1
|
Duroux D, Wohlfart C, Van Steen K, Vladimirova A, King M. Graph-based multi-modality integration for prediction of cancer subtype and severity. Sci Rep 2023; 13:19653. [PMID: 37949935 PMCID: PMC10638406 DOI: 10.1038/s41598-023-46392-6] [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: 07/18/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Personalised cancer screening before therapy paves the way toward improving diagnostic accuracy and treatment outcomes. Most approaches are limited to a single data type and do not consider interactions between features, leaving aside the complementary insights that multimodality and systems biology can provide. In this project, we demonstrate the use of graph theory for data integration via individual networks where nodes and edges are individual-specific. We showcase the consequences of early, intermediate, and late graph-based fusion of RNA-Seq data and histopathology whole-slide images for predicting cancer subtypes and severity. The methodology developed is as follows: (1) we create individual networks; (2) we compute the similarity between individuals from these graphs; (3) we train our model on the similarity matrices; (4) we evaluate the performance using the macro F1 score. Pros and cons of elements of the pipeline are evaluated on publicly available real-life datasets. We find that graph-based methods can increase performance over methods that do not study interactions. Additionally, merging multiple data sources often improves classification compared to models based on single data, especially through intermediate fusion. The proposed workflow can easily be adapted to other disease contexts to accelerate and enhance personalized healthcare.
Collapse
Affiliation(s)
- Diane Duroux
- BIO3 - Systems Genetics, GIGA-R Medical Genomics, University of Liège, 4000, Liège, Belgium.
- Post-Doctoral Fellow, ETH AI center, Zürich, Switzerland.
| | | | - Kristel Van Steen
- BIO3 - Systems Genetics, GIGA-R Medical Genomics, University of Liège, 4000, Liège, Belgium
- Department of Human Genetics, BIO3 - Systems Medicine, 3000, Leuven, Belgium
| | - Antoaneta Vladimirova
- Roche Information Solutions, Roche Diagnostics Corporation, Santa Clara, California, United States of America
| | | |
Collapse
|
2
|
Rabah Y, Francés R, Minatchy J, Guédon L, Desnous C, Plaçais PY, Preat T. Glycolysis-derived alanine from glia fuels neuronal mitochondria for memory in Drosophila. Nat Metab 2023; 5:2002-2019. [PMID: 37932430 PMCID: PMC10663161 DOI: 10.1038/s42255-023-00910-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/30/2022] [Accepted: 09/20/2023] [Indexed: 11/08/2023]
Abstract
Glucose is the primary source of energy for the brain; however, it remains controversial whether, upon neuronal activation, glucose is primarily used by neurons for ATP production or if it is partially oxidized in astrocytes, as proposed by the astrocyte-neuron lactate shuttle model for glutamatergic neurons. Thus, an in vivo picture of glucose metabolism during cognitive processes is missing. Here, we uncover in Drosophila melanogaster a glia-to-neuron alanine transfer involving alanine aminotransferase that sustains memory formation. Following associative conditioning, glycolysis in glial cells produces alanine, which is back-converted into pyruvate in cholinergic neurons of the olfactory memory center to uphold their increased mitochondrial needs. Alanine, as a mediator of glia-neuron coupling, could be an alternative to lactate in cholinergic systems. In parallel, a dedicated glial glucose transporter imports glucose specifically for long-term memory, by directly transferring it to neurons for use by the pentose phosphate pathway. Our results demonstrate in vivo the compartmentalization of glucose metabolism between neurons and glial cells during memory formation.
Collapse
Affiliation(s)
- Yasmine Rabah
- Energy & Memory, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Raquel Francés
- Energy & Memory, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Julia Minatchy
- Energy & Memory, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Laura Guédon
- Energy & Memory, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Coraline Desnous
- Energy & Memory, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Pierre-Yves Plaçais
- Energy & Memory, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL Research University, Paris, France.
| | - Thomas Preat
- Energy & Memory, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL Research University, Paris, France.
| |
Collapse
|
3
|
Wei C, Zeng H, Zhong Z, Cai X, Teng J, Liu Y, Zhao Y, Wu X, Li J, Zhang Z. Integration of non-additive genome-wide association study with a multi-tissue transcriptome analysis of growth and carcass traits in Duroc pigs. Animal 2023; 17:100817. [PMID: 37196577 DOI: 10.1016/j.animal.2023.100817] [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: 12/08/2022] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 05/19/2023] Open
Abstract
Growth and carcass traits are of economic importance in the pig production, which affect pork quality and profitability of finishing pig production. This study used whole-genome and transcriptome sequencing technologies to identify potential candidate genes affecting growth and carcass traits in Duroc pigs. The medium (50-60 k) single nucleotide polymorphism (SNP) arrays of 4 154 Duroc pigs from three populations were imputed to whole-genome sequence data, yielding 10 463 227 markers on 18 autosomes. The dominance heritabilities estimated for growth and carcass traits ranged from 0.000 ± 0.041 to 0.161 ± 0.054. Using non-additive genome-wide association study (GWAS), we identified 80 dominance quantitative trait loci for growth and carcass traits at genome-wide significance (false discovery rate < 5%), 15 of which were also detected in our additive GWAS. After fine mapping, 31 candidate genes for dominance GWAS were annotated, and 8 of them were highlighted that have been previously reported to be associated with growth and development (e.g. SNX14, RELN and ENPP2), autosomal recessive diseases (e.g. AMPH, SNX14, RELN and CACNB4) and immune response (e.g. UNC93B1 and PPM1D). By integrating the lead SNPs with RNA-seq data of 34 pig tissues from the Pig Genotype-Tissue Expression project (https://piggtex.farmgtex.org/), we found that the rs691128548, rs333063869, and rs1110730611 have significantly dominant effects for the expression of SNX14, AMPH and UNC93B1 genes in tissues related to growth and development for pig, respectively. Finally, the identified candidate genes were significantly enriched for biological processes involved in the cell and organ development, lipids catabolic process and phosphatidylinositol 3-kinase signalling (P < 0.05). These results provide new molecular markers for meat production and quality selection of pig as well as basis for deciphering the genetic mechanisms of growth and carcass traits.
Collapse
Affiliation(s)
- Chen Wei
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China
| | - Haonan Zeng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China
| | - Zhanming Zhong
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China
| | - Xiaodian Cai
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China
| | - Jingyan Teng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China
| | - Yuqiang Liu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China
| | - Yunxiang Zhao
- School of Life Science and Engineering, Foshan University, Foshan 528225, PR China
| | - Xibo Wu
- Guangxi Guiken Yongxin Animal Husbandry Group Co. Ltd, Nanning 530000, PR China
| | - Jiaqi Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China
| | - Zhe Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, PR China.
| |
Collapse
|
4
|
Fink JK. The hereditary spastic paraplegias. Handb Clin Neurol 2023; 196:59-88. [PMID: 37620092 DOI: 10.1016/b978-0-323-98817-9.00022-3] [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] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
The hereditary spastic paraplegias (HSPs) are a group of more than 90 genetic disorders in which lower extremity spasticity and weakness are either the primary neurologic impairments ("uncomplicated HSP") or when accompanied by other neurologic deficits ("complicated HSP"), important features of the clinical syndrome. Various genetic types of HSP are inherited such as autosomal dominant, autosomal recessive, X-linked, and maternal (mitochondrial) traits. Symptoms that begin in early childhood may be nonprogressive and resemble spastic diplegic cerebral palsy. Symptoms that begin later, typically progress insidiously over a number of years. Genetic testing is able to confirm the diagnosis for many subjects. Insights from gene discovery indicate that abnormalities in diverse molecular processes underlie various forms of HSP, including disturbance in axon transport, endoplasmic reticulum morphogenesis, vesicle transport, lipid metabolism, and mitochondrial function. Pathologic studies in "uncomplicated" HSP have shown axon degeneration particularly involving the distal ends of corticospinal tracts and dorsal column fibers. Treatment is limited to symptom reduction including amelioration of spasticity, reducing urinary urgency, proactive physical therapy including strengthening, stretching, balance, and agility exercise.
Collapse
Affiliation(s)
- John K Fink
- Department of Neurology, University of Michigan, Ann Arbor, MI, United States.
| |
Collapse
|
5
|
Liu J, Chen B, Liu Y, Kong J, Zhang B, Han L, Mei D, Ma CY, Shang Q, Xie Z, Xiao M, Mei S, Zhang Y, Gao C, Li D. Paternal uniparental disomy of chromosome 16 resulting in homozygosity of a GPT2 mutation causes intellectual and developmental disability. Eur J Med Genet 2022; 65:104554. [DOI: 10.1016/j.ejmg.2022.104554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/16/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022]
|
6
|
Cicatiello AG, Sagliocchi S, Nappi A, Di Cicco E, Miro C, Murolo M, Stornaiuolo M, Dentice M. Thyroid hormone regulates glutamine metabolism and anaplerotic fluxes by inducing mitochondrial glutamate aminotransferase GPT2. Cell Rep 2022; 38:110409. [PMID: 35196498 PMCID: PMC8889437 DOI: 10.1016/j.celrep.2022.110409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/29/2021] [Accepted: 01/27/2022] [Indexed: 12/27/2022] Open
Abstract
Thyroid hormones (THs) are key metabolic regulators coordinating short- and long-term energy needs. In skeletal muscle, THs modulate energy metabolism in pathophysiological conditions. Indeed, hypo- and hyperthyroidism are leading causes of muscle weakness and strength; however, the metabolic pathways underlying these effects are still poorly understood. Using molecular, biochemical, and isotope-tracing approaches combined with mass spectrometry and denervation experiments, we find that THs regulate glutamine metabolism and anaplerotic fluxes by up-regulating the glutamate pyruvate transaminase 2 (GPT2) gene. In humans, GPT2 autosomal recessive mutations cause a neurological syndrome characterized by intellectual disability, microcephaly, and progressive motor symptoms. Here, we demonstrate a role of the TH/GPT2 axis in skeletal muscle in which it regulates muscle weight and fiber diameter in resting and atrophic conditions and results in protection from muscle loss during atrophy. These results describe an anabolic route by which THs rewire glutamine metabolism toward the maintenance of muscle mass. THs induce the expression of the mitochondrial GPT2 gene in skeletal muscle The GPT2 up-regulation by THs enhances anaplerotic cycles and α-KG production GPT2 is reduced during muscle atrophy and is reactivated by THs treatment GPT2 KO+/– mice undergo muscle loss that is partially attenuated by THs
Collapse
Affiliation(s)
| | - Serena Sagliocchi
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", Naples, NA 80138 Italy
| | - Annarita Nappi
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", Naples, NA 80138 Italy
| | - Emery Di Cicco
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", Naples, NA 80138 Italy
| | - Caterina Miro
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", Naples, NA 80138 Italy
| | - Melania Murolo
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", Naples, NA 80138 Italy
| | - Mariano Stornaiuolo
- Department of Pharmacy, University of Naples "Federico II", Naples, NA 80138 Italy
| | - Monica Dentice
- Department of Clinical Medicine and Surgery, University of Naples "Federico II", Naples, NA 80138 Italy; CEINGE-Biotecnologie Avanzate Scarl, Naples, NA 80131, Italy.
| |
Collapse
|
7
|
Iwata R, Vanderhaeghen P. Regulatory roles of mitochondria and metabolism in neurogenesis. Curr Opin Neurobiol 2021; 69:231-240. [PMID: 34171617 PMCID: PMC8415079 DOI: 10.1016/j.conb.2021.05.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 01/14/2023]
Abstract
Neural stem cells (NSCs) undergo massive molecular and cellular changes during neuronal differentiation. These include mitochondria and metabolism remodelling, which were thought to be mostly permissive cues, but recent work indicates that they are causally linked to neurogenesis. Striking remodelling of mitochondria occurs right after mitosis of NSCs, which influences the postmitotic daughter cells towards self-renewal or differentiation. The transitioning to neuronal fate requires metabolic rewiring including increased oxidative phosphorylation activity, which drives transcriptional and epigenetic effects to influence cell fate. Mitochondria metabolic pathways also contribute in an essential way to the regulation of NSC proliferation and self-renewal. The influence of mitochondria and metabolism on neurogenesis is conserved from fly to human systems, but also displays striking differences linked to cell context or species. These new findings have important implications for our understanding of neurodevelopmental diseases and possibly human brain evolution.
Collapse
Affiliation(s)
- Ryohei Iwata
- VIB KULeuven Center for Brain & Disease Research, KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, 3000, Belgium; Université Libre de Bruxelles (ULB), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), ULB Neuroscience Institute (UNI), Brussels, 1070, Belgium
| | - Pierre Vanderhaeghen
- VIB KULeuven Center for Brain & Disease Research, KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, 3000, Belgium; Université Libre de Bruxelles (ULB), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), ULB Neuroscience Institute (UNI), Brussels, 1070, Belgium.
| |
Collapse
|
8
|
Ruaud L, Keren B, Debs R, Mignot C, Mochel F. Demyelinating motor neuropathy associated with a homozygous GPT2 pathogenic variant. Muscle Nerve 2021; 63:E41-E44. [PMID: 33501685 DOI: 10.1002/mus.27183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/07/2021] [Accepted: 01/24/2021] [Indexed: 12/25/2022]
Affiliation(s)
- Lyse Ruaud
- INSERM UMR 1141, Neurodiderot, University of Paris, Paris, France.,Department of Genetics, APHP, Robert-Debré Hospital, Paris, France
| | - Boris Keren
- Department of Genetics, APHP, Sorbonne Université, Pitié-Salpêtrière University Hospital, Paris, France
| | - Rabab Debs
- Department of Clinical Neurophysiology, APHP, Sorbonne Université, Pitié-Salpêtrière University Hospital, Paris, France
| | - Cyril Mignot
- Department of Genetics, APHP, Sorbonne Université, Pitié-Salpêtrière University Hospital, Paris, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpêtrière University Hospital, Paris, France
| | - Fanny Mochel
- Department of Genetics, APHP, Sorbonne Université, Pitié-Salpêtrière University Hospital, Paris, France.,INSERM U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| |
Collapse
|
9
|
Hengel H, Buchert R, Sturm M, Haack TB, Schelling Y, Mahajnah M, Sharkia R, Azem A, Balousha G, Ghanem Z, Falana M, Balousha O, Ayesh S, Keimer R, Deigendesch W, Zaidan J, Marzouqa H, Bauer P, Schöls L. First-line exome sequencing in Palestinian and Israeli Arabs with neurological disorders is efficient and facilitates disease gene discovery. Eur J Hum Genet 2020; 28:1034-43. [PMID: 32214227 DOI: 10.1038/s41431-020-0609-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 02/26/2020] [Accepted: 03/10/2020] [Indexed: 12/22/2022] Open
Abstract
A high rate of consanguinity leads to a high prevalence of autosomal recessive disorders in inbred populations. One example of inbred populations is the Arab communities in Israel and the Palestinian Authority. In the Palestinian Authority in particular, due to limited access to specialized medical care, most patients do not receive a genetic diagnosis and can therefore neither receive genetic counseling nor possibly specific treatment. We used whole-exome sequencing as a first-line diagnostic tool in 83 Palestinian and Israeli Arab families with suspected neurogenetic disorders and were able to establish a probable genetic diagnosis in 51% of the families (42 families). Pathogenic, likely pathogenic or highly suggestive candidate variants were found in the following genes extending and refining the mutational and phenotypic spectrum of these rare disorders: ACO2, ADAT3, ALS2, AMPD2, APTX, B4GALNT1, CAPN1, CLCN1, CNTNAP1, DNAJC6, GAMT, GPT2, KCNQ2, KIF11, LCA5, MCOLN1, MECP2, MFN2, MTMR2, NT5C2, NTRK1, PEX1, POLR3A, PRICKLE1, PRKN, PRX, SCAPER, SEPSECS, SGCG, SLC25A15, SPG11, SYNJ1, TMCO1, and TSEN54. Further, this cohort has proven to be ideal for prioritization of new disease genes. Two separately published candidate genes (WWOX and PAX7) were identified in this study. Analyzing the runs of homozygosity (ROHs) derived from the Exome sequencing data as a marker for the rate of inbreeding, revealed significantly longer ROHs in the included families compared with a German control cohort. The total length of ROHs correlated with the detection rate of recessive disease-causing variants. Identification of the disease-causing gene led to new therapeutic options in four families.
Collapse
|
10
|
Binaafar S, Razmara E, Mahdieh N, Sahebjame H, Tavasoli AR, Garshasbi M. A novel missense variant in GPT2 causes non-syndromic autosomal recessive intellectual disability in a consanguineous Iranian family. Eur J Med Genet 2020; 63:103853. [PMID: 31978613 DOI: 10.1016/j.ejmg.2020.103853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 10/26/2019] [Revised: 12/15/2019] [Accepted: 01/17/2020] [Indexed: 12/28/2022]
Abstract
Intellectual disability (ID) affects 1-3% of the general population worldwide. Genetic factors play an undeniable role in the etiology of Non-Syndromic Intellectual disability (NS-ID). Nowadays, whole-exome sequencing (WES) technique is used frequently to identify the causative genes in such heterogeneous diseases. Herein, we subjected four patients with initial diagnostics of NS-ID in a consanguineous Iranian family. To find the possible genetic cause(s), Trio-WES was performed on the proband and his both healthy parents. Sanger sequencing was performed to confirm the identified variant by WES and also investigate whether it co-segregates with the patients' phenotype in the family. Using several online in-silico predictors, the probable impacts of the variant on structure and function of GPT2 protein were predicted. A novel variant, c.266A>G; p.(Glu89Gly), in exon 3 of GPT2 (NM_133443.3) was identified using Trio-WES. The candidate variant was also verified by Sanger sequencing. All affected members showed the common clinical features suffering from a non-progressive mild-to-severe ID. Also, different clinical observations compared to previously reported cases such as no facial features, no obvious structural malformations, ability to speak but with difficulty, and lack of any morphological defects were noted for the first time in this family. The c.266A>G; p.(Glu89Gly) variant reported here is the sixth variant identified up to now in the GPT2 gene, to be associated with NS-ID. Our data support the potential malfunction of the substituted GPT2 protein resulted from the novel variant, however, we strongly suggest confirming this finding more by doing functional analysis.
Collapse
Affiliation(s)
- Sima Binaafar
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Ehsan Razmara
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Nejat Mahdieh
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Sahebjame
- Department of Biology, Faculty of Basic Science, Gonbad Kavous University, Gonbad Kavous, Golestan, Iran
| | - Ali Reza Tavasoli
- Myelin Disorders Clinic, Pediatric Neurology Division, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| |
Collapse
|
11
|
Ouyang Q, Kavanaugh BC, Joesch-Cohen L, Dubois B, Wu Q, Schmidt M, Baytas O, Pastore SF, Harripaul R, Mishra S, Hussain A, Kim KH, Holler-Managan YF, Ayub M, Mir A, Vincent JB, Liu JS, Morrow EM. GPT2 mutations in autosomal recessive developmental disability: extending the clinical phenotype and population prevalence estimates. Hum Genet 2019; 138:1183-1200. [PMID: 31471722 PMCID: PMC6748651 DOI: 10.1007/s00439-019-02057-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/24/2019] [Indexed: 10/26/2022]
Abstract
The glutamate pyruvate transaminase 2 (GPT2) gene produces a nuclear-encoded mitochondrial enzyme that catalyzes the reversible transfer of an amino group from glutamate to pyruvate, generating alanine and alpha-ketoglutarate. Recessive mutations in GPT2 have been recently identified in a new syndrome involving intellectual and developmental disability (IDD), postnatal microcephaly, and spastic paraplegia. We have identified additional families with recessive GPT2 mutations and expanded the phenotype to include small stature. GPT2 loss-of-function mutations were identified in four families, nine patients total, including: a homozygous mutation in one child [c.775T>C (p.C259R)]; compound heterozygous mutations in two siblings [c.812A>C (p.N271T)/c.1432_1433delGT (p.V478Rfs*73)]; a novel homozygous, putative splicing mutation [c.1035C>T (p.G345=)]; and finally, a recurrent mutation, previously identified in a distinct family [c.1210C>T (p.R404*)]. All patients were diagnosed with IDD. A majority of patients had remarkably small stature throughout development, many < 1st percentile for height and weight. Given the potential biological function of GPT2 in cellular growth, this phenotype is strongly suggestive of a newly identified clinical susceptibility. Further, homozygous GPT2 mutations manifested in at least 2 of 176 families with IDD (approximately 1.1%) in a Pakistani cohort, thereby representing a relatively common cause of recessive IDD in this population, with recurrence of the p.R404* mutation in this population. Based on variants in the ExAC database, we estimated that approximately 1 in 248 individuals are carriers of moderately or severely deleterious variants in GPT2.
Collapse
Affiliation(s)
- Qing Ouyang
- Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University and Emma Pendleton Bradley Hospital, East Providence, RI, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI, USA.,Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI, USA
| | - Brian C Kavanaugh
- Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University and Emma Pendleton Bradley Hospital, East Providence, RI, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI, USA
| | - Lena Joesch-Cohen
- Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI, USA.,Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI, USA
| | - Bethany Dubois
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Qing Wu
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI, USA
| | - Michael Schmidt
- Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University and Emma Pendleton Bradley Hospital, East Providence, RI, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI, USA.,Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI, USA
| | - Ozan Baytas
- Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University and Emma Pendleton Bradley Hospital, East Providence, RI, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI, USA.,Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI, USA
| | - Stephen F Pastore
- Molecular Neuropsychiatry and Development (MiND) Lab, Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, Toronto, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Ricardo Harripaul
- Molecular Neuropsychiatry and Development (MiND) Lab, Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, Toronto, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Sasmita Mishra
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Abrar Hussain
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Katherine H Kim
- Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yolanda F Holler-Managan
- Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Muhammad Ayub
- Department of Psychiatry, Queens University Kingston, Kingston, ON, Canada
| | - Asif Mir
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - John B Vincent
- Molecular Neuropsychiatry and Development (MiND) Lab, Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, Toronto, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Judy S Liu
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI, USA.,Department of Neurology, Rhode Island Hospital and Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Eric M Morrow
- Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University and Emma Pendleton Bradley Hospital, East Providence, RI, USA. .,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI, USA. .,Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA. .,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI, USA. .,Laboratories for Molecular Medicine, Brown University, 70 Ship Street, Box G-E4, Providence, RI, 02912, USA.
| |
Collapse
|