
4
14
10
4
9
5
7
9
9
10
12
 Stoploss
1
1
0
0
1
2
2
1
1
1
1
 Startloss
0
1
0
0
2
0
2
1
0
1
1
 Exonic
689
777
754
702
772
869
832
754
782
715
751
 Splicing
62
58
57
59
62
60
60
63
61
57
66
 NcRNA
238
229
240
235
233
249
259
239
223
222
248
 UTR5
178
194
188
180
186
198
216
174
172
174
203
 UTR3
1530
1510
1427
1276
1498
1471
1797
1372
1414
1382
1519
 Intronic
11,915
11,636
11,562
10,061
11,403
11,572
13,936
10,245
10,997
10,788
11,579
 Upstream
283
280
307
266
304
293
338
242
279
239
284
 Downstream
733
710
683
603
740
708
846
663
682
688
738
 Intergenic
302
296
271
241
250
258
329
276
263
255
269
SNP analysis
 Total
134,311
134,225
136,378
129,878
134,039
133,761
166,869
127,698
130,216
131,224
134,002
 1000genome and dbsnp
121,404
120,889
122,334
116,489
120,656
119,805
152,022
114,903
117,222
117,467
119,890
 1000genome specific
443
456
451
450
466
500
503
473
473
443
436
 dbSNP specific
4979
5030
5142
4963
5008
5188
5533
4875
5051
5034
5008
 dbSNP rate
94.10%
93.81%
93.47%
93.51%
93.75%
93.45%
94.42%
93.80%
93.90%
93.35%
93.21%
 Novel
7485
7850
8451
7976
7909
8268
8811
7447
7470
8280
8668
 Homozygous
51,982
53,569
52,947
51,462
51,793
50,013
32,944
48,638
50,529
51,424
51,815
 Heterozygous
82,329
80,656
83,431
78,416
82,246
83,748
133,925
79,060
79,687
79,800
82,187
 Synonymous
11,043
11,075
11,209
10,961
10,967
11,123
14,116
11,169
11,048
11,104
11,215
 Missense
10,750
10,857
10,991
10,820
10,768
11,029
13,713
10,878
10,892
10,768
10,992
 Stopgain
100
113
117
110
102
109
139
113
111
117
113
 Stoploss
30
33
31
30
28
35
34
33
31
35
27
 Startgain
506
509
496
468
524
491
639
466
487
495
503
 Startloss
30
29
26
27
30
30
36
24
29
30
32
 Exonic
21,979
22,126
22,390
21,970
21,916
22,346
28,067
22,241
22,131
22,075
22,402
 Splicing
159
162
166
149
150
156
191
168
157
157
158
 NcRNA
3252
3279
3410
3233
3381
3329
3809
3283
3281
3245
3284
 UTR5
1981
2028
2080
1993
2015
2096
2498
1908
1948
1968
2061
 UTR3
7707
7707
7821
7485
7825
7652
9778
7461
7527
7610
7820
 Intronic
89,844
89,674
91,108
86,065
89,445
88,742
111,479
83,963
86,127
87,172
89,093
 Upstream
2248
2299
2339
2195
2262
2344
2743
2040
2170
2152
2237
 Downstream
4596
4483
4540
4325
4523
4471
5408
4202
4364
4429
4516
 Intergenic
2545
2467
2524
2463
2522
2625
2896
2432
2511
2416
2431
 SIFT
1859
1905
1934
1819
1833
1939
2556
1918
1866
1892
1904
After filtering and samples comparison, one heterozygous change was confirmed in all affected individuals in congenital cataract family, G > A, at position 139 (c.139 G > A) in exon 2 of GJA8 (Cx50). This change led to the substitution of aspartic acid by asparagine at position 47 (p. D47N). This mutation was further confirmed by Sanger sequencing (Fig. 2). The D47N substitution co-segregated with all 14 affected individuals, while it was not found in the unaffected family members or in the 100 healthy controls.

Bioinformatics analysis

The potential structure and function impact of the D47N mutation was predicted to affect protein function with a score of 0.00, and could probably be damaging with a score of 1.0 by SIFT and PolyPhen-2, respectively. As shown in Fig. 3, the secondary structure of mutant Cx50 protein was different with wild type. The results stated clearly that the wild-type sheet in COOH- terminal portion is likely missing in the D47N mutant. Took the structure of Cx-26 as template, the model structure of the mutant Cx50 have distinct changes (Fig. 4). There are additional helix (red arrow) and shortened sheet (green arrow) in the D47N mutant.

Discussion

In the current study, we confirmed a missense mutation c. 139 G > A in Cx50 (GJA8) in a six-generation Chinese pedigree with congenital cataract. This mutation resulted in an asparagine substitution for aspartic at amino acid residue 47 (D47N).
Cataracts are defined as opacification of the normally transparent crystalline lens, and are the leading cause of vision loss in the world. Congenital cataract is a type of cataract that emerges at birth or during early childhood [5, 18]. The abnormality of lens can interfere with normal development of eyes [5, 19]. Congenital cataracts can be inherited or familial, either as an isolated lens phenotype or as part of a genetic/metabolic disorder, commonly with full penetrance and autosomal dominant transmission [19]. Genetic factors play an important role in congenital cataract [20]. Gene mutations that affecting the lens development during embryonic period are considered to be the main cause [18]. Up to now, more than 39 genes and loci have been confirmed to be involved in the formation of isolate cataract [21, 22], including crystallins, such as α-, β-, γ-crystallins (e.g., CRYAA, CRYBB1, CRYBB2, CRYGD), membrane transport and channel proteins, such as α-connexins (GJA3, GJA8).
Intercellular gap junction channels provide pathways for metabolic and electrical coupling between cells in different tissues, and they are permeable to ions and small solutes, such as ions (K+, Ca2+), nutrients and small metabolites [23]. Gap junction channels consist of connexin protein subunits. Connexin proteins also known as gap junction proteins have four transmembrane domins with two extracellular loops (E1 and E2) and three intracellular regions (the NH2-terminus, a cytoplasmic loop and the COOH-terminus) [24]. Three isoforms of the connexin gene family- Cx43 (GJA1), Cx46 (GJA3) and Cx50 (GJA8) are abundantly expressed in the vertebrate lens.
Cx50 is an important protein and play an important role during lens growth, maturation of lens fiber cells, and lens transparency [25]. Cx50 comprises two exons with exon-2 coding for the entire 433 amino acid residues of gap junction protein α8 (GJA8). Up to date, at least 32 mutations in Cx50 have been identified to contribute to cataract. Of the 32 coding mutations, 29 result in missense substitutions that are involved in autosomal dominant cataract, and two are frameshift mutation associated with autosomal recessive cataract [6]. The majority of missense substitution are situated in the N-terminal half of the protein, which also contains the conserved connexin domain (amino acids 3–109) [6]. Three types of mutation: D47N, D47H and D47Y indicate that the amino acid at position 47 in GJA8 is a mutational hot spot [2628]. Functional findings showed that D47N mutant expressed in Xenopus oocyte pairs could not form functional gap junction channels. Moreover, co-expression of Cx50D47N with wild-type Cx50 did not inhibit the activity of wild-type Cx50 [29]. The similar behavior was also observed in the mouse Cx50D47A, a mutation underlying the cataracts in the No2 mouse [30]. D47N and D47A mutants were loss-of-function mutants. Cellular level studies showed that the mutation of Cx50 prevented its localization to the plasma membrane. And this may lead to a capacity deficiency of Connexin 50, triggering a complex sequence of events, such as disruption of transmembrane ion gradients, loss of membrane potential, decreased cell growth and subsequent decreased metabolic activity [25, 31]. Cx50 is critical for ball-and-socket structures, actin distribution and fiber cell morphology. Cx50 gap junctional communication through ball-and-socket is important for lens development, especially during rapid, early fiber cell growth [32].
Some limitations of this study should be addressed. First, we did not collect all of pedigree samples, especially the affected individuals in the congenital cataract family. Secondly, we did not perform more experiments, such as cell function experiment of D47N mutant and animal model experiments. Both of these limit our knowledge of more information of the D47N mutant. Nonetheless, advantages in our study should also be acknowledged. Exome sequencing and next-generation sequencing provide a rational approach to screen all candidate genes for inherited cataract or other inherited disease. In addition, exome sequencing and next-generation sequencing are suitable for molecular diagnosis of hereditary diseases. Our finding supports the enormous potential of exome sequencing in molecular diagnosis of single gene disease.

Conclusions

In conclusion, the present research confirmed a recurrent mutation, c.139 G > A (p.D47N) in Cx50 in a six-generation Chinese family with autosomal dominant congenital cataract. This result provided further evidence for Cx50 in association with congenital cataract, and the amino acid at position 47 is a mutational hot-spot. The function of D47N mutation needs to be further certificated in animal mode. In addition, exome sequencing and next-generation sequencing are suitable for molecular diagnosis of hereditary diseases.

Acknowledgments

We thank all participants including healthy control peoples, patients and their families in this study. We also thank all the people who helped us to complete the research successfully.
Informed written consent was obtained from all participants of the family. If the participants are children (under 16 years of age), the informed consent was signed by their parents.

Funding

This work was supported by a grant from Daqing Oil Field Innovation Fund (No.2015018).

Availability of data and materials

The datasets in the current study are available from the corresponding author on reasonable request.

Authors’ contributions

CS, HM and XC conceived and designed the experiments; CS, JW, XW, and FW performed the experiments; CS, JW, XG, YC, YL, and LZ analyzed the data; HM contributed reagents/materials/analysis tools; CS wrote the paper; All authors have read and approved the final manuscript.

Competing interests

The authors announce that they have no affiliations with or involvement in any organization or entity with any financial interest, or non-financial interest in the materials or subject matter discussed in this paper.
This research was approved by the ethics committee of General Hospital of Daqing Oil Field and was conducted according to the Declaration of Helsinki of the World Medical Association. Informed written consent was obtained from the participants or their legal guardians (if the participant was underage).

Publisher’s Note

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Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://​creativecommons.​org/​licenses/​by/​4.​0/​), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://​creativecommons.​org/​publicdomain/​zero/​1.​0/​) applies to the data made available in this article, unless otherwise stated.
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Metadaten
Titel
Next-generation sequencing for D47N mutation in Cx50 analysis associated with autosomal dominant congenital cataract in a six-generation Chinese family
verfasst von
Chao Shen
Jingbing Wang
Xiaotang Wu
Fuchao Wang
Yang Liu
Xiaoying Guo
Lina Zhang
Yanfei Cao
Xiuhua Cao
Hongxing Ma
Publikationsdatum
01.12.2017
Verlag
BioMed Central
Erschienen in
BMC Ophthalmology / Ausgabe 1/2017
Elektronische ISSN: 1471-2415
DOI
https://doi.org/10.1186/s12886-017-0476-5

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