Abstract
Glycosylphosphatidylinositol (GPI)-anchored proteins are located at the cell surface by a covalent attachment between protein and GPI embedded in the plasma membrane. This attachment is catalyzed by GPI transamidase comprising five subunits (PIGK, PIGS, PIGT, PIGU, and GPAA1) in the endoplasmic reticulum. Loss of either subunit of GPI transamidase eliminates cell surface localization of GPI-anchored proteins. In humans, pathogenic variants in either subunit of GPI transamidase cause neurodevelopmental disorders. However, how the loss of GPI-anchored proteins triggers neurodevelopmental defects remains largely unclear. Here, we identified a novel homozygous variant of PIGK, NM_005482:c.481A > G,p. (Met161Val), in a Japanese female patient with neurodevelopmental delay, hypotonia, cerebellar atrophy, febrile seizures, hearing loss, growth impairment, dysmorphic facial features, and brachydactyly. The missense variant was found heterozygous in her father, but not in her mother. Zygosity analysis revealed that the homozygous PIGK variant in the patient was caused by paternal isodisomy. Rescue experiments using PIGK-deficient CHO cells revealed that the p.Met161Val variant of PIGK reduced GPI transamidase activity. Rescue experiments using pigk mutant zebrafish confirmed that the p.Met161Val variant compromised PIGK function in tactile-evoked motor response. We also demonstrated that axonal localization of voltage-gated sodium channels and concomitant generation of action potentials were impaired in pigk-deficient neurons in zebrafish, suggesting a link between GPI-anchored proteins and neuronal defects. Taken together, the missense p.Met161Val variant of PIGK is a novel pathogenic variant that causes the neurodevelopmental disorder.
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References
Kinoshita T, Fujita M, Maeda Y. Biosynthesis, remodelling and functions of mammalian GPI-anchored proteins: recent progress. J Biochem. 2008;144:287–94.
Benghezal M, Benachour A, Rusconi S, Aebi M, Conzelmann A. Yeast Gpi8p is essential for GPI anchor attachment onto proteins. EMBO J. 1996;15:6575–83.
Yu J, Nagarajan S, Knez JJ, Udenfriend S, Chen R, Medof ME. The affected gene underlying the class K glycosylphosphatidylinositol (GPI) surface protein defect codes for the GPI transamidase. Proc Natl Acad Sci USA. 1997;94:12580–5.
Chen X, Yin W, Chen S, Zhang W, Li H, Kuang H, et al. Loss of PIGK function causes severe infantile encephalopathy and extensive neuronal apoptosis. Hum Genet. 2021;140:791–803.
Nguyen TTM, Murakami Y, Mobilio S, Niceta M, Zampino G, Philippe C, et al. Bi-allelic variants in the GPI transamidase subunit PIGK cause a neurodevelopmental syndrome with hypotonia, cerebellar atrophy, and epilepsy. Am J Hum Genet. 2020;106:484–95.
Efthymiou S, Dutra-Clarke M, Maroofian R, Kaiyrzhanov R, Scala M, Reza Alvi J, et al. Expanding the phenotype of PIGS-associated early onset epileptic developmental encephalopathy. Epilepsia. 2021;62:e35–41.
Nguyen TTM, Murakami Y, Wigby KM, Baratang NV, Rousseau J, St-Denis A, et al. Mutations in PIGS, encoding a GPI transamidase, cause a neurological syndrome ranging from fetal akinesia to epileptic encephalopathy. Am J Hum Genet. 2018;103:602–11.
Zhang L, Mao X, Long H, Xiao B, Luo Z, Xiao W, et al. Compound heterozygous PIGS variants associated with infantile spasm, global developmental delay, hearing loss, visual impairment, and hypotonia. Front Genet. 2020;11:564.
Kohashi K, Ishiyama A, Yuasa S, Tanaka T, Miya K, Adachi Y, et al. Epileptic apnea in a patient with inherited glycosylphosphatidylinositol anchor deficiency and PIGT mutations. Brain Dev. 2018;40:53–7.
Kvarnung M, Nilsson D, Lindstrand A, Korenke GC, Chiang SC, Blennow E, et al. A novel intellectual disability syndrome caused by GPI anchor deficiency due to homozygous mutations in PIGT. J Med Genet. 2013;50:521–8.
Lam C, Golas GA, Davids M, Huizing M, Kane MS, Krasnewich DM, et al. Expanding the clinical and molecular characteristics of PIGT-CDG, a disorder of glycosylphosphatidylinositol anchors. Mol Genet Metab. 2015;115:128–40.
Nakashima M, Kashii H, Murakami Y, Kato M, Tsurusaki Y, Miyake N, et al. Novel compound heterozygous PIGT mutations caused multiple congenital anomalies-hypotonia-seizures syndrome 3. Neurogenetics. 2014;15:193–200.
Nobrega PR, Castro MAA, de Paiva ARB, Kok F. Mystery solved after 23 years: M syndrome is PIGT-associated multiple congenital anomalies-hypotonia-seizures syndrome 3. Am J Med Genet A. 2022;188:3567–8.
Skauli N, Wallace S, Chiang SC, Baroy T, Holmgren A, Stray-Pedersen A, et al. Novel PIGT variant in two brothers: expansion of the multiple congenital anomalies-hypotonia seizures syndrome 3 phenotype. Genes. 2016;7:108.
Knaus A, Kortum F, Kleefstra T, Stray-Pedersen A, Dukic D, Murakami Y, et al. Mutations in PIGU impair the function of the GPI transamidase complex, causing severe intellectual disability, epilepsy, and brain anomalies. Am J Hum Genet. 2019;105:395–402.
Nguyen TTM, Murakami Y, Sheridan E, Ehresmann S, Rousseau J, St-Denis A, et al. Mutations in GPAA1, encoding a GPI transamidase complex protein, cause developmental delay, epilepsy, cerebellar atrophy, and osteopenia. Am J Hum Genet. 2017;101:856–65.
Bellai-Dussault K, Nguyen TTM, Baratang NV, Jimenez-Cruz DA, Campeau PM. Clinical variability in inherited glycosylphosphatidylinositol deficiency disorders. Clin Genet. 2019;95:112–21.
Iida T, Igarashi A, Fukunaga K, Aoki T, Hidai T, Yanagi K, et al. Functional analysis of RRAS2 pathogenic variants with a Noonan-like phenotype. Front Genet. 2024;15:1383176.
Ueda K, Ogawa S, Matsuda K, Hasegawa Y, Nishi E, Yanagi K, et al. Blended phenotype of combination of HERC2 and AP3B2 deficiency and Angelman syndrome caused by paternal isodisomy of chromosome 15. Am J Med Genet A. 2021;185:3092–8.
Xu Y, Jia G, Li T, Zhou Z, Luo Y, Chao Y, et al. Molecular insights into biogenesis of glycosylphosphatidylinositol anchor proteins. Nat Commun. 2022;13:2617.
Xu Y, Li T, Zhou Z, Hong J, Chao Y, Zhu Z, et al. Structures of liganded glycosylphosphatidylinositol transamidase illuminate GPI-AP biogenesis. Nat Commun. 2023;14:5520.
Ashida H, Hong Y, Murakami Y, Shishioh N, Sugimoto N, Kim YU, et al. Mammalian PIG-X and yeast Pbn1p are the essential components of glycosylphosphatidylinositol-mannosyltransferase I. Mol Biol Cell. 2005;16:1439–48.
Carmean V, Yonkers MA, Tellez MB, Willer JR, Willer GB, Gregg RG, et al. pigk Mutation underlies macho behavior and affects Rohon-Beard cell excitability. J Neurophysiol. 2015;114:1146–57.
Uemura O, Okada Y, Ando H, Guedj M, Higashijima S, Shimazaki T, et al. Comparative functional genomics revealed conservation and diversification of three enhancers of the isl1 gene for motor and sensory neuron-specific expression. Dev Biol. 2005;278:587–606.
Ogino K, Low SE, Yamada K, Saint-Amant L, Zhou W, Muto A, et al. RING finger protein 121 facilitates the degradation and membrane localization of voltage-gated sodium channels. Proc Natl Acad Sci USA. 2015;112:2859–64.
Hirata H, Ogino K, Yamada K, Leacock S, Harvey RJ. Defective escape behavior in DEAH-box RNA helicase mutants improved by restoring glycine receptor expression. J Neurosci. 2013;33:14638–44.
Nakano Y, Fujita M, Ogino K, Saint-Amant L, Kinoshita T, Oda Y, et al. Biogenesis of GPI-anchored proteins is essential for surface expression of sodium channels in zebrafish Rohon-Beard neurons to respond to mechanosensory stimulation. Development. 2010;137:1689–98.
Hirata H, Watanabe T, Hatakeyama J, Sprague SM, Saint-Amant L, Nagashima A, et al. Zebrafish relatively relaxed mutants have a ryanodine receptor defect, show slow swimming and provide a model of multi-minicore disease. Development. 2007;134:2771–81.
Low SE, Zhou W, Choong I, Saint-Amant L, Sprague SM, Hirata H, et al. Na(v)1.6a is required for normal activation of motor circuits normally excited by tactile stimulation. Dev Neurobiol. 2010;70:508–22.
Escayg A, MacDonald BT, Meisler MH, Baulac S, Huberfeld G, An-Gourfinkel I, et al. Mutations of SCN1A, encoding a neuronal sodium channel, in two families with GEFS+2. Nat Genet. 2000;24:343–5.
Wallace RH, Wang DW, Singh R, Scheffer IE, George AL Jr., Phillips HA, et al. Febrile seizures and generalized epilepsy associated with a mutation in the Na+-channel beta1 subunit gene SCN1B. Nat Genet. 1998;19:366–70.
Acknowledgements
We thank Ms. Tomomi Hidai for sample preparation for genetic analysis and Dr. Kazuhito Satou for data analysis of WES. We also thank the Hirata laboratory members for fish care. This work was supported by the grants from the Japan Agency for Medical Research and Development (AMED) (18ek0109301 and 19ek0109288s0103), KAKENHI (Grant-in-Aid for Scientific Research B from MEXT, Japan: 19H03329), the Takeda Science Foundation, the Naito Foundation and the Long-Range Research Initiatives of the Japan Chemical Industry Association to HH, and grants from the Ministry of Health, Labour and Welfare, and Practical Research Project for Rare/Intractable Diseases (20FC1025 and 21ek0109418h0003) and the Initiative on Rare and Undiagnosed Disease (IROD: https://www.amed.go.jp/en/index.html) (23ek0109549s0203 and 22ek0109549s0202) from the AMED to YM.
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KY, YH, Y Murakami, SEL, Y Matsubara, NO, TK and HH designed research. YH and NO performed clinical studies. KY, Y Matsubara and TK performed genetic experiments and analyzed data with structural modeling. Y Murakami performed CHO cell experiments and analyzed data. KS, SEL, DO and HH performed zebrafish experiments and analyzed data. KS, KY, YH, Y Murakami, TK and HH wrote manuscript. All authors reviewed and approved the manuscript.
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The study including comprehensive genome analysis was approved by the ethical committee of the National Research Institute for Child Health and Development. Experimental procedures were also approved by the institutional review boards for ethics of the Research Institute for Microbial Diseases, Osaka University. Zebrafish experiments have been approved by the Animal Care and Ethics Committee of Aoyama Gakuin University (A9/2020) and carried out in accordance with the Aoyama Gakuin University Animal Care and Use Guidelines, the Animal Research Reporting of In Vivo Experiments (ARRIVE) guidelines and relevant regulations.
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Sadamitsu, K., Yanagi, K., Hasegawa, Y. et al. A novel homozygous variant of the PIGK gene caused by paternal disomy in a patient with neurodevelopmental disorder, cerebellar atrophy, and seizures. J Hum Genet (2024). https://doi.org/10.1038/s10038-024-01264-3
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DOI: https://doi.org/10.1038/s10038-024-01264-3
