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Fujihira H, Sato K, Nishiuchi Y, Murase T, Matsuda Y, Yoshida Y, Kamei T, Suzuki T. ELISA-based highly sensitive assay system for the detection of endogenous NGLY1 activity. Biochem Biophys Res Commun 2024; 710:149826. [PMID: 38581946 DOI: 10.1016/j.bbrc.2024.149826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/21/2024] [Accepted: 03/24/2024] [Indexed: 04/08/2024]
Abstract
Cytosolic peptide:N-glycanase (NGLY1, PNGase) is an enzyme that cleaves N-glycans from misfolded glycoproteins. In 2012, a human genetic disorder, NGLY1 deficiency, was first reported to be caused by mutations of the NGLY1 gene. Since then, there has been rapid progresses on NGLY1 biology, and gene therapy has been proposed as a promising therapeutic option for NGLY1 deficiency. While a plasma/urine biomarker has also been developed for this disease, detection of NGLY1 activity could be another viable option for early diagnosis of NGLY1 deficiency. Thus far, several in vitro and in cellulo NGLY1 assays have been reported, but those assay systems have several issues that must be addressed in order to develop an assay system compatible for routine clinical examination. Here, we show a facile, highly sensitive in vitro assay system that could be used to detect NGLY1 activity by utilizing its sequence editing function, i.e. conversion of glycosylated Asn into Asp, followed by a detection of newly generated epitope (HA)-tag by anti-HA antibody. Using this ELISA-based assay, we detected endogenous NGLY1 activity in as little as 2 μg of crude extract, which is the equivalent of 5 × 103 cells. Our system also detects NGLY1 activity from cells with compromised NGLY1 activity, such as iPS cells from patient samples. This assay system could be applied in future clinical examinations to achieve an early diagnosis of NGLY1 deficiency.
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Affiliation(s)
- Haruhiko Fujihira
- Glycometabolic Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, 351-0198, Japan; Division of Glycobiologics, Juntendo University Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Keiko Sato
- Glycometabolic Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, 351-0198, Japan
| | | | | | | | - Yukiko Yoshida
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Takayuki Kamei
- Global Advanced Platform, Takeda Pharmaceutical Co. Ltd., Kanagawa, 251-8555, Japan; NGLY1 Deficiency Project, T-CiRA Joint Program, Kanagawa, 251-8555, Japan
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, 351-0198, Japan; NGLY1 Deficiency Project, T-CiRA Joint Program, Kanagawa, 251-8555, Japan.
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2
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Yuan S, Chen Y, Zou L, Lu X, Liu R, Zhang S, Zhang Y, Chen C, Cheng D, Chen L, Sun G. Functional prediction of the potential NGLY1 mutations associated with rare disease CDG. Heliyon 2024; 10:e28787. [PMID: 38628705 PMCID: PMC11016977 DOI: 10.1016/j.heliyon.2024.e28787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
Genetic diseases are currently diagnosed by functional mutations. However, only some mutations are associated with disease. It is necessary to establish a quick prediction model for clinical screening. Pathogenic mutations in NGLY1 cause a rare autosomal recessive disease known as congenital disorder of deglycosylation (NGLY1-CDDG). Although NGLY1-CDDG can be diagnosed through gene sequencing, clinical relevance of a detected mutation in NGLY1 needs to be further confirmed. In this study, taken NGLY1-CDDG as an example, a comprehensive and practical predictive model for pathogenic mutations on NGLY1 through an NGLY1/Glycopeptide complex model was constructed, the binding sites of NGLY1 and glycopeptides were simulated, and an in vitro enzymatic assay system was established to facilitate quick clinical decisions for NGLY1-CDDG patients. The docking model covers 42 % of reported NGLY1-CDDG missense mutations (5/12). All reported mutations were subjected to in vitro enzymatic assay in which 18 mutations were dysfunctional (18/30). In addition, a full spectrum of functional R328 mutations was assayed and 11 mutations were dysfunctional (11/19). In this study, a model of NGLY1 and glycopeptides was built for potential functional mutations in NGLY1. In addition, the effect of potential regulatory compounds, including N-acetyl-l-cysteine and dithiothreitol, on NGLY1 was examined. The established in vitro assay may serve as a standard protocol to facilitate rapid diagnosis of all mutations in NGLY1-CDDG. This method could also be applied as a comprehensive and practical predictive model for the other rare genetic diseases.
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Affiliation(s)
- Shuying Yuan
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Yanwen Chen
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Lin Zou
- Department of Medical Microbiology and Parasitology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xinrong Lu
- Department of Medical Microbiology and Parasitology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Ruijie Liu
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Shaoxing Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Yuxin Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Cuiying Chen
- Department of Research and Development, SysDiagno Biotech, Nanjing, 211800, Jiangsu Province, China
| | - Dongqing Cheng
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Li Chen
- Department of Medical Microbiology and Parasitology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Guiqin Sun
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
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Frater CH, Ruzhnikov MRZ, Beres S, Alcorn D, Shue A, Levy RJ. Ocular features of NGLY1 deficiency from a prospective longitudinal cohort. J AAPOS 2024:103925. [PMID: 38697387 DOI: 10.1016/j.jaapos.2024.103925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 05/05/2024]
Abstract
BACKGROUND NGLY1 deficiency is a rare autosomal recessive disorder with core features of global developmental delay, liver enzyme abnormalities, movement disorder, polyneuropathy, and hypo- or alacrima. We characterized the full spectrum and evolution of the ocular phenotype in a prospective natural history of NGLY1 deficiency. METHODS We collected ophthalmological data on 29 individuals with NGLY1 deficiency in a natural history study. Medical records were reviewed to confirm caregiver-reported symptoms. Of the 29, 15 participants appeared for at least one ophthalmological examination. RESULTS Caregivers reported at least one ocular sign or symptom in 90% of participants (26/29), most commonly decreased tears, refractive error, and chronic infection. Daily eye medication, including artificial tears, ophthalmic ointment, and topical antibiotics were used by 62%. Ophthalmological examination confirmed refractive errors in 93% (14/15) and corneal abnormalities in 73% (11/15). CONCLUSIONS Given nearly universal hypolacrima and additional prominent ocular findings in NGLY1 deficiency, a targeted ocular history and ophthalmologic examination may facilitate prompt diagnosis and early initiation of preventive eye care, preserving vision and overall ocular health.
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Affiliation(s)
- Christina H Frater
- Neurology and Neurological Sciences, Stanford University, Palo Alto, California
| | - Maura R Z Ruzhnikov
- Neurology and Neurological Sciences, Stanford University, Palo Alto, California; Division of Medical Genetics, Stanford University, Palo Alto, California
| | - Shannon Beres
- Neurology and Neurological Sciences, Stanford University, Palo Alto, California; Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California
| | - Deborah Alcorn
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California; Department of Pediatrics, Stanford University, Palo Alto, California
| | - Ann Shue
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California
| | - Rebecca J Levy
- Neurology and Neurological Sciences, Stanford University, Palo Alto, California.
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Makita Y, Asahina M, Fujinawa R, Yukitake H, Suzuki T. Intranasal oxytocin suppresses seizure-like behaviors in a mouse model of NGLY1 deficiency. Commun Biol 2024; 7:460. [PMID: 38649481 PMCID: PMC11035592 DOI: 10.1038/s42003-024-06131-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/01/2024] [Indexed: 04/25/2024] Open
Abstract
NGLY1 deficiency is a genetic disease caused by biallelic mutations of the Ngly1 gene. Although epileptic seizure is one of the most severe symptoms in patients with NGLY1 deficiency, preclinical studies have not been conducted due to the lack of animal models for epileptic seizures in NGLY1 deficiency. Here, we observed the behaviors of male and female Ngly1-/- mice by video monitoring and found that these mice exhibit spontaneous seizure-like behaviors. Gene expression analyses and enzyme immunoassay revealed significant decreases in oxytocin, a well-known neuropeptide, in the hypothalamus of Ngly1-/- mice. Seizure-like behaviors in Ngly1-/- mice were transiently suppressed by a single intranasal administration of oxytocin. These findings suggest the therapeutic potential of oxytocin for epileptic seizure in patients with NGLY1 deficiency and contribute to the clarification of the disease mechanism.
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Affiliation(s)
- Yukimasa Makita
- Takeda-CiRA Joint Program, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
- Global Advanced Platform, R&D Research, Takeda Pharmaceutical Co., Ltd. 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Makoto Asahina
- Takeda-CiRA Joint Program, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
- Global Advanced Platform, R&D Research, Takeda Pharmaceutical Co., Ltd. 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Reiko Fujinawa
- Global Advanced Platform, R&D Research, Takeda Pharmaceutical Co., Ltd. 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
- Glycometabolic Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako Saitama, 351-0198, Japan
| | - Hiroshi Yukitake
- Takeda-CiRA Joint Program, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
- Global Advanced Platform, R&D Research, Takeda Pharmaceutical Co., Ltd. 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Tadashi Suzuki
- Global Advanced Platform, R&D Research, Takeda Pharmaceutical Co., Ltd. 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan.
- Glycometabolic Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako Saitama, 351-0198, Japan.
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Saito-Koyama R, Tamai K, Yasuda J, Okamura Y, Yamazaki Y, Inoue C, Miki Y, Abe J, Oishi H, Sato I, Sasano H. Morphometric analysis of nuclear shape irregularity as a novel predictor of programmed death-ligand 1 expression in lung squamous cell carcinoma. Virchows Arch 2024; 484:609-620. [PMID: 37171482 DOI: 10.1007/s00428-023-03548-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/11/2023] [Accepted: 04/17/2023] [Indexed: 05/13/2023]
Abstract
Immune checkpoint inhibitor (ICI) therapy has been established as one of the key treatment strategies for lung squamous cell carcinoma (LUSQ). The status of programmed death-ligand 1 (PD-L1) in tumor cells and/or immune cells using immunohistochemistry has been primarily used as a surrogate marker for determining ICI treatment; however, when the tissues to be examined are small, false-negative results could be unavoidable due to the heterogeneity of PD-L1 immunoreactivity. To overcome this practical limitation, we attempted to explore the status of nuclear atypia evaluated using morphometry as a potential predictor of PD-L1 status in LUSQ. We correlated the parameters related to nuclear atypia with PD-L1 status using two different cohorts of LUSQ patients (95 cases from The Cancer Genome Atlas database and 30 cases from the Miyagi Cancer Center). Furthermore, we studied the gene mutation status to elucidate the genetic profile of PD-L1 predictable cases. The results revealed that nuclear atypia, especially morphometric parameters related to nuclear shape irregularity, including aspect ratio, circularity, roundness, and solidity, were all significantly associated with PD-L1 status. Additionally, LUSQ cases with high PD-L1 expression and pronounced nuclear atypia were significantly associated with C10orf71 and COL14A1 mutations compared with those with low PD-L1 expression and mild nuclear atypia. We demonstrated for the first time that nuclear shape irregularity could represent a novel predictor of PD-L1 expression in LUSQ. Including the morphometric parameters related to nuclear atypia in conjunction with PD-L1 status could help determine an effective ICI therapeutic strategy; however, further investigation is required.
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Affiliation(s)
- Ryoko Saito-Koyama
- Department of Pathology, Tohoku University School of Medicine, Miyagi, Japan.
- Department of Pathology, National Hospital Organization, Sendai Medical Center, 2-11-12 Miyagino, Miyagino-ku, Sendai, Miyagi, 983-8520, Japan.
| | - Keiichi Tamai
- Division of Cancer Stem Cell, Miyagi Cancer Center Research Institute, Miyagi, Japan
| | - Jun Yasuda
- Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Miyagi, Japan
| | - Yasunobu Okamura
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Miyagi, Japan
| | - Yuto Yamazaki
- Department of Pathology, Tohoku University School of Medicine, Miyagi, Japan
| | - Chihiro Inoue
- Department of Pathology, Tohoku University School of Medicine, Miyagi, Japan
| | - Yasuhiro Miki
- Department of Pathology, Tohoku University School of Medicine, Miyagi, Japan
- Faculty of Medical Science & Welfare, Tohoku Bunka Gakuen University, Miyagi, Japan
| | - Jiro Abe
- Division of Thoracic Surgery, Miyagi Cancer Center, Miyagi, Japan
| | - Hisashi Oishi
- Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Miyagi, Japan
| | - Ikuro Sato
- Division of Pathology, Miyagi Cancer Center, Miyagi, Japan
| | - Hironobu Sasano
- Department of Pathology, Tohoku University School of Medicine, Miyagi, Japan
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Ulhaq ZS, Soraya GV, Istifiani LA, Pamungkas SA, Arisanti D, Dini B, Astari LF, Hasan YTN, Ayudianti P, Kusuma MAS, Shodry S, Herawangsa S, Nurputra DK, Idaiani S, Tse WKF. A Brief Analysis on Clinical Severity of Mandibulofacial Dysostosis Guion-Almeida Type. Cleft Palate Craniofac J 2024; 61:688-696. [PMID: 36317361 DOI: 10.1177/10556656221136177] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
Abstract
OBJECTIVE Genetic variants in EFTUD2 were proven to influence variable phenotypic expressivity in mandibulofacial dysostosis Guion-Almeida type (MFDGA) or mandibulofacial dysostosis with microcephaly (MFDM). Yet, the association between the severity of clinical findings with variants within the EFTUD2 gene has not been established. Thus, we aim to elucidate a possible genotype-phenotype correlation in MFDM. METHODS Forty articles comprising 156 patients were evaluated. The genotype-phenotype correlation was analyzed using a chi-square or Fisher's exact test. RESULTS The proportion of patients with MFDM was higher in Caucasian relative to Asian populations. Although, in general, there was no apparent genotype-phenotype correlation in patients with MFDM, Asians tended to have more severe clinical manifestations than Caucasians. In addition, cardiac abnormality presented in patients with intronic variants located in canonical splice sites was a predisposing factor in affecting MFDM severity. CONCLUSION Altogether, this article provides the pathogenic variants observed in EFTUD2 and possible genotype-phenotype relationships in this disease.
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Affiliation(s)
- Zulvikar Syambani Ulhaq
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Kyushu University, Faculty of Agriculture, Fukuoka, Fukuoka, Japan
- Research Center for Pre-Clinical and Clinical Medicine, National Research and Innovation Agency Republic of Indonesia, Cibinong, Indonesia
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Maulana Malik Ibrahim State Islamic University, Malang, East Java, Indonesia
| | - Gita Vita Soraya
- Department of Biochemistry, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
- Department of Neurology, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia
| | - Lola Ayu Istifiani
- Department of Nutrition, Faculty of Health Sciences, Brawijaya University, Malang, East Java, Indonesia
| | | | - Ditya Arisanti
- Department of Clinical Medicine, Faculty of Medicine and Health Science, Maulana Malik State Islamic University, Malang, Indonesia
| | - Badariyatud Dini
- Department of Clinical Medicine, Faculty of Medicine and Health Science, Maulana Malik State Islamic University, Malang, Indonesia
| | - Lina Fitria Astari
- Department of Clinical Medicine, Faculty of Medicine and Health Science, Maulana Malik State Islamic University, Malang, Indonesia
| | - Yuliono Trika Nur Hasan
- Department of Clinical Medicine, Faculty of Medicine and Health Science, Maulana Malik State Islamic University, Malang, Indonesia
| | - Prida Ayudianti
- Department of Clinical Medicine, Faculty of Medicine and Health Science, Maulana Malik State Islamic University, Malang, Indonesia
| | - Muhammad A'raaf Sirojan Kusuma
- Research Center for Pre-Clinical and Clinical Medicine, National Research and Innovation Agency Republic of Indonesia, Cibinong, Indonesia
| | - Syifaus Shodry
- Research Center for Pre-Clinical and Clinical Medicine, National Research and Innovation Agency Republic of Indonesia, Cibinong, Indonesia
| | - Sarah Herawangsa
- Research Center for Pre-Clinical and Clinical Medicine, National Research and Innovation Agency Republic of Indonesia, Cibinong, Indonesia
| | - Dian Kesumapramudya Nurputra
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Gadjah Mada University, Yogyakarta, Indonesia
| | - Sri Idaiani
- Research Center for Pre-Clinical and Clinical Medicine, National Research and Innovation Agency Republic of Indonesia, Cibinong, Indonesia
| | - William Ka Fai Tse
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Kyushu University, Faculty of Agriculture, Fukuoka, Fukuoka, Japan
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7
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Hirayama H, Tachida Y, Fujinawa R, Matsuda Y, Murase T, Nishiuchi Y, Suzuki T. Development of a fluorescence and quencher-based FRET assay for detection of endogenous peptide:N-glycanase/NGLY1 activity. J Biol Chem 2024; 300:107121. [PMID: 38417795 PMCID: PMC11065741 DOI: 10.1016/j.jbc.2024.107121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/17/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024] Open
Abstract
Cytosolic peptide:N-glycanase (PNGase/NGLY1 in mammals) catalyzes deglycosylation of N-glycans on glycoproteins. A genetic disorder caused by mutations in the NGLY1 gene leads to NGLY1 deficiency with symptoms including motor deficits and neurological problems. Effective therapies have not been established, though, a recent study used the administration of an adeno-associated viral vector expressing human NGLY1 to dramatically rescue motor functions in young Ngly1-/- rats. Thus, early therapeutic intervention may improve symptoms arising from central nervous system dysfunction, and assay methods for measuring NGLY1 activity in biological samples are critical for early diagnostics. In this study, we established an assay system for plate-based detection of endogenous NGLY1 activity using a FRET-based probe. Using this method, we revealed significant changes in NGLY1 activity in rat brains during aging. This novel assay offers reliable disease diagnostics and provides valuable insights into the regulation of PNGase/NGLY1 activity in diverse organisms under different stress conditions.
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Affiliation(s)
- Hiroto Hirayama
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, Wako Saitama, Japan; Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
| | - Yuriko Tachida
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, Wako Saitama, Japan; Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
| | - Reiko Fujinawa
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, Wako Saitama, Japan; Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan
| | | | | | | | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, Wako Saitama, Japan; Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, Japan.
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8
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Suzuki T. A commentary on 'Patient-derived gene and protein expression signatures of NGLY1 deficiency'. J Biochem 2024; 175:221-223. [PMID: 38156787 DOI: 10.1093/jb/mvad119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024] Open
Abstract
The cytosolic peptide:N-glycanase (PNGase; NGLY1 in human and PNG1 in budding yeast) is a deglycosylating enzyme widely conserved in eukaryotes. Initially, functional importance of this enzyme remained unknown as the png1Δ mutant in yeast did not exhibit any significant phenotypes. However, the discovery of NGLY1 deficiency, a rare genetic disorder with biallelic mutations in NGLY1 gene, prompted an intensification of research that has resulted in uncovering the significance of NGLY1 as well as the proteins under its influence that are involved in numerous cellular processes. A recent report by Rauscher et al. (Patient-derived gene and protein expression signatures of NGLY1 deficiency. J. Biochem. 2022; 171: 187-199) presented a comprehensive summary of transcriptome/proteome analyses of various cell types derived from NGLY1-deficient patients. The authors also provide a web application called 'NGLY1 browser', which will allow researchers to have access to a wealth of information on gene and protein expression signature for patients with NGLY1 deficiency.
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Affiliation(s)
- Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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9
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Suzuki T, Fujihira H. NGLY1: A fascinating, multifunctional molecule. Biochim Biophys Acta Gen Subj 2024; 1868:130379. [PMID: 37951368 DOI: 10.1016/j.bbagen.2023.130379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/04/2023] [Indexed: 11/14/2023]
Abstract
NGLY1, a cytoplasmic de-N-glycosylating enzyme is well conserved among eukaryotes. This enzyme has attracted considerable attention after mutations on the NGLY1 gene were found to cause a rare genetic disorder called NGLY1 deficiency. Recent explosive progress in NGLY1 research has revealed multi-functional aspects of this protein.
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Affiliation(s)
- Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Saitama, Japan; Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan.
| | - Haruhiko Fujihira
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Saitama, Japan
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10
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Dugger SA, Dhindsa RS, Sampaio GDA, Ressler AK, Rafikian EE, Petri S, Letts VA, Teoh J, Ye J, Colombo S, Peng Y, Yang M, Boland MJ, Frankel WN, Goldstein DB. Neurodevelopmental deficits and cell-type-specific transcriptomic perturbations in a mouse model of HNRNPU haploinsufficiency. PLoS Genet 2023; 19:e1010952. [PMID: 37782669 PMCID: PMC10569524 DOI: 10.1371/journal.pgen.1010952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 10/12/2023] [Accepted: 09/01/2023] [Indexed: 10/04/2023] Open
Abstract
Heterozygous de novo loss-of-function mutations in the gene expression regulator HNRNPU cause an early-onset developmental and epileptic encephalopathy. To gain insight into pathological mechanisms and lay the potential groundwork for developing targeted therapies, we characterized the neurophysiologic and cell-type-specific transcriptomic consequences of a mouse model of HNRNPU haploinsufficiency. Heterozygous mutants demonstrated global developmental delay, impaired ultrasonic vocalizations, cognitive dysfunction and increased seizure susceptibility, thus modeling aspects of the human disease. Single-cell RNA-sequencing of hippocampal and neocortical cells revealed widespread, yet modest, dysregulation of gene expression across mutant neuronal subtypes. We observed an increased burden of differentially-expressed genes in mutant excitatory neurons of the subiculum-a region of the hippocampus implicated in temporal lobe epilepsy. Evaluation of transcriptomic signature reversal as a therapeutic strategy highlights the potential importance of generating cell-type-specific signatures. Overall, this work provides insight into HNRNPU-mediated disease mechanisms and provides a framework for using single-cell RNA-sequencing to study transcriptional regulators implicated in disease.
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Affiliation(s)
- Sarah A. Dugger
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Ryan S. Dhindsa
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute of Texas Children’s Hospital, Houston, Texas, United States of America
| | - Gabriela De Almeida Sampaio
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Andrew K. Ressler
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Elizabeth E. Rafikian
- Mouse Neurobehavioral Core Facility, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Sabrina Petri
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Verity A. Letts
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - JiaJie Teoh
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Junqiang Ye
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York, United States of America
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, New York, United States of America
| | - Sophie Colombo
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Yueqing Peng
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Mu Yang
- Mouse Neurobehavioral Core Facility, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Michael J. Boland
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Wayne N. Frankel
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York, United States of America
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York, United States of America
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11
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Pandey A, Galeone A, Han SY, Story BA, Consonni G, Mueller WF, Steinmetz LM, Vaccari T, Jafar-Nejad H. Gut barrier defects, intestinal immune hyperactivation and enhanced lipid catabolism drive lethality in NGLY1-deficient Drosophila. Nat Commun 2023; 14:5667. [PMID: 37704604 PMCID: PMC10499810 DOI: 10.1038/s41467-023-40910-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 08/16/2023] [Indexed: 09/15/2023] Open
Abstract
Intestinal barrier dysfunction leads to inflammation and associated metabolic changes. However, the relative impact of gut bacteria versus non-bacterial insults on animal health in the context of barrier dysfunction is not well understood. Here, we establish that loss of Drosophila N-glycanase 1 (Pngl) in a specific intestinal cell type leads to gut barrier defects, causing starvation and JNK overactivation. These abnormalities, along with loss of Pngl in enterocytes and fat body, result in Foxo overactivation, leading to hyperactive innate immune response and lipid catabolism and thereby contributing to lethality. Germ-free rearing of Pngl mutants rescued their developmental delay but not lethality. However, raising Pngl mutants on isocaloric, fat-rich diets partially rescued lethality. Our data indicate that Pngl functions in Drosophila larvae to establish the gut barrier, and that the lethality caused by loss of Pngl is primarily mediated through non-bacterial induction of immune and metabolic abnormalities.
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Affiliation(s)
- Ashutosh Pandey
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, USA.
| | - Antonio Galeone
- Department of Biosciences, University of Milan, Milan, Italy
- Institute of Nanotechnology, National Research Council (CNR-NANOTEC), Lecce, Italy
| | - Seung Yeop Han
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, USA
| | - Benjamin A Story
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Gaia Consonni
- Department of Biosciences, University of Milan, Milan, Italy
| | - William F Mueller
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Lars M Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Genetics, School of Medicine, Stanford University, Stanford, USA
| | - Thomas Vaccari
- Department of Biosciences, University of Milan, Milan, Italy
| | - Hamed Jafar-Nejad
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, USA.
- Genetics & Genomic Graduate Program, Baylor College of Medicine, Houston, USA.
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, USA.
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12
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Aida N, Saito A, Azuma T. Current Status of Next-Generation Sequencing in Bone Genetic Diseases. Int J Mol Sci 2023; 24:13802. [PMID: 37762102 PMCID: PMC10530486 DOI: 10.3390/ijms241813802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The development of next-generation sequencing (NGS) has dramatically increased the speed and volume of genetic analysis. Furthermore, the range of applications of NGS is rapidly expanding to include genome, epigenome (such as DNA methylation), metagenome, and transcriptome analyses (such as RNA sequencing and single-cell RNA sequencing). NGS enables genetic research by offering various sequencing methods as well as combinations of methods. Bone tissue is the most important unit supporting the body and is a reservoir of calcium and phosphate ions, which are important for physical activity. Many genetic diseases affect bone tissues, possibly because metabolic mechanisms in bone tissue are complex. For instance, the presence of specialized immune cells called osteoclasts in the bone tissue, which absorb bone tissue and interact with osteoblasts in complex ways to support normal vital functions. Moreover, the many cell types in bones exhibit cell-specific proteins for their respective activities. Mutations in the genes encoding these proteins cause a variety of genetic disorders. The relationship between age-related bone tissue fragility (also called frailty) and genetic factors has recently attracted attention. Herein, we discuss the use of genomic, epigenomic, transcriptomic, and metagenomic analyses in bone genetic disorders.
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Affiliation(s)
- Natsuko Aida
- Department of Biochemistry, Tokyo Dental College, 2-9-18 Kandamisaki-cho, Chiyoda-ku, Tokyo 101-0061, Japan; (A.S.); (T.A.)
| | - Akiko Saito
- Department of Biochemistry, Tokyo Dental College, 2-9-18 Kandamisaki-cho, Chiyoda-ku, Tokyo 101-0061, Japan; (A.S.); (T.A.)
| | - Toshifumi Azuma
- Department of Biochemistry, Tokyo Dental College, 2-9-18 Kandamisaki-cho, Chiyoda-ku, Tokyo 101-0061, Japan; (A.S.); (T.A.)
- Oral Health Science Center, Tokyo Dental College, 2-9-18 Kandamisaki-cho, Chiyoda-ku, Tokyo 101-0061, Japan
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13
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Tong S, Ventola P, Frater CH, Klotz J, Phillips JM, Muppidi S, Dwight SS, Mueller WF, Beahm BJ, Wilsey M, Lee KJ. NGLY1 deficiency: a prospective natural history study. Hum Mol Genet 2023; 32:2787-2796. [PMID: 37379343 PMCID: PMC10481101 DOI: 10.1093/hmg/ddad106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 06/30/2023] Open
Abstract
N-glycanase 1 (NGLY1) deficiency is a debilitating, ultra-rare autosomal recessive disorder caused by loss of function of NGLY1, a cytosolic enzyme that deglycosylates other proteins. It is characterized by severe global developmental delay and/or intellectual disability, hyperkinetic movement disorder, transient elevation of transaminases, (hypo)alacrima and progressive, diffuse, length-dependent sensorimotor polyneuropathy. A prospective natural history study (NHS) was conducted to elucidate clinical features and disease course. Twenty-nine participants were enrolled (15 onsite, 14 remotely) and followed for up to 32 months, representing ~29% of the ~100 patients identified worldwide. Participants exhibited profound developmental delays, with almost all developmental quotients below 20 on the Mullen Scales of Early Learning, well below the normative score of 100. Increased difficulties with sitting and standing suggested decline in motor function over time. Most patients presented with (hypo)alacrima and reduced sweat response. Pediatric quality of life was poor except for emotional function. Language/communication and motor skill problems including hand use were reported by caregivers as the most bothersome symptoms. Levels of the substrate biomarker, GlcNAc-Asn (aspartylglucosamine; GNA), were consistently elevated in all participants over time, independent of age. Liver enzymes were elevated for some participants but improved especially in younger patients and did not reach levels indicating severe liver disease. Three participants died during the study period. Data from this NHS informs selection of endpoints and assessments for future clinical trials for NGLY1 deficiency interventions. Potential endpoints include GNA biomarker levels, neurocognitive assessments, autonomic and motor function (particularly hand use), (hypo)alacrima and quality of life.
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Affiliation(s)
- Sandra Tong
- Grace Science Foundation, Menlo Park, CA 94026, USA
| | - Pamela Ventola
- Cogstate, New Haven, CT 06510, USA
- Yale Child Study Center, New Haven, CT 06519, USA
| | | | - Jenna Klotz
- Department of Neurology, Stanford University, Stanford, CA 94305, USA
| | | | - Srikanth Muppidi
- Department of Neurology, Stanford University, Stanford, CA 94305, USA
| | | | | | | | - Matt Wilsey
- Grace Science Foundation, Menlo Park, CA 94026, USA
| | - Kevin J Lee
- Grace Science Foundation, Menlo Park, CA 94026, USA
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14
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Chung CCY, Hue SPY, Ng NYT, Doong PHL, Chu ATW, Chung BHY. Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations. Genet Med 2023; 25:100896. [PMID: 37191093 DOI: 10.1016/j.gim.2023.100896] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
PURPOSE This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations. METHODS A meta-analysis was conducted to identify studies from 2011 to 2021. RESULTS One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations. Diagnostic rates of ES (0.38, 95% CI 0.36-0.40) and GS (0.34, 95% CI 0.30-0.38) were similar (P = .1). Within-cohort comparison illustrated 1.2-times odds of diagnosis by GS over ES (95% CI 0.79-1.83, P = .38). GS studies discovered a higher range of novel genes than ES studies; yet, the rate of variant of unknown significance did not differ (P = .78). Among high-quality studies, clinical utility of GS (0.77, 95% CI 0.64-0.90) was higher than that of ES (0.44, 95% CI 0.30-0.58) (P < .01). CONCLUSION This meta-analysis provides an important update to demonstrate the similar diagnostic rates between ES and GS and the higher clinical utility of GS over ES. With the newly published recommendations for clinical interpretation of variants found in noncoding regions of the genome and the trend of decreasing variant of unknown significance and GS cost, it is expected that GS will be more widely used in clinical settings.
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Affiliation(s)
| | - Shirley P Y Hue
- Hong Kong Genome Institute, Hong Kong Special Administrative Region
| | - Nicole Y T Ng
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Annie T W Chu
- Hong Kong Genome Institute, Hong Kong Special Administrative Region.
| | - Brian H Y Chung
- Hong Kong Genome Institute, Hong Kong Special Administrative Region; Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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15
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Rogerson D, Alkelai A, Giordano J, Pantrangi M, Hsiao MC, Nhan-Chang CL, Motelow JE, Aggarwal V, Goldstein D, Wapner R, Shawber CJ. Investigation into the genetics of fetal congenital lymphatic anomalies. Prenat Diagn 2023; 43:703-716. [PMID: 36959127 PMCID: PMC10330091 DOI: 10.1002/pd.6345] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/10/2023] [Accepted: 03/12/2023] [Indexed: 03/25/2023]
Abstract
OBJECTIVE Congenital lymphatic anomalies (LAs) arise due to defects in lymphatic development and often present in utero as pleural effusion, chylothorax, nuchal and soft tissue edema, ascites, or hydrops. Many LAs are caused by single nucleotide variants, which are not detected on routine prenatal testing. METHODS Demographic data were compared between two subcohorts, those with clinically significant fetal edema (CSFE) and isolated fetal edema. A targeted variant analysis of LA genes was performed using American College of Medical Genetics criteria on whole exome sequencing (WES) data generated for 71 fetal edema cases who remained undiagnosed after standard workup. RESULTS CSFE cases had poor outcomes, including preterm delivery, demise, and maternal preeclampsia. Pathogenic and likely pathogenic variants were identified in 7% (5/71) of cases, including variants in RASopathy genes, RASA1, SOS1, PTPN11, and a novel PIEZO1 variant. Variants of uncertain significance (VOUS) were identified in 45% (32/71) of cases. In CSFEs, VOUS were found in CELSR1, EPHB4, TIE1, PIEZO1, ITGA9, RASopathy genes, SOS1, SOS2, and RAF1. CONCLUSIONS WES identified pathogenic and likely pathogenic variants and VOUS in LA genes in 51% of fetal edema cases, supporting WES and expanded hydrops panels in cases of idiopathic fetal hydrops and fluid collections.
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Affiliation(s)
- Daniella Rogerson
- Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Jessica Giordano
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Madhulatha Pantrangi
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Meng-Chang Hsiao
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Chia-Ling Nhan-Chang
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Joshua E. Motelow
- Department of Pediatrics, Columbia University Vagelos College of Physicians andSurgeons, New York, New York, USA
| | - Vimla Aggarwal
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - David Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Ron Wapner
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Carrie J. Shawber
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Department of Surgery, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
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16
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Pandey A, Galeone A, Han SY, Story BA, Consonni G, Mueller WF, Steinmetz LM, Vaccari T, Jafar-Nejad H. Gut barrier defects, increased intestinal innate immune response, and enhanced lipid catabolism drive lethality in N -glycanase 1 deficient Drosophila. bioRxiv 2023:2023.04.07.536022. [PMID: 37066398 PMCID: PMC10104161 DOI: 10.1101/2023.04.07.536022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Intestinal barrier dysfunction leads to inflammation and associated metabolic changes. However, the relative impact of infectious versus non-infectious mechanisms on animal health in the context of barrier dysfunction is not well understood. Here, we establish that loss of Drosophila N -glycanase 1 (Pngl) leads to gut barrier defects, which cause starvation and increased JNK activity. These defects result in Foxo overactivation, which induces a hyperactive innate immune response and lipid catabolism, thereby contributing to lethality associated with loss of Pngl . Notably, germ-free rearing of Pngl mutants did not rescue lethality. In contrast, raising Pngl mutants on isocaloric, fat-rich diets improved animal survival in a dosage-dependent manner. Our data indicate that Pngl functions in Drosophila larvae to establish the gut barrier, and that the immune and metabolic consequences of loss of Pngl are primarily mediated through non-infectious mechanisms.
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17
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Spillmann RC, Tan QKG, Reuter C, Schoch K, Kohler J, Bonner D, Zastrow D, Alkelai A, Baugh E, Cope H, Marwaha S, Wheeler MT, Bernstein JA, Shashi V. A concurrent dual analysis of genomic data augments diagnoses: Experiences of 2 clinical sites in the Undiagnosed Diseases Network. Genet Med 2023; 25:100353. [PMID: 36481303 PMCID: PMC10506157 DOI: 10.1016/j.gim.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Next-generation sequencing (NGS) has revolutionized the diagnostic process for rare/ultrarare conditions. However, diagnosis rates differ between analytical pipelines. In the National Institutes of Health-Undiagnosed Diseases Network (UDN) study, each individual's NGS data are concurrently analyzed by the UDN sequencing core laboratory and the clinical sites. We examined the outcomes of this practice. METHODS A retrospective review was performed at 2 UDN clinical sites to compare the variants and diagnoses/candidate genes identified with the dual analyses of the NGS data. RESULTS In total, 95 individuals had 100 diagnoses/candidate genes. There was 59% concordance between the UDN sequencing core laboratories and the clinical sites in identifying diagnoses/candidate genes. The core laboratory provided more diagnoses, whereas the clinical sites prioritized more research variants/candidate genes (P < .001). The clinical sites solely identified 15% of the diagnoses/candidate genes. The differences between the 2 pipelines were more often because of variant prioritization disparities than variant detection. CONCLUSION The unique dual analysis of NGS data in the UDN synergistically enhances outcomes. The core laboratory provided a clinical analysis with more diagnoses and the clinical sites prioritized more research variants/candidate genes. Implementing such concurrent dual analyses in other genomic research studies and clinical settings can improve both variant detection and prioritization.
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Affiliation(s)
- Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Queenie K-G Tan
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Chloe Reuter
- Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA; Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Jennefer Kohler
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Devon Bonner
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Diane Zastrow
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Anna Alkelai
- Institute for Genome Medicine, Columbia University Medical Center, New York, NY
| | - Evan Baugh
- Institute for Genome Medicine, Columbia University Medical Center, New York, NY
| | - Heidi Cope
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Shruti Marwaha
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Matthew T Wheeler
- Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA; Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Jonathan A Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC.
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18
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Alharbi H, Daniel EJP, Thies J, Chang I, Goldner DL, Ng BG, Witters P, Aqul A, Velez-Bartolomei F, Enns GM, Hsu E, Kichula E, Lee E, Lourenco C, Poskanzer SA, Rasmussen S, Saarela K, Wang YM, Raymond KM, Schultz MJ, Freeze HH, Lam C, Edmondson AC, He M. Fractionated plasma N-glycan profiling of novel cohort of ATP6AP1-CDG subjects identifies phenotypic association. J Inherit Metab Dis 2023; 46:300-312. [PMID: 36651831 PMCID: PMC10047170 DOI: 10.1002/jimd.12589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023]
Abstract
ATP6AP1-CDG is an X-linked disorder typically characterized by hepatopathy, immunodeficiency, and an abnormal type II transferrin glycosylation pattern. Here, we present 11 new patients and clinical updates with biochemical characterization on one previously reported patient. We also document intrafamilial phenotypic variability and atypical presentations, expanding the symptomatology of ATP6AP1-CDG to include dystonia, hepatocellular carcinoma, and lysosomal abnormalities on hepatic histology. Three of our subjects received successful liver transplantation. We performed N-glycan profiling of total and fractionated plasma proteins for six patients and show associations with varying phenotypes, demonstrating potential diagnostic and prognostic value of fractionated N-glycan profiles. The aberrant N-linked glycosylation in purified transferrin and remaining plasma glycoprotein fractions normalized in one patient post hepatic transplant, while the increases of Man4GlcNAc2 and Man5GlcNAc2 in purified immunoglobulins persisted. Interestingly, in the single patient with isolated immune deficiency phenotype, elevated high-mannose glycans were detected on purified immunoglobulins without glycosylation abnormalities on transferrin or the remaining plasma glycoprotein fractions. Given the diverse and often tissue specific clinical presentations and the need of clinical management post hepatic transplant in ATP6AP1-CDG patients, these results demonstrate that fractionated plasma N-glycan profiling could be a valuable tool in diagnosis and disease monitoring.
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Affiliation(s)
- Hana Alharbi
- Department of Pediatrics, Faculty of Medicine, University of Tabuk, Tabuk, Saudi Arabia
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Earnest James Paul Daniel
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jenny Thies
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, Washington, USA
| | - Irene Chang
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Dana L Goldner
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Columbia University Medical Center, New York, New York, USA
| | - Bobby G Ng
- Human Genetics Program, Sanford Burnham Prebys, La Jolla, California, USA
| | - Peter Witters
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, Center for Metabolic Diseases, University Hospital Leuven, Leuven, Belgium
- Department of Development and Regeneration, Faculty of Medicine, KU Leuven, University Hospitals Leuven, Leuven, Belgium
| | - Amal Aqul
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, University of Texas Southwestern/Children's Medical Center, Dallas, Texas, USA
| | - Frances Velez-Bartolomei
- Genetics Section, San Jorge Children and Women's Hospital in San Juan, San Juan, Puerto Rico, USA
- Division of Medical Genetics, Department of Pediatrics, Lucile Packard Children's Hospital and Stanford University, Stanford, California, USA
| | - Gregory M Enns
- Division of Medical Genetics, Department of Pediatrics, Lucile Packard Children's Hospital and Stanford University, Stanford, California, USA
| | - Evelyn Hsu
- Division of Gastroenterology and Hepatology, Department of Pediatrics, Seattle Children's Hospital, University of Washington School of Medicine, Seattle, Washington, USA
| | - Elizabeth Kichula
- Division of Neurology, Departments of Pediatrics and Neurology, Children's Hospital of Philadelphia and the Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Esther Lee
- Genetic Services, Kaiser Permanente of Washington, Seattle, Washington, USA
| | - Charles Lourenco
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São Jose do Rio Preto - São Paulo, Brazil
- Personalized Medicine area, Special Education Sector at DLE/Grupo Pardini, Belo Horizonte - MG, Brazil
| | - Sheri A Poskanzer
- St. Luke's Health System, Boise, Idaho, USA
- Department of Pediatrics, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Sara Rasmussen
- Transplant Center, Department of Surgery, Seattle Children's Hospital University of Washington School of Medicine Seattle, Seattle, Washington, USA
| | - Katelyn Saarela
- Division of Gastroenterology and Hepatology, Department of Pediatrics, Seattle Children's Hospital, University of Washington School of Medicine, Seattle, Washington, USA
| | - YunZu M Wang
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Kimiyo M Raymond
- Department of Laboratory Medicine and Pathology, Laboratory Genetics and Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew J Schultz
- Department of Laboratory Medicine and Pathology, Laboratory Genetics and Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Hudson H Freeze
- Human Genetics Program, Sanford Burnham Prebys, La Jolla, California, USA
| | - Christina Lam
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Andrew C Edmondson
- Department of Pediatrics, Division of Human Genetics, Section of Metabolism, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Miao He
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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19
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Abstract
Exome sequencing (ES) and genome sequencing (GS) have radically transformed the diagnostic approach to undiagnosed rare/ultrarare Mendelian diseases. Next-generation sequencing (NGS), the technology integral for ES, GS, and most large (100+) gene panels, has enabled previously unimaginable diagnoses, changes in medical management, new treatments, and accurate reproductive risk assessments for patients, as well as new disease gene discoveries. Yet, challenges remain, as most individuals remain undiagnosed with current NGS. Improved NGS technology has resulted in long-read sequencing, which may resolve diagnoses in some patients who do not obtain a diagnosis with current short-read ES and GS, but its effectiveness is unclear, and it is expensive. Other challenges that persist include the resolution of variants of uncertain significance, the urgent need for patients with ultrarare disorders to have access to therapeutics, the need for equity in patient access to NGS-based testing, and the study of ethical concerns. However, the outlook for undiagnosed disease resolution is bright, due to continual advancements in the field.
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Affiliation(s)
- Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
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20
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Guedj M, Rosier M, Calvas P, Julia S, Garnier C, Cambon-Thomsen A, Munoz Sastre MT. Chapitre 8. Annoncer ou pas la découverte d’anomalies non sollicitées lors d’un test génétique à séquençage haut débit ? J Int Bioethique Ethique Sci 2023; 34:121-130. [PMID: 37684199 DOI: 10.3917/jibes.342.0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
OBJECTIVE New genome sequencing techniques allow new approaches in medical genetics, in particular by facilitating the diagnosis of genetic diseases. However, their use also leads to unsolicited genetic findings being uncovered. This type of discovery raises ethical, legal and psychological considerations. The objective of this psychological research was to study the different positions of patients, health professionals and general public regarding the acceptability of the announcement of unsolicited findings revealed during a high-throughput sequencing genetic test. METHOD the first exploratory study aimed, through non-directive research interviews conducted with 13 patients of a medical genetics service, to understand the psychological repercussions linked to the announcement of a result of a targeted genetic test and to know the patients’ desires regarding the announcement of unsolicited findings if the test had been a high-throughput genetic test. The second study, using a quantitative methodology, aimed to identify the judgment policies of 144 patients, 94 healthcare professionals and 211 people from the general public concerning the acceptability of this type of disclosure. RESULTS The cluster analyses highlighted six judgment policies as to whether or not to disclose the discovery of unsolicited anomalies: “Tell everything”, “Tell even in part”, “Tell everything unless desperate”, “Undecided”, “Do not tell” and “Do not tell if no prevention”. The participants positioned themselves differently, in particular according to the patient’s consent. CONCLUSION This research shows the variability of positioning and the importance of consent in the acceptability of the disclosure of unsolicited findings. However, one of the limitations of the study lies in the fact that in medical clinic, acceptability and acceptance may vary over time. A longitudinal study would undoubtedly afford a better understanding of the psychological progress of patients in this type of care pathway..
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Budhraja R, Saraswat M, De Graef D, Ranatunga W, Ramarajan MG, Mousa J, Kozicz T, Pandey A, Morava E. N-glycoproteomics reveals distinct glycosylation alterations in NGLY1-deficient patient-derived dermal fibroblasts. J Inherit Metab Dis 2023; 46:76-91. [PMID: 36102038 PMCID: PMC10092224 DOI: 10.1002/jimd.12557] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 01/19/2023]
Abstract
Congenital disorders of glycosylation are genetic disorders that occur due to defects in protein and lipid glycosylation pathways. A deficiency of N-glycanase 1, encoded by the NGLY1 gene, results in a congenital disorder of deglycosylation. The NGLY1 enzyme is mainly involved in cleaving N-glycans from misfolded, retro-translocated glycoproteins in the cytosol from the endoplasmic reticulum before their proteasomal degradation or activation. Despite the essential role of NGLY1 in deglycosylation pathways, the exact consequences of NGLY1 deficiency on global cellular protein glycosylation have not yet been investigated. We undertook a multiplexed tandem mass tags-labeling-based quantitative glycoproteomics and proteomics analysis of fibroblasts from NGLY1-deficient individuals carrying different biallelic pathogenic variants in NGLY1. This quantitative mass spectrometric analysis detected 8041 proteins and defined a proteomic signature of differential expression across affected individuals and controls. Proteins that showed significant differential expression included phospholipid phosphatase 3, stromal cell-derived factor 1, collagen alpha-1 (IV) chain, hyaluronan and proteoglycan link protein 1, and thrombospondin-1. We further detected a total of 3255 N-glycopeptides derived from 550 glycosylation sites of 407 glycoproteins by multiplexed N-glycoproteomics. Several extracellular matrix glycoproteins and adhesion molecules showed altered abundance of N-glycopeptides. Overall, we observed distinct alterations in specific glycoproteins, but our data revealed no global accumulation of glycopeptides in the patient-derived fibroblasts, despite the genetic defect in NGLY1. Our findings highlight new molecular and system-level insights for understanding NGLY1-CDDG.
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Affiliation(s)
- Rohit Budhraja
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Mayank Saraswat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Diederik De Graef
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Wasantha Ranatunga
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Madan G Ramarajan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Jehan Mousa
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Tamas Kozicz
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Eva Morava
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
- Department of Medical Genetics and Department of Biophysics, University of Pecs Medical School, Pecs, Hungary
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22
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Hetz R, Magaway C, Everett J, Li L, Willard BB, Freeze HH, He P. Comparative proteomics reveals elevated CCN2 in NGLY1-deficient cells. Biochem Biophys Res Commun 2022; 632:165-172. [PMID: 36209585 PMCID: PMC9677521 DOI: 10.1016/j.bbrc.2022.09.100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/13/2022] [Accepted: 09/25/2022] [Indexed: 01/05/2023]
Abstract
N-glycanase 1(NGLY1) catalyzes the removal of N-linked glycans from newly synthesized or misfolded protein. NGLY1 deficiency is a recently diagnosed rare genetic disorder. The affected individuals present a broad spectrum of clinical features. Recent studies explored several possible molecular mechanisms of NGLY1 deficiency including defects in proteostasis, mitochondrial homeostasis, innate immunity, and water/ion transport. We demonstrate abnormal accumulation of endoplasmic reticulum-associated degradation (ERAD) substrates in NGLY1-deficient cells. Global quantitative proteomics discovered elevated levels of endogenous proteins in NGLY1-defective human and mouse cells. Further biological validation assays confirmed the altered abundance of several key candidates that were subjected to isobarically labeled proteomic analysis. CCN2 was selected for further analysis due to its significant increase in different cell models of NGLY1 deficiency. Functional assays show elevated CCN2 and over-stimulated TGF-β signaling in NGLY1-deficient cells. Given the important role of CCN2 and TGF-β pathway in mediating systemic fibrosis, we propose a potential link of increased CCN2 and TGF-β signaling to microscopic liver fibrosis in NGLY1 patients.
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Affiliation(s)
- Rebecca Hetz
- Department of Biochemistry, Lake Erie College of Osteopathic Medicine, Erie, PA, USA
| | - Carlo Magaway
- Department of Biochemistry, Lake Erie College of Osteopathic Medicine, Erie, PA, USA
| | - Jaylene Everett
- Department of Biochemistry, Lake Erie College of Osteopathic Medicine, Erie, PA, USA
| | - Ling Li
- Proteomics and Metabolomics Core, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA
| | - Belinda B. Willard
- Proteomics and Metabolomics Core, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA
| | - Hudson H. Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Ping He
- Department of Biochemistry, Lake Erie College of Osteopathic Medicine, Erie, PA, USA,Correspondence: Department of Pre-Clinical Medicine, Lake Erie College of Osteopathic Medicine, 2000 West Grandview Boulevard, Room: 2-107, Erie, PA 16509, USA,
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23
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Walber S, Partalidou G, Gerling‐Driessen UIM. NGLY1 Deficiency: A Rare Genetic Disorder Unlocks Therapeutic Potential for Common Diseases. Isr J Chem 2022. [DOI: 10.1002/ijch.202200068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Simon Walber
- Institute of Organic and Macromolecular Chemistry Heinrich Heine University Duesseldorf Universitaetsstrasse 1 40225 Duesseldorf Germany
| | - Georgia Partalidou
- Institute of Organic and Macromolecular Chemistry Heinrich Heine University Duesseldorf Universitaetsstrasse 1 40225 Duesseldorf Germany
| | - Ulla I. M. Gerling‐Driessen
- Institute of Organic and Macromolecular Chemistry Heinrich Heine University Duesseldorf Universitaetsstrasse 1 40225 Duesseldorf Germany
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24
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Sasserath T, Robertson AL, Mendez R, Hays TT, Smith E, Cooper H, Akanda N, Rumsey JW, Guo X, Farkhondeh A, Pradhan M, Baumgaertel K, Might M, Rodems S, Zheng W, Hickman JJ. An induced pluripotent stem cell-derived NMJ platform for study of the NGLY1-Congenital Disorder of Deglycosylation. Adv Ther (Weinh) 2022; 5:2200009. [PMID: 36589922 PMCID: PMC9798846 DOI: 10.1002/adtp.202200009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Indexed: 01/05/2023]
Abstract
There are many neurological rare diseases where animal models have proven inadequate or do not currently exist. NGLY1 Deficiency, a congenital disorder of deglycosylation, is a rare disease that predominantly affects motor control, especially control of neuromuscular action. In this study, NGLY1-deficient, patient-derived induced pluripotent stem cells (iPSCs) were differentiated into motoneurons (MNs) to identify disease phenotypes analogous to clinical disease pathology with significant deficits apparent in the NGLY1-deficient lines compared to the control. A neuromuscular junction (NMJ) model was developed using patient and wild type (WT) MNs to study functional differences between healthy and diseased NMJs. Reduced axon length, increased and shortened axon branches, MN action potential (AP) bursting and decreased AP firing rate and amplitude were observed in the NGLY1-deficient MNs in monoculture. When transitioned to the NMJ-coculture system, deficits in NMJ number, stability, failure rate, and synchronicity with indirect skeletal muscle (SkM) stimulation were observed. This project establishes a phenotypic NGLY1 model for investigation of possible therapeutics and investigations into mechanistic deficits in the system.
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Affiliation(s)
- Trevor Sasserath
- Hesperos, Inc., 12501 Research Parkway, Suite 100, Orlando, FL 32826 USA
| | - Ashley L Robertson
- Hesperos, Inc., 12501 Research Parkway, Suite 100, Orlando, FL 32826 USA
| | - Roxana Mendez
- University of Central Florida, NanoScience Technology Center, 12424 Research Parkway, Suite 400, Orlando, FL 32826 USA
| | - Tristan T Hays
- Hesperos, Inc., 12501 Research Parkway, Suite 100, Orlando, FL 32826 USA
| | - Ethan Smith
- Hesperos, Inc., 12501 Research Parkway, Suite 100, Orlando, FL 32826 USA
| | - Helena Cooper
- Hesperos, Inc., 12501 Research Parkway, Suite 100, Orlando, FL 32826 USA
| | - Nesar Akanda
- University of Central Florida, NanoScience Technology Center, 12424 Research Parkway, Suite 400, Orlando, FL 32826 USA
| | - John W Rumsey
- Hesperos, Inc., 12501 Research Parkway, Suite 100, Orlando, FL 32826 USA
| | - Xiufang Guo
- University of Central Florida, NanoScience Technology Center, 12424 Research Parkway, Suite 400, Orlando, FL 32826 USA
| | - Atena Farkhondeh
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Building C, Room 310W Rockville, MD 20850, USA
| | - Manisha Pradhan
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Building C, Room 310W Rockville, MD 20850, USA
| | - Karsten Baumgaertel
- Travere Therapeutics, 3611 Valley Centre Drive, Suite 300, San Diego, CA, USA
| | - Matthew Might
- University of Alabama at Birmingham, Hugh Kaul Precision Medicine Institute, 510 20th St S, Office 858B, Birmingham, AL 35210, USA
| | - Steven Rodems
- Travere Therapeutics, 3611 Valley Centre Drive, Suite 300, San Diego, CA, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Building C, Room 310W Rockville, MD 20850, USA
| | - James J Hickman
- Hesperos, Inc., 12501 Research Parkway, Suite 100, Orlando, FL 32826 USA
- University of Central Florida, NanoScience Technology Center, 12424 Research Parkway, Suite 400, Orlando, FL 32826 USA
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25
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Hitomi Y, Aiba Y, Ueno K, Nishida N, Kawai Y, Kawashima M, Tsuiji M, Iwabuchi C, Takada S, Miyake N, Nagasaki M, Tokunaga K, Nakamura M. rs2013278 in the multiple immunological-trait susceptibility locus CD28 regulates the production of non-functional splicing isoforms. Hum Genomics 2022; 16:46. [PMID: 36271469 DOI: 10.1186/s40246-022-00419-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/30/2022] [Indexed: 11/22/2022] Open
Abstract
Background Ligation of CD28 with ligands such as CD80 or CD86 provides a critical second signal alongside antigen presentation by class II major histocompatibility complex expressed on antigen-presenting cells through the T cell antigen receptor for naïve T cell activation. A number of studies suggested that CD28 plays an important role in the pathogenesis of various human diseases. Recent genome-wide association studies (GWASs) identified CD28 as a susceptibility locus for lymphocyte and eosinophil counts, multiple sclerosis, ulcerative colitis, celiac disease, rheumatoid arthritis, asthma, and primary biliary cholangitis. However, the primary functional variant and molecular mechanisms of disease susceptibility in this locus remain to be elucidated. This study aimed to identify the primary functional variant from thousands of genetic variants in the CD28 locus and elucidate its functional effect on the CD28 molecule. Results Among the genetic variants exhibiting stronger linkage disequilibrium (LD) with all GWAS-lead variants in the CD28 locus, rs2013278, located in the Rbfox binding motif related to splicing regulation, was identified as a primary functional variant related to multiple immunological traits. Relative endogenous expression levels of CD28 splicing isoforms (CD28i and CD28Δex2) compared with full-length CD28 in allele knock-in cell lines generated using CRISPR/Cas9 were directly regulated by rs2013278 (P < 0.05). Although full-length CD28 protein expressed on Jurkat T cells showed higher binding affinity for CD80/CD86, both CD28i and CD28Δex2 encoded loss-of-function isoforms. Conclusion The present study demonstrated for the first time that CD28 has a shared disease-related primary functional variant (i.e., rs2013278) that regulates the CD28 alternative splicing that generates loss-of-function isoforms. They reduce disease risk by inducing anergy of effector T cells that over-react to autoantigens and allergens. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-022-00419-7.
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26
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Nolan DK, Pastore MT, McBride KL. Expanding the NGLY1 deficiency phenotype: Case report of an atypical patient. Eur J Med Genet 2022; 65:104558. [PMID: 35779835 DOI: 10.1016/j.ejmg.2022.104558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/06/2022] [Accepted: 06/27/2022] [Indexed: 11/03/2022]
Abstract
NGLY1 deficiency is a rare congenital disorder of deglycosylation with a unique constellation of symptoms that include hypo- or alacrima, movement disorder, epilepsy, and severe intellectual disability (OMIM #615273). Here we report a patient with NGLY1 deficiency whose clinical presentation lacks many of the features associated with the disease and has a much milder intellectual disability than had been previously reported, expanding the phenotypic spectrum.
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Affiliation(s)
- D K Nolan
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Anthropology, The Ohio State University, Columbus, OH, USA.
| | - M T Pastore
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - K L McBride
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA; Center for Cardiovascular Research, Nationwide Children's Hospital, Columbus, OH, USA
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27
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Mesika A, Nadav G, Shochat C, Kalfon L, Jackson K, Khalaileh A, Karasik D, Falik-Zaccai TC. NGLY1 Deficiency Zebrafish Model Manifests Abnormalities of the Nervous and Musculoskeletal Systems. Front Cell Dev Biol 2022; 10:902969. [PMID: 35769264 PMCID: PMC9234281 DOI: 10.3389/fcell.2022.902969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022] Open
Abstract
Background: NGLY1 is an enigmatic enzyme with multiple functions across a wide range of species. In humans, pathogenic genetic variants in NGLY1 are linked to a variable phenotype of global neurological dysfunction, abnormal tear production, and liver disease presenting the rare autosomal recessive disorder N-glycanase deficiency. We have ascertained four NGLY1 deficiency patients who were found to carry a homozygous nonsense variant (c.1294G > T, p.Glu432*) in NGLY1. Methods: We created an ngly1 deficiency zebrafish model and studied the nervous and musculoskeletal (MSK) systems to further characterize the phenotypes and pathophysiology of the disease. Results: Nervous system morphology analysis has shown significant loss of axon fibers in the peripheral nervous system. In addition, we found muscle structure abnormality of the mutant fish. Locomotion behavior analysis has shown hypersensitivity of the larval ngly1(−/−) fish during stress conditions. Conclusion: This first reported NGLY1 deficiency zebrafish model might add to our understanding of NGLY1 role in the development of the nervous and MSK systems. Moreover, it might elucidate the natural history of the disease and be used as a platform for the development of novel therapies.
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Affiliation(s)
- Aviv Mesika
- Institute of Human Genetics, Galilee Medical Center, Nahariya, Israel
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Golan Nadav
- Institute of Human Genetics, Galilee Medical Center, Nahariya, Israel
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Chen Shochat
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Limor Kalfon
- Institute of Human Genetics, Galilee Medical Center, Nahariya, Israel
| | - Karen Jackson
- MIGAL, Galilee Research Institute, Kiryat Shmona, Israel
| | - Ayat Khalaileh
- Institute of Human Genetics, Galilee Medical Center, Nahariya, Israel
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - David Karasik
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Tzipora C. Falik-Zaccai
- Institute of Human Genetics, Galilee Medical Center, Nahariya, Israel
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
- *Correspondence: Tzipora C. Falik-Zaccai,
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28
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Hope KA, Berman AR, Peterson RT, Chow CY. An in vivo drug repurposing screen and transcriptional analyses reveals the serotonin pathway and GSK3 as major therapeutic targets for NGLY1 deficiency. PLoS Genet 2022; 18:e1010228. [PMID: 35653343 PMCID: PMC9162339 DOI: 10.1371/journal.pgen.1010228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/02/2022] [Indexed: 11/19/2022] Open
Abstract
NGLY1 deficiency, a rare disease with no effective treatment, is caused by autosomal recessive, loss-of-function mutations in the N-glycanase 1 (NGLY1) gene and is characterized by global developmental delay, hypotonia, alacrima, and seizures. We used a Drosophila model of NGLY1 deficiency to conduct an in vivo, unbiased, small molecule, repurposing screen of FDA-approved drugs to identify therapeutic compounds. Seventeen molecules partially rescued lethality in a patient-specific NGLY1 deficiency model, including multiple serotonin and dopamine modulators. Exclusive dNGLY1 expression in serotonin and dopamine neurons, in an otherwise dNGLY1 deficient fly, was sufficient to partially rescue lethality. Further, genetic modifier and transcriptomic data supports the importance of serotonin signaling in NGLY1 deficiency. Connectivity Map analysis identified glycogen synthase kinase 3 (GSK3) inhibition as a potential therapeutic mechanism for NGLY1 deficiency, which we experimentally validated with TWS119, lithium, and GSK3 knockdown. Strikingly, GSK3 inhibitors and a serotonin modulator rescued size defects in dNGLY1 deficient larvae upon proteasome inhibition, suggesting that these compounds act through NRF1, a transcription factor that is regulated by NGLY1 and regulates proteasome expression. This study reveals the importance of the serotonin pathway in NGLY1 deficiency, and serotonin modulators or GSK3 inhibitors may be effective therapeutics for this rare disease. NGLY1 deficiency is a rare disease with no effective treatment. We conducted a drug repurposing screen and used the Connectivity Map, a transcriptional-based computational approach, to identify compounds that may serve as therapeutics for NGLY1 deficient individuals. The drug repurposing screen identified FDA-approved compounds acting through the serotonin and dopamine pathway that partially rescued lethality in an NGLY1 deficiency fly model. We also found that expressing dNGLY1 (the Drosophila ortholog of NGLY1) exclusively in serotonin neurons, in an otherwise dNGLY1 deficient fly, partially rescued lethality. These data indicate the importance of the serotonin and dopamine systems in NGLY1 deficiency. The Connectivity Map analyses found GSK3 inhibitors as potential therapeutic compounds, which were validated in vivo in the fly. Furthermore, knockdown of sgg (the Drosophila ortholog of GSK3) partially rescued lethality in dNGLY1 deficient flies, suggesting GSK3 as a therapeutic target for NGLY1 deficiency. Taken together, this work identifies therapeutic strategies for NGLY1 deficiency.
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Sakthivel D, Bolívar BE, Bouchier‐Hayes L. Cellular autophagy, an unbidden effect of caspase inhibition by zVAD‐fmk. FEBS J 2022; 289:3097-3100. [DOI: 10.1111/febs.16346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/05/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Dharaniya Sakthivel
- Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA
- Division of Hematology‐Oncology, Department of Pediatrics Baylor College of Medicine Houston TX USA
- Texas Children’s Hospital Houston William T. Shearer Center for Human Immunobiology TX USA
| | - Beatriz E. Bolívar
- Division of Hematology‐Oncology, Department of Pediatrics Baylor College of Medicine Houston TX USA
- Texas Children’s Hospital Houston William T. Shearer Center for Human Immunobiology TX USA
| | - Lisa Bouchier‐Hayes
- Division of Hematology‐Oncology, Department of Pediatrics Baylor College of Medicine Houston TX USA
- Texas Children’s Hospital Houston William T. Shearer Center for Human Immunobiology TX USA
- Department of Molecular and Cellular Biology Baylor College of Medicine Houston TX USA
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30
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Miao X, Wu J, Chen H, Lu G. Comprehensive Analysis of the Structure and Function of Peptide:N-Glycanase 1 and Relationship with Congenital Disorder of Deglycosylation. Nutrients 2022; 14:nu14091690. [PMID: 35565658 PMCID: PMC9102325 DOI: 10.3390/nu14091690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 02/01/2023] Open
Abstract
The cytosolic PNGase (peptide:N-glycanase), also known as peptide-N4-(N-acetyl-β-glucosaminyl)-asparagine amidase, is a well-conserved deglycosylation enzyme (EC 3.5.1.52) which catalyzes the non-lysosomal hydrolysis of an N(4)-(acetyl-β-d-glucosaminyl) asparagine residue (Asn, N) into a N-acetyl-β-d-glucosaminyl-amine and a peptide containing an aspartate residue (Asp, D). This enzyme (NGLY1) plays an essential role in the clearance of misfolded or unassembled glycoproteins through a process named ER-associated degradation (ERAD). Accumulating evidence also points out that NGLY1 deficiency can cause an autosomal recessive (AR) human genetic disorder associated with abnormal development and congenital disorder of deglycosylation. In addition, the loss of NGLY1 can affect multiple cellular pathways, including but not limited to NFE2L1 pathway, Creb1/Atf1-AQP pathway, BMP pathway, AMPK pathway, and SLC12A2 ion transporter, which might be the underlying reasons for a constellation of clinical phenotypes of NGLY1 deficiency. The current comprehensive review uncovers the NGLY1’ssdetailed structure and its important roles for participation in ERAD, involvement in CDDG and potential treatment for NGLY1 deficiency.
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Affiliation(s)
- Xiangguang Miao
- Queen Mary School, Nanchang University, No. 1299 Xuefu Avenue, Honggutan New District, Nanchang 330036, China;
| | - Jin Wu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People’s Hospital, No. 173 First Section of Taishanbei Road, Jingyang District, Deyang 618000, China;
- Deyang Key Laboratory of Tumor Molecular Research, No. 173 First Section of Taishanbei Road, Jingyang District, Deyang 618000, China
- Department of Molecular & Cellular Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Hongping Chen
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang 330006, China
- Correspondence: (H.C.); (G.L.); Tel.: +86-188-0147-4087 (G.L.)
| | - Guanting Lu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People’s Hospital, No. 173 First Section of Taishanbei Road, Jingyang District, Deyang 618000, China;
- Deyang Key Laboratory of Tumor Molecular Research, No. 173 First Section of Taishanbei Road, Jingyang District, Deyang 618000, China
- Correspondence: (H.C.); (G.L.); Tel.: +86-188-0147-4087 (G.L.)
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31
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Pandey A, Adams JM, Han SY, Jafar-Nejad H. NGLY1 Deficiency, a Congenital Disorder of Deglycosylation: From Disease Gene Function to Pathophysiology. Cells 2022; 11:1155. [PMID: 35406718 DOI: 10.3390/cells11071155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 02/01/2023] Open
Abstract
N-Glycanase 1 (NGLY1) is a cytosolic enzyme involved in removing N-linked glycans of misfolded N-glycoproteins and is considered to be a component of endoplasmic reticulum-associated degradation (ERAD). The 2012 identification of recessive NGLY1 mutations in a rare multisystem disorder has led to intense research efforts on the roles of NGLY1 in animal development and physiology, as well as the pathophysiology of NGLY1 deficiency. Here, we present a review of the NGLY1-deficient patient phenotypes, along with insights into the function of this gene from studies in rodent and invertebrate animal models, as well as cell culture and biochemical experiments. We will discuss critical processes affected by the loss of NGLY1, including proteasome bounce-back response, mitochondrial function and homeostasis, and bone morphogenetic protein (BMP) signaling. We will also cover the biologically relevant targets of NGLY1 and the genetic modifiers of NGLY1 deficiency phenotypes in animal models. Together, these discoveries and disease models have provided a number of avenues for preclinical testing of potential therapeutic approaches for this disease.
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Lin VJT, Hu J, Zolekar A, Salick MR, Mittal P, Bird JT, Hoffmann P, Kaykas A, Byrum SD, Wang Y. Deficiency of N-glycanase 1 perturbs neurogenesis and cerebral development modeled by human organoids. Cell Death Dis 2022; 13:262. [PMID: 35322011 PMCID: PMC8942998 DOI: 10.1038/s41419-022-04693-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 12/23/2022]
Abstract
AbstractMutations in N-glycanase 1 (NGLY1), which deglycosylates misfolded glycoproteins for degradation, can cause NGLY1 deficiency in patients and their abnormal fetal development in multiple organs, including microcephaly and other neurological disorders. Using cerebral organoids (COs) developed from human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs), we investigate how NGLY1 dysfunction disturbs early brain development. While NGLY1 loss had limited impact on the undifferentiated cells, COs developed from NGLY1-deficient hESCs showed defective formation of SATB2-positive upper-layer neurons, and attenuation of STAT3 and HES1 signaling critical for sustaining radial glia. Bulk and single-cell transcriptomic analysis revealed premature neuronal differentiation accompanied by downregulation of secreted and transcription factors, including TTR, IGFBP2, and ID4 in NGLY1-deficient COs. NGLY1 malfunction also dysregulated ID4 and enhanced neuronal differentiation in CO transplants developed in vivo. NGLY1-deficient CO cells were more vulnerable to multiple stressors; treating the deficient cells with recombinant TTR reduced their susceptibility to stress from proteasome inactivation, likely through LRP2-mediated activation of MAPK signaling. Expressing NGLY1 led to IGFBP2 and ID4 upregulation in CO cells developed from NGLY1-deficiency patient’s hiPSCs. In addition, treatment with recombinant IGFBP2 enhanced ID4 expression, STAT3 signaling, and proliferation of NGLY1-deficient CO cells. Overall, our discoveries suggest that dysregulation of stress responses and neural precursor differentiation underlies the brain abnormalities observed in NGLY1-deficient individuals.
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Alkelai A, Greenbaum L, Docherty AR, Shabalin AA, Povysil G, Malakar A, Hughes D, Delaney SL, Peabody EP, McNamara J, Gelfman S, Baugh EH, Zoghbi AW, Harms MB, Hwang HS, Grossman-Jonish A, Aggarwal V, Heinzen EL, Jobanputra V, Pulver AE, Lerer B, Goldstein DB. The benefit of diagnostic whole genome sequencing in schizophrenia and other psychotic disorders. Mol Psychiatry 2022; 27:1435-1447. [PMID: 34799694 DOI: 10.1038/s41380-021-01383-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 01/04/2023]
Abstract
Schizophrenia has a multifactorial etiology, involving a polygenic architecture. The potential benefit of whole genome sequencing (WGS) in schizophrenia and other psychotic disorders is not well studied. We investigated the yield of clinical WGS analysis in 251 families with a proband diagnosed with schizophrenia (N = 190), schizoaffective disorder (N = 49), or other conditions involving psychosis (N = 48). Participants were recruited in Israel and USA, mainly of Jewish, Arab, and other European ancestries. Trio (parents and proband) WGS was performed for 228 families (90.8%); in the other families, WGS included parents and at least two affected siblings. In the secondary analyses, we evaluated the contribution of rare variant enrichment in particular gene sets, and calculated polygenic risk score (PRS) for schizophrenia. For the primary outcome, diagnostic rate was 6.4%; we found clinically significant, single nucleotide variants (SNVs) or small insertions or deletions (indels) in 14 probands (5.6%), and copy number variants (CNVs) in 2 (0.8%). Significant enrichment of rare loss-of-function variants was observed in a gene set of top schizophrenia candidate genes in affected individuals, compared with population controls (N = 6,840). The PRS for schizophrenia was significantly increased in the affected individuals group, compared to their unaffected relatives. Last, we were also able to provide pharmacogenomics information based on CYP2D6 genotype data for most participants, and determine their antipsychotic metabolizer status. In conclusion, our findings suggest that WGS may have a role in the setting of both research and genetic counseling for individuals with schizophrenia and other psychotic disorders and their families.
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Affiliation(s)
- Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA.
| | - Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anna R Docherty
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Andrey A Shabalin
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Ayan Malakar
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Daniel Hughes
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Shannon L Delaney
- New York State Psychiatric Institute, Columbia University, New York City, NY, USA
| | - Emma P Peabody
- Psychology Research Laboratory, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - James McNamara
- Psychology Research Laboratory, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Sahar Gelfman
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Evan H Baugh
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Anthony W Zoghbi
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- New York State Psychiatric Institute, Columbia University, New York City, NY, USA
- New York State Psychiatric Institute, Office of Mental Health, New York, NY, USA
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew B Harms
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY, USA
| | - Hann-Shyan Hwang
- Department of Medicine, National Taiwan University School of Medicine, Taipei, Taiwan
| | - Anat Grossman-Jonish
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Vimla Aggarwal
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Erin L Heinzen
- Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vaidehi Jobanputra
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Ann E Pulver
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bernard Lerer
- Biological Psychiatry Laboratory, Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
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McConkie-Rosell A, Schoch K, Sullivan J, Spillmann RC, Cope H, Tan QKG, Palmer CGS, Hooper SR, Shashi V. Clinical application of a scale to assess genomic healthcare empowerment (GEmS): Process and illustrative case examples. J Genet Couns 2022; 31:59-70. [PMID: 34115423 PMCID: PMC8664895 DOI: 10.1002/jgc4.1451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 05/04/2021] [Accepted: 05/09/2021] [Indexed: 02/03/2023]
Abstract
The Genome Empowerment Scale (GEmS), developed as a research tool, assesses perspectives of parents of children with undiagnosed disorders about to undergo exome or genome sequencing related to the process of empowerment. We defined genomic healthcare empowerment as follows: perceived ability to understand and seek new information related to the genomic sequencing, manage emotions related to the diagnostic process and outcomes, and utilize genomic sequencing information to the betterment of the individual/child and family. The GEmS consists of four scales, two are primarily emotion-focused (Meaning of a Diagnosis, and Emotional Management of the Process) and two are action-oriented (Seeking Information and Support, and Implications and Planning). The purpose of this research was to provide a strategy for interpreting results from the GEmS and present illustrative cases. These illustrations should serve to facilitate use of the GEmS in the clinical and research arena, particularly with respect to guiding genetic counseling processes for parents of children with undiagnosed conditions.
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Affiliation(s)
- Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Jennifer Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Rebecca C. Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Heidi Cope
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Queenie K.-G. Tan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Christina G. S. Palmer
- Department of Psychiatry and Biobehavioral Sciences, Department of Human Genetics, Institute for Society and Genetics, UCLA, Los Angeles, CA, USA
| | | | - Stephen R. Hooper
- Department of Allied Health Sciences, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
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李 晓, 洪 梦, 戴 朴, 袁 永. [Clinical case analysis and literature review of mandibulofacial dysostosis with microcephaly syndrome]. Lin Chuang Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2022; 36:36-40. [PMID: 34979617 PMCID: PMC10128212 DOI: 10.13201/j.issn.2096-7993.2022.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Indexed: 06/14/2023]
Abstract
Objective:To explore the clinical diagnosis, otological treatment and molecular etiology in a rare syndromic hearing loss case characterized by mandibulofacial dysostosis with microcephaly(MFDM). Methods: The proband underwent detailed history collection, systematic physical examination and phenotypic analysis, as well as audiological examination, chest X-ray, temporal bone CT and brain MRI and other imaging examinations. The blood DNA of the proband and his parents was extracted and tested by the whole exom sequencing. The EFTUD2-related-MFDM literatures published by the end of 2020 were searched and sifted in PubMed and CNKI databases,the clinical characteristics of MFDM were summarized. Results:In this study, the patient presented with hypoplasia of auricle, micrognathia, microcephaly, developmental retardation, severe sensorineural hearing loss in both ears, and developmental malformation of middle and inner ear. Genetic analysis revealed a de novo deletion c.623_624delAT in EFTUD2 gene. According to the clinical features and genetic test results, the patient was diagnosed as MFDM. In order to solve the problem of hearing loss, the patient was further performed bilateral cochlear implantation, and part of the electrodes responded well during and after operation. Conclusion:This is the first domestic reported case of MFDM caused by EFTUD2 gene mutation. The key problem of cochlear implantation for this kind of patient is to avoid damaging the malformed facial nerve during the operation.The effect of speech rehabilitation after cochlear implant operation is related to many factors such as intelligence development of the patients.
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Affiliation(s)
- 晓雨 李
- 国家耳鼻咽喉疾病临床医学研究中心 解放军总医院第六医学中心耳鼻咽喉头颈外科医学部 解放军总医院第六医学中心耳显微外科(北京,100048)National Clinical Research Center for Otolaryngologic Diseases, College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Department of Otomicrosurgery, Sixth Medical Center of the PLA General Hospital, Beijing, 100048, China
| | - 梦迪 洪
- 解放军总医院第一医学中心耳鼻咽喉头颈外科听觉植入中心Auditory Implant Center, Department of Otolaryngology Head and Neck Surgery, First Medical Center of the PLA General Hospital
| | - 朴 戴
- 国家耳鼻咽喉疾病临床医学研究中心 解放军总医院第六医学中心耳鼻咽喉头颈外科医学部 解放军总医院第六医学中心耳显微外科(北京,100048)National Clinical Research Center for Otolaryngologic Diseases, College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Department of Otomicrosurgery, Sixth Medical Center of the PLA General Hospital, Beijing, 100048, China
| | - 永一 袁
- 国家耳鼻咽喉疾病临床医学研究中心 解放军总医院第六医学中心耳鼻咽喉头颈外科医学部 解放军总医院第六医学中心耳显微外科(北京,100048)National Clinical Research Center for Otolaryngologic Diseases, College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Department of Otomicrosurgery, Sixth Medical Center of the PLA General Hospital, Beijing, 100048, China
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Athanasopoulou K, Boti MA, Adamopoulos PG, Skourou PC, Scorilas A. Third-Generation Sequencing: The Spearhead towards the Radical Transformation of Modern Genomics. Life (Basel) 2021; 12:life12010030. [PMID: 35054423 PMCID: PMC8780579 DOI: 10.3390/life12010030] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022] Open
Abstract
Although next-generation sequencing (NGS) technology revolutionized sequencing, offering a tremendous sequencing capacity with groundbreaking depth and accuracy, it continues to demonstrate serious limitations. In the early 2010s, the introduction of a novel set of sequencing methodologies, presented by two platforms, Pacific Biosciences (PacBio) and Oxford Nanopore Sequencing (ONT), gave birth to third-generation sequencing (TGS). The innovative long-read technologies turn genome sequencing into an ease-of-handle procedure by greatly reducing the average time of library construction workflows and simplifying the process of de novo genome assembly due to the generation of long reads. Long sequencing reads produced by both TGS methodologies have already facilitated the decipherment of transcriptional profiling since they enable the identification of full-length transcripts without the need for assembly or the use of sophisticated bioinformatics tools. Long-read technologies have also provided new insights into the field of epitranscriptomics, by allowing the direct detection of RNA modifications on native RNA molecules. This review highlights the advantageous features of the newly introduced TGS technologies, discusses their limitations and provides an in-depth comparison regarding their scientific background and available protocols as well as their potential utility in research and clinical applications.
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Rauscher B, Mueller WF, Clauder-Münster S, Jakob P, Islam MS, Sun H, Ghidelli-Disse S, Boesche M, Bantscheff M, Pflaumer H, Collier P, Haase B, Chen S, Hoffman R, Wang G, Benes V, Drewes G, Snyder M, Steinmetz LM. Patient-derived gene and protein expression signatures of NGLY1 deficiency. J Biochem 2021; 171:187-199. [PMID: 34878535 DOI: 10.1093/jb/mvab131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/13/2021] [Indexed: 11/14/2022] Open
Abstract
N-Glycanase 1 (NGLY1) deficiency is a rare and complex genetic disorder. Although recent studies have shed light on the molecular underpinnings of NGLY1 deficiency, a systematic characterization of gene and protein expression changes in patient-derived cells has been lacking. Here, we performed RNA-sequencing and mass spectrometry to determine the transcriptomes and proteomes of 66 cell lines representing 4 different cell types derived from 14 NGLY1 deficient patients and 17 controls. Although NGLY1 protein levels were up to 9.5-fold downregulated in patients compared to parents, residual and likely non-functional NGLY1 protein was detectable in all patient-derived lymphoblastoid cell lines. Consistent with the role of NGLY1 as a regulator of the transcription factor Nrf1, we observed a cell type-independent downregulation of proteasomal genes in NGLY1 deficient cells. In contrast, genes involved in ribosome biogenesis and mRNA processing were upregulated in multiple cell types. In addition, we observed cell type-specific effects. For example, genes and proteins involved in glutathione synthesis, such as the glutamate-cysteine ligase subunits GCLC and GCLM, were downregulated specifically in lymphoblastoid cells. We provide a web application that enables access to all results generated in this study at https://apps.embl.de/ngly1browser. This resource will guide future studies of NGLY1 deficiency in directions that are most relevant to patients.
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Affiliation(s)
- Benedikt Rauscher
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | | | - Sandra Clauder-Münster
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Petra Jakob
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - M Saiful Islam
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Han Sun
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Sonja Ghidelli-Disse
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Markus Boesche
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Marcus Bantscheff
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Hannah Pflaumer
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Paul Collier
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Bettina Haase
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Songjie Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Rene Hoffman
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Guangwen Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Vladimir Benes
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Gerard Drewes
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Lars M Steinmetz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
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Stuut T, Popescu O, Oviedo A. N-Glycanase 1 Deficiency Is a Rare Cause of Pediatric Neurodegeneration With Neuronal Inclusions and Liver Steatosis. Cureus 2021; 13:e19126. [PMID: 34858763 PMCID: PMC8614178 DOI: 10.7759/cureus.19126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2021] [Indexed: 11/05/2022] Open
Abstract
Pediatric neurodegeneration is extremely rare and devastating to the families involved. We describe a rare case of pediatric neurodegeneration in a child with N-glycanase 1 (NGLY1) deficiency. This child had an autosomal recessive mutation in NGLY1, the gene coding for the enzyme NGLY1 that was found with exome sequencing. NGLY1 catalyzes protein deglycosylation by cleaving the -aspartyl glycosylamine bond of N-linked glycoproteins and is thereby a component of the endoplasmic reticulum-associated degradation pathway. This child passed away at five years of age after a prolonged clinical course with myoclonic epilepsy, choreoathetosis-like movements, lacrimal duct problems, and severe developmental delay. This autopsy case report shows images of the neuronal inclusions and liver steatosis found in this patient with NGLY1 deficiency and offers a detailed clinical history.
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Affiliation(s)
- Thomas Stuut
- Family Medicine, Central Michigan University College of Medicine, Mount Pleasant, USA
| | - Oana Popescu
- Pathology and Laboratory Medicine, Vernon Jubilee Hospital, Vernon, CAN
| | - Angelica Oviedo
- Pathology and Laboratory Medicine, Burrell College of Osteopathic Medicine, Las Cruces, USA
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Abstract
Whole exome sequences have now been collected for millions of humans, with the related goals of identifying pathogenic mutations in patients and establishing reference repositories of data from unaffected individuals. As a result, we are approaching an important limit, in which datasets are large enough that, in the absence of natural selection, every highly mutable site will have experienced at least one mutation in the genealogical history of the sample. Here, we focus on CpG sites that are methylated in the germline and experience mutations to T at an elevated rate of ~10-7 per site per generation; considering synonymous mutations in a sample of 390,000 individuals, ~ 99 % of such CpG sites harbor a C/T polymorphism. Methylated CpG sites provide a natural mutation saturation experiment for fitness effects: as we show, at nt sample sizes, not seeing a non-synonymous polymorphism is indicative of strong selection against that mutation. We rely on this idea in order to directly identify a subset of CpG transitions that are likely to be highly deleterious, including ~27 % of possible loss-of-function mutations, and up to 20 % of possible missense mutations, depending on the type of functional site in which they occur. Unlike methylated CpGs, most mutation types, with rates on the order of 10-8 or 10-9, remain very far from saturation. We discuss what these findings imply for interpreting the potential clinical relevance of mutations from their presence or absence in reference databases and for inferences about the fitness effects of new mutations.
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Affiliation(s)
- Ipsita Agarwal
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Molly Przeworski
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
- Department of Systems Biology, Columbia UniversityNew YorkUnited States
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Hirayama H, Suzuki T. Assay for the peptide:N-glycanase/NGLY1 and disease-specific biomarkers for diagnosing NGLY1 deficiency. J Biochem 2021; 171:169-176. [PMID: 34791337 DOI: 10.1093/jb/mvab127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/11/2021] [Indexed: 11/13/2022] Open
Abstract
Cytosolic peptide:N-glycanase (NGLY1 in mammals), a highly conserved enzyme in eukaryotes, catalyzes the deglycosylation of N-glycans that are attached to glycopeptide/glycoproteins. In 2012, an autosomal recessive disorder related to the NGLY1 gene, which was referred to as NGLY1 deficiency, was reported. Since then, more than 100 patients have been identified. Patients with this disease exhibit various symptoms, including various motor deficits and other neurological problems. Effective therapeutic treatments for this disease, however, have not been established. Most recently, it was demonstrated that the intracerebroventricular administration of an adeno-associated virus 9 vector expressing human NGLY1 during the weaning period allowed some motor functions to be recovered in Ngly1-/- rats. This observation led us to hypothesize that a therapeutic intervention for improving these motor deficits or other neurological symptoms found in the patients might be possible. To achieve this, it is critical to establish robust and facile methods for assaying NGLY1 activity in biological samples, for the early diagnosis and evaluation of the therapeutic efficacy for the treatment of NGLY1 deficiency. In this mini-review, we summarize progress made in the development of various assay methods for NGLY1 activity, as well as a recent progress in the identification of NGLY1 deficiency-specific biomarkers.
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Affiliation(s)
- Hiroto Hirayama
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Japan.,Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Japan.,Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan
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Hirayama H, Tachida Y, Seino J, Suzuki T. A method for assaying peptide: N-glycanase/N-Glycanase 1 activities in crude extracts using an N-glycosylated cyclopeptide. Glycobiology 2021; 32:110-122. [PMID: 34939090 PMCID: PMC8934141 DOI: 10.1093/glycob/cwab115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/09/2021] [Accepted: 10/31/2021] [Indexed: 11/13/2022] Open
Abstract
Cytosolic peptide: N-glycanase (PNGase; NGLY1), an enzyme responsible for de-glycosylation of N-glycans on glycoproteins, is known to play pivotal roles in a variety of biological processes. In 2012, NGLY1 deficiency, a rare genetic disorder, was reported and since then, more than 100 patients have now been identified worldwide. Patients with this disease exhibit several common symptoms that are caused by the dysfunction of NGLY1. However, correlation between the severity of patient symptoms and the extent of the reduction in NGLY1 activity in these patients remains to be clarified, mainly due to the absence of a facile quantitative assay system for this enzyme, especially in a crude extract as an enzyme source. In this study, a quantitative, non-radioisotope (RI)-based assay method for measuring recombinant NGLY1 activity was established using a BODIPY-labeled asialoglycopeptide (BODIPY-ASGP) derived from hen eggs. With this assay, the activities of 27 recombinant NGLY1 mutants that are associated with the deficiency were examined. It was found that the activities of 3 (R469X, R458fs, and H494fs) out of the 27 recombinant mutant proteins were 30-70 percent of the activities of wild-type NGLY1. We further developed a method for measuring endogenous NGLY1 activity in crude extracts derived from cultured cells, patients' fibroblasts, iPS cells or peripheral blood mononuclear cells (PBMCs), using a glycosylated cyclopeptide (GCP) that exhibited resistance to the endogenous proteases in the extract. Our methods will not only provide new insights into the molecular mechanism responsible for this disease but also promises to be applicable for its diagnosis.
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Affiliation(s)
- Hiroto Hirayama
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, Japan.,Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan
| | - Yuriko Tachida
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, Japan.,Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan
| | - Junichi Seino
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, Japan
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, Japan.,Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan
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42
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Abstract
Peptide:N-glycanase is an evolutionarily conserved deglycosylating enzyme that catalyzes the removal of N-linked glycans from cytosolic glycoproteins. Recessive mutations that inactivate this enzyme cause NGLY1 deficiency, a multisystemic disorder with symptoms including developmental delay and defects in cognition and motor control. Developing treatments for NGLY1 deficiency will require an understanding of how failure to deglycosylate NGLY1 substrates perturbs cellular and organismal function. In this review, I highlight insights into peptide:N-glycanase biology gained by studies in the highly tractable genetic model animal C. elegans. I focus on the recent discovery of SKN-1A/Nrf1, an N-glycosylated transcription factor, as a peptide:N-glycanase substrate critical for regulation of the proteasome. I describe the elaborate post-translational mechanism that culminates in activation of SKN-1A/Nrf1 via NGLY1-dependent 'sequence editing' and discuss the implications of these findings for our understanding of NGLY1 deficiency.
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43
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Fujihira H, Asahina M, Suzuki T. Physiological importance of NGLY1, as revealed by rodent model analyses. J Biochem 2021; 171:161-167. [PMID: 34580715 DOI: 10.1093/jb/mvab101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/01/2021] [Indexed: 12/29/2022] Open
Abstract
Cytosolic peptide:N-glycanase (NGLY1) is an enzyme that cleaves N-glycans from glycoproteins that has been retrotranslocated from the endoplasmic reticulum (ER) lumen into the cytosol. It is known that NGLY1 is involved in the degradation of cytosolic glycans (non-lysosomal glycan degradation) as well as ER-associated degradation (ERAD), a quality control system for newly synthesized glycoproteins. The discovery of NGLY1 deficiency, which is caused by mutations in the human NGLY1 gene and results in multisystemic symptoms, has attracted interest in the physiological functions of NGLY1 in mammals. Studies using various animal models led to the identification of possible factors that contribute to the pathogenesis of NGLY1 deficiency. In this review, we summarize phenotypic consequences that have been reported for various Ngly1-deficient rodent models, and discuss future perspectives to provide more insights into the physiological functions of NGLY1.
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Affiliation(s)
- Haruhiko Fujihira
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, 3510198 Saitama, Japan.,Division of Glycobiologics, Intractable Disease Research Center, Juntendo University Graduate School of Medicine, 1138421 Tokyo, Japan
| | - Makoto Asahina
- T-CiRA Discovery, Takeda Pharmaceutical Company Ltd, 2518555 Kanagawa, Japan
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, 3510198 Saitama, Japan.,T-CiRA Discovery, Takeda Pharmaceutical Company Ltd, 2518555 Kanagawa, Japan
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44
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Asahina M, Fujinawa R, Nakamura S, Yokoyama K, Tozawa R, Suzuki T. Ngly1 -/- rats develop neurodegenerative phenotypes and pathological abnormalities in their peripheral and central nervous systems. Hum Mol Genet 2021; 29:1635-1647. [PMID: 32259258 PMCID: PMC7322575 DOI: 10.1093/hmg/ddaa059] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/10/2020] [Accepted: 03/30/2020] [Indexed: 12/13/2022] Open
Abstract
N-glycanase 1 (NGLY1) deficiency, an autosomal recessive disease caused by mutations in the NGLY1 gene, is characterized by developmental delay, hypolacrima or alacrima, seizure, intellectual disability, movement disorders and other neurological phenotypes. Because of few animal models that recapitulate these clinical signatures, the mechanisms of the onset of the disease and its progression are poorly understood, and the development of therapies is hindered. In this study, we generated the systemic Ngly1-deficient rodent model, Ngly1−/− rats, which showed developmental delay, movement disorder, somatosensory impairment and scoliosis. These phenotypes in Ngly1−/− rats are consistent with symptoms in human patients. In accordance with the pivotal role played by NGLY1 in endoplasmic reticulum-associated degradation processes, cleaving N-glycans from misfolded glycoproteins in the cytosol before they can be degraded by the proteasome, loss of Ngly1 led to accumulation of cytoplasmic ubiquitinated proteins, a marker of misfolded proteins in the neurons of the central nervous system of Ngly1−/− rats. Histological analysis identified prominent pathological abnormalities, including necrotic lesions, mineralization, intra- and extracellular eosinophilic bodies, astrogliosis, microgliosis and significant loss of mature neurons in the thalamic lateral and the medial parts of the ventral posterior nucleus and ventral lateral nucleus of Ngly1−/− rats. Axonal degradation in the sciatic nerves was also observed, as in human subjects. Ngly1−/− rats, which mimic the symptoms of human patients, will be a useful animal model for preclinical testing of therapeutic options and understanding the detailed mechanisms of NGLY1 deficiency.
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Affiliation(s)
- Makoto Asahina
- Takeda-CiRA Joint Program (T-CiRA), Kanagawa 2518555, Japan.,T-CiRA Discovery, Takeda Pharmaceutical Company Ltd., Kanagawa 2518555, Japan
| | - Reiko Fujinawa
- Takeda-CiRA Joint Program (T-CiRA), Kanagawa 2518555, Japan.,Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 3510198, Japan
| | - Sayuri Nakamura
- Nonclinical Safety Research, Axcelead Drug Discovery Partners Inc., Kanagawa 2510012, Japan
| | - Kotaro Yokoyama
- Nonclinical Safety Research, Axcelead Drug Discovery Partners Inc., Kanagawa 2510012, Japan
| | - Ryuichi Tozawa
- Takeda-CiRA Joint Program (T-CiRA), Kanagawa 2518555, Japan.,T-CiRA Discovery, Takeda Pharmaceutical Company Ltd., Kanagawa 2518555, Japan
| | - Tadashi Suzuki
- Takeda-CiRA Joint Program (T-CiRA), Kanagawa 2518555, Japan.,Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 3510198, Japan
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45
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Akgün M, Ünal AB, Ergüner B, Pfeifer N, Kohlbacher O. Identifying disease-causing mutations with privacy protection. Bioinformatics 2021; 36:5205-5213. [PMID: 32683440 PMCID: PMC7850099 DOI: 10.1093/bioinformatics/btaa641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 06/16/2020] [Accepted: 07/13/2020] [Indexed: 12/14/2022] Open
Abstract
Motivation The use of genome data for diagnosis and treatment is becoming increasingly common. Researchers need access to as many genomes as possible to interpret the patient genome, to obtain some statistical patterns and to reveal disease–gene relationships. The sensitive information contained in the genome data and the high risk of re-identification increase the privacy and security concerns associated with sharing such data. In this article, we present an approach to identify disease-associated variants and genes while ensuring patient privacy. The proposed method uses secure multi-party computation to find disease-causing mutations under specific inheritance models without sacrificing the privacy of individuals. It discloses only variants or genes obtained as a result of the analysis. Thus, the vast majority of patient data can be kept private. Results Our prototype implementation performs analyses on thousands of genomic data in milliseconds, and the runtime scales logarithmically with the number of patients. We present the first inheritance model (recessive, dominant and compound heterozygous) based privacy-preserving analyses of genomic data to find disease-causing mutations. Furthermore, we re-implement the privacy-preserving methods (MAX, SETDIFF and INTERSECTION) proposed in a previous study. Our MAX, SETDIFF and INTERSECTION implementations are 2.5, 1122 and 341 times faster than the corresponding operations of the state-of-the-art protocol, respectively. Availability and implementation https://gitlab.com/DIFUTURE/privacy-preserving-genomic-diagnosis. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mete Akgün
- Translational Bioinformatics, University Hospital Tübingen, Tübingen 72026, Germany.,Methods in Medical Informatics, Dept. of Computer Science, University of Tübingen, Tübingen 72026, Germany
| | - Ali Burak Ünal
- Methods in Medical Informatics, Dept. of Computer Science, University of Tübingen, Tübingen 72026, Germany
| | - Bekir Ergüner
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Nico Pfeifer
- Methods in Medical Informatics, Dept. of Computer Science, University of Tübingen, Tübingen 72026, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen 72026, Germany.,Statistical Learning in Computational Biology, Max Planck Institute for Informatics, Saarbrücken 66123, Germany
| | - Oliver Kohlbacher
- Translational Bioinformatics, University Hospital Tübingen, Tübingen 72026, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen 72026, Germany.,Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Tübingen 72026, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen 72026, Germany
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Abstract
Although nearly 10% of Americans suffer from a rare disease, clinical progress in individual rare diseases is severely compromised by lack of attention and research resources compared to common diseases. It is thus imperative to investigate these diseases at their most basic level to build a foundation and provide the opportunity for understanding their mechanisms and phenotypes, as well as potential treatments. One strategy for effectively and efficiently studying rare diseases is using genetically tractable organisms to model the disease and learn about the essential cellular processes affected. Beyond investigating dysfunctional cellular processes, modeling rare diseases in simple organisms presents the opportunity to screen for pharmacological or genetic factors capable of ameliorating disease phenotypes. Among the small model organisms that excel in rare disease modeling is the nematode Caenorhabditis elegans. With a staggering breadth of research tools, C. elegans provides an ideal system in which to study human disease. Molecular and cellular processes can be easily elucidated, assayed and altered in ways that can be directly translated to humans. When paired with other model organisms and collaborative efforts with clinicians, the power of these C. elegans studies cannot be overstated. This Review highlights studies that have used C. elegans in diverse ways to understand rare diseases and aid in the development of treatments. With continuing and advancing technologies, the capabilities of this small round worm will continue to yield meaningful and clinically relevant information for human health.
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Affiliation(s)
| | | | | | | | - Andy Golden
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Pandey A, Jafar-Nejad H. Tracing the NGLY1 footprints: Insights from Drosophila. J Biochem 2021; 171:153-160. [PMID: 34270726 DOI: 10.1093/jb/mvab084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/11/2021] [Indexed: 02/03/2023] Open
Abstract
Recessive mutations in human N-glycanase 1 (NGLY1) cause a multisystem disorder with various phenotypes including global developmental delay. One of the models utilized to understand the biology of NGLY1 and the pathophysiology of NGLY1 deficiency is Drosophila melanogaster, a well-established, genetically tractable organism broadly used to study various biological processes and human diseases. Loss of the Drosophila NGLY1 homolog (Pngl) causes a host of phenotypes including developmental delay and lethality. Phenotypic, transcriptomic and genome-wide association analyses on Drosophila have revealed links between NGLY1 and several critical developmental and cellular pathways/processes. Further, repurposing screens of FDA-approved drugs have identified potential candidates to ameliorate some of the Pngl mutant phenotypes. Here, we will summarize the insights gained into the functions of NGLY1 from Drosophila studies. We hope that the current review article will encourage additional studies in Drosophila and other model systems towards establishing a therapeutic strategy for NGLY1 deficiency patients.
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Affiliation(s)
- Ashutosh Pandey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, United States of America
| | - Hamed Jafar-Nejad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, United States of America.,Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA.,Genetics & Genomics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
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48
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Kawame H, Fukushima A, Fuse N, Nagami F, Suzuki Y, Sakurai-Yageta M, Yasuda J, Yamaguchi-Kabata Y, Kinoshita K, Ogishima S, Takai T, Kuriyama S, Hozawa A, Nakaya N, Nakamura T, Minegishi N, Sugawara J, Suzuki K, Tomita H, Uruno A, Kobayashi T, Aizawa Y, Tokutomi T, Yamamoto K, Ohneda K, Kure S, Aoki Y, Katagiri H, Ishigaki Y, Sawada S, Sasaki M, Yamamoto M. The return of individual genomic results to research participants: design and pilot study of Tohoku Medical Megabank Project. J Hum Genet 2021; 67:9-17. [PMID: 34234266 DOI: 10.1038/s10038-021-00952-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/08/2021] [Accepted: 06/14/2021] [Indexed: 12/21/2022]
Abstract
Certain large genome cohort studies attempt to return the individual genomic results to the participants; however, the implementation process and psychosocial impacts remain largely unknown. The Tohoku Medical Megabank Project has conducted large genome cohort studies of general residents. To implement the disclosure of individual genomic results, we extracted the potential challenges and obstacles. Major challenges include the determination of genes/disorders based on the current medical system in Japan, the storage of results, prevention of misunderstanding, and collaboration of medical professionals. To overcome these challenges, we plan to conduct multilayer pilot studies, which deal with different disorders/genes. We finally chose familial hypercholesterolemia (FH) as a target disease for the first pilot study. Of the 665 eligible candidates, 33.5% were interested in the pilot study and provided consent after an educational "genetics workshop" on the basic genetics and medical facts of FH. The genetics professionals disclosed the results to the participants. All positive participants were referred to medical care, and a serial questionnaire revealed no significant psychosocial distress after the disclosure. Return of genomic results to research participants was implemented using a well-prepared protocol. To further elucidate the impact of different disorders, we will perform multilayer pilot studies with different disorders, including actionable pharmacogenomics and hereditary tumor syndromes.
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Affiliation(s)
- Hiroshi Kawame
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan.
| | - Akimune Fukushima
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Yoichi Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | | | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | | | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Takako Takai
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Naoki Nakaya
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Tomohiro Nakamura
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Junichi Sugawara
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Kichiya Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Hiroaki Tomita
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Akira Uruno
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Tomoko Kobayashi
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Yayoi Aizawa
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Tomoharu Tokutomi
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Kayono Yamamoto
- Department of Clinical Genetics, Iwate Medical University, Iwate, Japan
| | - Kinuko Ohneda
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan.
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Hideki Katagiri
- Department of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yasushi Ishigaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Shojiro Sawada
- Department of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan.
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49
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Asahina M, Fujinawa R, Hirayama H, Tozawa R, Kajii Y, Suzuki T. Reversibility of motor dysfunction in the rat model of NGLY1 deficiency. Mol Brain 2021; 14:91. [PMID: 34120625 PMCID: PMC8201687 DOI: 10.1186/s13041-021-00806-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/07/2021] [Indexed: 12/26/2022] Open
Abstract
N-glycanase 1 (NGLY1) deficiency is a rare inherited disorder characterized by developmental delay, hypolacrima or alacrima, seizure, intellectual disability, motor deficits, and other neurological symptoms. The underlying mechanisms of the NGLY1 phenotype are poorly understood, and no effective therapy is currently available. Similar to human patients, the rat model of NGLY1 deficiency, Ngly1-/-, shows developmental delay, movement disorder, somatosensory impairment, scoliosis, and learning disability. Here we show that single intracerebroventricular administration of AAV9 expressing human NGLY1 cDNA (AAV9-hNGLY1) to Ngly1-/- rats during the weaning period restored NGLY1 expression in the brain and spinal cord, concomitant with increased enzymatic activity of NGLY1 in the brain. hNGLY1 protein expressed by AAV9 was found predominantly in mature neurons, but not in glial cells, of Ngly1-/- rats. Strikingly, intracerebroventricular administration of AAV9-hNGLY1 normalized the motor phenotypes of Ngly1-/- rats assessed by the rota-rod test and gait analysis. The reversibility of motor deficits in Ngly1-/- rats by central nervous system (CNS)-restricted gene delivery suggests that the CNS is the primary therapeutic target organs for NGLY1 deficiency, and that the Ngly1-/- rat model may be useful for evaluating therapeutic treatments in pre-clinical studies.
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Affiliation(s)
- Makoto Asahina
- T-CiRA Discovery, Takeda Pharmaceutical Company Ltd., Fujisawa, Kanagawa, 2518555, Japan
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, 2518555, Japan
| | - Reiko Fujinawa
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, 2518555, Japan
| | - Hiroto Hirayama
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, 2518555, Japan
| | - Ryuichi Tozawa
- T-CiRA Discovery, Takeda Pharmaceutical Company Ltd., Fujisawa, Kanagawa, 2518555, Japan
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, 2518555, Japan
| | - Yasushi Kajii
- T-CiRA Discovery, Takeda Pharmaceutical Company Ltd., Fujisawa, Kanagawa, 2518555, Japan
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa, 2518555, Japan.
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50
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Edwards NA, Shacham-Silverberg V, Weitz L, Kingma PS, Shen Y, Wells JM, Chung WK, Zorn AM. Developmental basis of trachea-esophageal birth defects. Dev Biol 2021; 477:85-97. [PMID: 34023332 DOI: 10.1016/j.ydbio.2021.05.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/13/2021] [Accepted: 05/16/2021] [Indexed: 02/07/2023]
Abstract
Trachea-esophageal defects (TEDs), including esophageal atresia (EA), tracheoesophageal fistula (TEF), and laryngeal-tracheoesophageal clefts (LTEC), are a spectrum of life-threatening congenital anomalies in which the trachea and esophagus do not form properly. Up until recently, the developmental basis of these conditions and how the trachea and esophagus arise from a common fetal foregut was poorly understood. However, with significant advances in human genetics, organoids, and animal models, and integrating single cell genomics with high resolution imaging, we are revealing the molecular and cellular mechanisms that orchestrate tracheoesophageal morphogenesis and how disruption in these processes leads to birth defects. Here we review the current understanding of the genetic and developmental basis of TEDs. We suggest future opportunities for integrating developmental mechanisms elucidated from animals and organoids with human genetics and clinical data to gain insight into the genotype-phenotype basis of these heterogeneous birth defects. Finally, we envision how this will enhance diagnosis, improve treatment, and perhaps one day, lead to new tissue replacement therapy.
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Affiliation(s)
- Nicole A Edwards
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Vered Shacham-Silverberg
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Leelah Weitz
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA; Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Paul S Kingma
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA
| | - James M Wells
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA; Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Center for Stem Cell & Organoid Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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