1
|
Zhang C, Yan Y, Zhou B, Wang Y, Tian X, Hao S, Ma P, Zheng L, Zhang Q, Hui L, Wang Y, Cao Z, Ma X. Identification of deep intronic variants of PAH in phenylketonuria using full-length gene sequencing. Orphanet J Rare Dis 2023; 18:128. [PMID: 37237386 PMCID: PMC10214626 DOI: 10.1186/s13023-023-02742-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Phenylketonuria (PKU) is an autosomal recessive congenital metabolic disorder caused by PAH variants. Previously, approximately 5% of PKU patients remained undiagnosed after Sanger sequencing and multiplex ligation-dependent probe amplification. To date, increasing numbers of pathogenic deep intronic variants have been reported in more than 100 disease-associated genes. METHODS In this study, we performed full-length sequencing of PAH to investigate the deep intronic variants in PAH of PKU patients without definite genetic diagnosis. RESULTS We identified five deep intronic variants (c.1199+502A>T, c.1065+241C>A, c.706+368T>C, c.706+531>C, and c.706+608A>C). Of these, the c.1199+502A>T variant was found at high frequency and may be a hotspot PAH variant in Chinese PKU. c.706+531T>C and c.706+608A>C are two novel variants that extend the deep intronic variant spectrum of PAH. CONCLUSION Deep intronic variant pathogenicity analysis can further improve the genetic diagnosis of PKU patients. In silico prediction and minigene analysis are powerful approaches for studying the functions and effects of deep intronic variants. Targeted sequencing after full-length gene amplification is an economical and effective tool for the detection of deep intron variation in genes with small fragments.
Collapse
Affiliation(s)
- Chuan Zhang
- Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
- National Research Institute for Health and Family Planning, National Human Genetic Resources Center, Beijing, China
- Graduate School of Peking, Union Medical College, Beijing, China
| | - Yousheng Yan
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University; Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Bingbo Zhou
- Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Yupei Wang
- Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Xinyuan Tian
- Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Shengju Hao
- Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Panpan Ma
- Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Lei Zheng
- Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Qinghua Zhang
- Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Ling Hui
- Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Yan Wang
- Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Zongfu Cao
- National Research Institute for Health and Family Planning, National Human Genetic Resources Center, Beijing, China.
| | - Xu Ma
- National Research Institute for Health and Family Planning, National Human Genetic Resources Center, Beijing, China.
- Graduate School of Peking, Union Medical College, Beijing, China.
| |
Collapse
|
2
|
Zhang C, Zhang P, Yan Y, Zhou B, Wang Y, Tian X, Hao S, Ma P, Zheng L, Zhang Q, Hui L, Wang Y, Cao Z, Ma X. The spectrum of phenylalanine hydroxylase variants and genotype-phenotype correlation in phenylketonuria patients in Gansu, China. Hum Genomics 2023; 17:36. [PMID: 37098607 PMCID: PMC10127316 DOI: 10.1186/s40246-023-00475-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/15/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND Phenylketonuria (PKU) is a common, congenital, autosomal recessive, metabolic disorder caused by Phenylalanine hydroxylase (PAH) variants. METHODS 967 PKU patients from Gansu, China were genotyped by Sanger sequencing, multiplex ligation-dependent probe amplification, and whole exome sequencing. We analyzed the variants of PAH exons, their flanking sequences, and introns. RESULTS The detection of deep intronic variants in PAH gene can significantly improve the genetic diagnostic rate of PKU. The distribution of PAH variants among PKU subtypes may be related to the unique genetic background in Gansu, China. CONCLUSION The identification of PAH hotspot variants will aid the development of large-scale neonatal genetic screening for PKU. The five new PAH variants found in this study further expand the spectrum of PAH variants. Genotype-phenotype correlation analysis may help predict the prognosis of PKU patients and enable precise treatment regimens to be developed.
Collapse
Affiliation(s)
- Chuan Zhang
- Gansu Province Medical Genetics Center,Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
- National Research Institute for Family Planning , National Human Genetic Resources Center, Beijing, China
| | - Pei Zhang
- Department of Nosocomial Infection Management, Lanzhou University Second Hospital, Lanzhou, China
| | - Yousheng Yan
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Bingbo Zhou
- Gansu Province Medical Genetics Center,Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Yupei Wang
- Gansu Province Medical Genetics Center,Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Xinyuan Tian
- Gansu Province Medical Genetics Center,Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Shengju Hao
- Gansu Province Medical Genetics Center,Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Panpan Ma
- Gansu Province Medical Genetics Center,Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Lei Zheng
- Gansu Province Medical Genetics Center,Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Qinghua Zhang
- Gansu Province Medical Genetics Center,Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Ling Hui
- Gansu Province Medical Genetics Center,Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Yan Wang
- Gansu Province Medical Genetics Center,Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Zongfu Cao
- National Research Institute for Family Planning , National Human Genetic Resources Center, Beijing, China.
| | - Xu Ma
- National Research Institute for Family Planning , National Human Genetic Resources Center, Beijing, China.
| |
Collapse
|
3
|
Chaudhary AK, Gholse A, Nagarajaram HA, Dalal AB, Gupta N, Dutta AK, Danda S, Gupta R, Sankar HV, Bhavani GS, Girisha KM, Phadke SR, Ranganath P, Bashyam MD. Ectodysplasin pathogenic variants affecting the furin-cleavage site and unusual clinical features define X-linked hypohidrotic ectodermal dysplasia in India. Am J Med Genet A 2021; 188:788-805. [PMID: 34863015 DOI: 10.1002/ajmg.a.62579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/20/2021] [Accepted: 11/02/2021] [Indexed: 11/09/2022]
Abstract
Hypohidrotic ectodermal dysplasia (HED) is a rare genetic disorder caused by mutational inactivation of a developmental pathway responsible for generation of tissues of ectodermal origin. The X-linked form accounts for the majority of HED cases and is caused by Ectodysplasin (EDA) pathogenic variants. We performed a combined analysis of 29 X-linked hypohidrotic ectodermal dysplasia (XLHED) families (including 12 from our previous studies). In addition to the classical triad of symptoms including loss (or reduction) of ectodermal structures, such as hair, teeth, and sweat glands, we detected additional HED-related clinical features including facial dysmorphism and hyperpigmentation in several patients. Interestingly, global developmental delay was identified as an unusual clinical symptom in many patients. More importantly, we identified 22 causal pathogenic variants that included 15 missense, four small in-dels, and one nonsense, splice site, and large deletion each. Interestingly, we detected 12 unique (India-specific) pathogenic variants. Of the 29 XLHED families analyzed, 11 (38%) harbored pathogenic variant localized to the furin cleavage site. A comparison with HGMD revealed significant differences in the frequency of missense pathogenic variants; involvement of specific exons and/or protein domains and transition/transversion ratios. A significantly higher proportion of missense pathogenic variants (33%) localized to the EDA furin cleavage when compared to HGMD (7%), of which p.R155C, p.R156C, and p.R156H were detected in three families each. Therefore, the first comprehensive analysis of XLHED from India has revealed several unique features including unusual clinical symptoms and high frequency of furin cleavage site pathogenic variants.
Collapse
Affiliation(s)
- Ajay Kumar Chaudhary
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Aishwarya Gholse
- Laboratory of Computational Biology, Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Hampapathalu Adimurthy Nagarajaram
- Laboratory of Computational Biology, Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Ashwin Bhikaji Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Atanu Kumar Dutta
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, India
| | - Sumita Danda
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, India
| | - Rekha Gupta
- Department of Medical Genetics, Mahatma Gandhi Medical College and Hospital, Jaipur, India
| | - Hariharan V Sankar
- Department of Pediatrics, SAT Hospital, Medical College, Trivandrum, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Shubha Rao Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Prajnya Ranganath
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Murali Dharan Bashyam
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| |
Collapse
|
4
|
Vieira Neto E, Laranjeira F, Quelhas D, Ribeiro I, Seabra A, Mineiro N, d. M. Carvalho L, Lacerda L, G. Ribeiro M. Mutation analysis of the PAH gene in phenylketonuria patients from Rio de Janeiro, Southeast Brazil. Mol Genet Genomic Med 2018; 6:575-591. [PMID: 29749107 PMCID: PMC6081236 DOI: 10.1002/mgg3.408] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/29/2018] [Accepted: 04/06/2018] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Phenylketonuria (PKU) is an autosomal recessive disease resulting from mutations in the PAH gene. Most of the patients are compound heterozygotes, and genotype is a major factor in determining the phenotypic variability of PKU. More than 1,000 variants have been described in the PAH gene. Rio de Janeiro's population has a predominance of Iberian, followed by African and Amerindian ancestries. It is expected that most PKU variants in this Brazilian state have originated in the Iberian Peninsula. However, rare European, African or pathogenic variants that are characteristic of the admixed population of the state might also be found. METHODS A total of 102 patients were included in this study. Genomic DNA was isolated from dried blood spots. Sanger sequencing was used for PAH gene variant identification. Deletions and duplications were also screened using MLPA analysis. Haplotypes were also determined. RESULTS Nine (8.8%) homozygous and 93 (91.2%) compound heterozygous patients were found. The spectrum included 37 causative mutations. Missense, nonsense, and splicing pathogenic variants corresponded to 63.7%, 2.9%, and 22.6% of the mutant alleles, respectively. Large (1.5%), and small deletions, inframe (5.4%) and with frameshift (3.9%), comprised the remainder. The most frequent pathogenic variants were: p.V388M (12.7%), p.R261Q (11.8%), IVS10-11G>A (10.3%), IVS2+5G>C (6.4%), p.S349P (6.4%), p.R252W (5.4%), p.I65T (4.4%), p.T323del (4.4%), and p.P281L (3.4%). One novel variant was detected: c.934G>T (p.G312C) [rs763115697]. CONCLUSION The three most frequent pathogenic variants in our study (34.8% of the alleles) were also the most common in other Brazilian states, Portugal, and Spain (p.V388M, p.R261Q, IVS10-11G>A), corroborating that the Iberian Peninsula is the major source of PAH mutations in Rio de Janeiro. Pathogenic variants that have other geographical origins, such IVS2+5G>C, p.G352Vfs*48, and IVS12+1G>A were also detected. Genetic drift and founder effect may have also played a role in the mutation spectrum we observed.
Collapse
Affiliation(s)
- Eduardo Vieira Neto
- Gerência de Monitoramento AssistencialAgência Nacional de Saúde SuplementarRio de JaneiroBrazil
- Serviço de Genética MédicaInstituto de Puericultura e Pediatria Martagão GesteiraUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Francisco Laranjeira
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
| | - Dulce Quelhas
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
| | - Isaura Ribeiro
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
| | - Alexandre Seabra
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
| | - Nicole Mineiro
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
| | - Lilian d. M. Carvalho
- Serviço de MetabologiaInstituto de Diabetes e Endocrinologia Luiz CapriglioneRio de JaneiroBrazil
| | - Lúcia Lacerda
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
| | - Márcia G. Ribeiro
- Serviço de Genética MédicaInstituto de Puericultura e Pediatria Martagão GesteiraUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| |
Collapse
|
5
|
Sanayama Y, Matsumoto A, Shimojo N, Kohno Y, Nakaya H. Phenylalanine sensitive K562-D cells for the analysis of the biochemical impact of excess amino acid. Sci Rep 2014; 4:6941. [PMID: 25373594 PMCID: PMC4221789 DOI: 10.1038/srep06941] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/20/2014] [Indexed: 12/31/2022] Open
Abstract
Although it is recognized that the abnormal accumulation of amino acid is a cause of the symptoms in metabolic disease such as phenylketonuria (PKU), the relationship between disease severity and serum amino acid levels is not well understood due to the lack of experimental model. Here, we present a novel in vitro cellular model using K562-D cells that proliferate slowly in the presence of excessive amount of phenylalanine within the clinically observed range, but not phenylpyruvate. The increased expression of the L-type amino acid transporter (LAT2) and its adapter protein 4F2 heavy chain appeared to be responsible for the higher sensitivity to phenylalanine in K562-D cells. Supplementation with valine over phenylalanine effectively restored cell proliferation, although other amino acids did not improve K562-D cell proliferation over phenylalanine. Biochemical analysis revealed mammalian target of rapamycin complex (mTORC) as a terminal target of phenylalanine in K562-D cell proliferation, and supplementation of valine restored mTORC1 activity. Our results show that K562-D cell can be a potent tool for the investigation of PKU at the molecular level and to explore new therapeutic approaches to the disease.
Collapse
Affiliation(s)
- Yoshitami Sanayama
- 1] Department of Pharmacology, Graduate School of Medicine, Chiba University, Chiba [2] Department of Pediatrics, National Hospital Organization, Shimoshizu Hospital, Chiba
| | - Akio Matsumoto
- Department of Pharmacology, Graduate School of Medicine, Chiba University, Chiba
| | - Naoki Shimojo
- Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yoichi Kohno
- Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Haruaki Nakaya
- Department of Pharmacology, Graduate School of Medicine, Chiba University, Chiba
| |
Collapse
|