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. 2020 Aug 6;107(2):311-324.
doi: 10.1016/j.ajhg.2020.06.016. Epub 2020 Jul 31.

De Novo and Bi-allelic Pathogenic Variants in NARS1 Cause Neurodevelopmental Delay Due to Toxic Gain-of-Function and Partial Loss-of-Function Effects

Andreea Manole  1 Stephanie Efthymiou  1 Emer O'Connor  1 Marisa I Mendes  2 Matthew Jennings  3 Reza Maroofian  1 Indran Davagnanam  4 Kshitij Mankad  5 Maria Rodriguez Lopez  6 Vincenzo Salpietro  1 Ricardo Harripaul  7 Lauren Badalato  8 Jagdeep Walia  8 Christopher S Francklyn  9 Alkyoni Athanasiou-Fragkouli  1 Roisin Sullivan  1 Sonal Desai  10 Kristin Baranano  10 Faisal Zafar  11 Nuzhat Rana  11 Muhammed Ilyas  12 Alejandro Horga  1 Majdi Kara  13 Francesca Mattioli  14 Alice Goldenberg  15 Helen Griffin  3 Amelie Piton  14 Lindsay B Henderson  16 Benyekhlef Kara  17 Ayca Dilruba Aslanger  17 Joost Raaphorst  18 Rolph Pfundt  19 Ruben Portier  20 Marwan Shinawi  21 Amelia Kirby  22 Katherine M Christensen  22 Lu Wang  23 Rasim O Rosti  23 Sohail A Paracha  24 Muhammad T Sarwar  24 Dagan Jenkins  25 SYNAPS Study Group  26 Jawad Ahmed  24 Federico A Santoni  27 Emmanuelle Ranza  28 Justyna Iwaszkiewicz  29 Cheryl Cytrynbaum  30 Rosanna Weksberg  30 Ingrid M Wentzensen  16 Maria J Guillen Sacoto  16 Yue Si  16 Aida Telegrafi  16 Marisa V Andrews  21 Dustin Baldridge  21 Heinz Gabriel  31 Julia Mohr  31 Barbara Oehl-Jaschkowitz  32 Sylvain Debard  33 Bruno Senger  33 Frédéric Fischer  33 Conny van Ravenwaaij  34 Annemarie J M Fock  34 Servi J C Stevens  35 Jürg Bähler  6 Amina Nasar  8 John F Mantovani  36 Adnan Manzur  25 Anna Sarkozy  25 Desirée E C Smith  2 Gajja S Salomons  2 Zubair M Ahmed  37 Shaikh Riazuddin  38 Saima Riazuddin  37 Muhammad A Usmani  37 Annette Seibt  39 Muhammad Ansar  40 Stylianos E Antonarakis  41 John B Vincent  7 Muhammad Ayub  8 Mona Grimmel  42 Anne Marie Jelsig  43 Tina Duelund Hjortshøj  43 Helena Gásdal Karstensen  43 Marybeth Hummel  44 Tobias B Haack  45 Yalda Jamshidi  46 Felix Distelmaier  39 Rita Horvath  3 Joseph G Gleeson  23 Hubert Becker  33 Jean-Louis Mandel  14 David A Koolen  19 Henry Houlden  47
Affiliations

De Novo and Bi-allelic Pathogenic Variants in NARS1 Cause Neurodevelopmental Delay Due to Toxic Gain-of-Function and Partial Loss-of-Function Effects

Andreea Manole et al. Am J Hum Genet. .

Abstract

Aminoacyl-tRNA synthetases (ARSs) are ubiquitous, ancient enzymes that charge amino acids to cognate tRNA molecules, the essential first step of protein translation. Here, we describe 32 individuals from 21 families, presenting with microcephaly, neurodevelopmental delay, seizures, peripheral neuropathy, and ataxia, with de novo heterozygous and bi-allelic mutations in asparaginyl-tRNA synthetase (NARS1). We demonstrate a reduction in NARS1 mRNA expression as well as in NARS1 enzyme levels and activity in both individual fibroblasts and induced neural progenitor cells (iNPCs). Molecular modeling of the recessive c.1633C>T (p.Arg545Cys) variant shows weaker spatial positioning and tRNA selectivity. We conclude that de novo and bi-allelic mutations in NARS1 are a significant cause of neurodevelopmental disease, where the mechanism for de novo variants could be toxic gain-of-function and for recessive variants, partial loss-of-function.

Keywords: aminoacyl-tRNA synthetase; developmental delay; epilepsy; neurodevelopment; neuropathy; next generation sequencing.

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Conflict of interest statement

Maria J. Guillen Sacoto, Lindsay B. Henderson, Yue Si, Aida Telegrafi, and Ingrid M. Wentzensen are employees of GeneDx. The other authors declare no competing interests.

Figures

Figure 1
Figure 1
AsnRS1 Protein Structure and Function (A) AA asparagine (Asn) is ligated to tRNAAsn and catalyzed by AsnRS1 and ATP to produce Asn-tRNA (Asn), AMP, and pyrophosphate. (B) NARS1 mutations and their predicted functional effect. (C) Schematic representation of human ARS1 primary structure. Three main domains are depicted: the unique domain (UNE-N), the anticodon binding domain (ABD), and the catalytic domain (CAT). The nature and position of the mutants are shown above the primary structure, de novo boxed in red, and the positions of the domains are indicated below, including motif 1 (involved in AsnRS1 dimerization) and motifs 2 and 3 (which form the active site). (D) Bar graph summarizing proportions of various clinical findings affecting individuals with NARS1 mutations.
Figure 2
Figure 2
Pedigrees of the 21 Families and 32 Affected Individuals Identified in This Study with de novo and Bi-allelic Mutations in NARS1 Filled symbols represent affected individuals and double bars represent consanguinity in the family. −/−, +/−, and +/+ represent wild-type, heterozygous, and homozygous variants, respectively.
Figure 3
Figure 3
Radiological Findings of Individuals in Our Cohort Set 1: Individual homozygous for c.32G>C (p.Arg11Pro). Upper row images (coronal T2-WI [1A] and axial T1-WI [1B]) at the age of 10 months show severely delayed myelination and fronto-temporal atrophy. Lower row images (axial T2-WI [1C] and axial T1-WI [1D]) repeated at the age of 18 months show progressive and global brain atrophy with an emerging pattern of severe hypomyelination. Set 2: An additional homozygous c.32G>C (p.Arg11Pro) individual. Upper row images (axial T2-WI [2A] and axial T1-WI [2B]) at the age of 8 months show mild fronto-temporal underdevelopment and severely delayed myelination. Lower row images (axial T2-WI [2C] and axial T1-W1 [2D]) repeated at the age of 2 years shows progressive and global brain atrophy along with severe hypomyelination. Set 3: Individual homozygous for c.50C>T (p.Thr17Met). Axial fluid-attenuated inversion recovery (FLAIR) images at the age of 9 months show global atrophy involving the cerebral and cerebellar hemispheres along with severe hypomyelination. Set 4: MRI images of an individual with the homozygous c.1633C>T (p.Arg545Cyc) variant. Coronal T1-WI (4A), axial T2-WI (4B), and sagittal T1-WI (4C) at the age of 4 years; coronal T1-WI (4D), axial T2-WI (4E), and sagittal T1-WI (4F) at the age of 11 years; and coronal T2-WI (4G), axial FLAIR (4H), and sagittal T2-WI (4I) at the age of 20 years. These demonstrate normal intracranial appearances across the three different ages. This individual had an upper thoracic scoliosis, which was operatively corrected at the age of 4, demonstrated on the sagittal T2-WI of the spine (4J) and frontal projection radiograph of the chest/thoracic spine (4K).
Figure 4
Figure 4
Protein Levels of AsnRS1 Are Reduced in Individual-Derived Cells (A) RT-PCR of the de novo c.1600C>T (p.Arg534) variant in P2 and parents (B) western blotting and (C) quantification graph of individuals with NARS1 mutations compared with controls. Ctrl = control, P10 = homozygous c.1633C>T (p.Arg545Cys), P26 = homozygous c.50C>T (p.Thr17Met), P29 = compound heterozygous (c.1067A>C (p.Asp356Ala) and c.203dupA (p.Met69Aspfs4) (F denotes father of individuals), P24 = homozygous c.32G>C (p.Arg11Pro).
Figure 5
Figure 5
BN-PAGE and iNPC RNA-Sequencing (A) iNPCs from P26 (c.50C>T [p.Thr17Met]) and P29 (c.203dupA [p.Met69Aspfs4] and c.1067A>C [p.Asp356Ala]) exhibit increased expression of most iNPC markers (sox1, sox2, nestin, snail1, pax6, DKK3, twist2, and Musashi-1) compared to fibroblast (fbb) as measured by qPCR, shown with hierarchal clustering. (B) Heatmap with hierarchal clustering generated using all gene counts from RNaseq distinction of control (Ctrl1 a–c, Ctrl2 a–c) and individual-derived (P26 a–b, P29 a–c) iNPCs. (C) Volcano plot showing log2 of fold change in NARS mutant iNPCs compared to controls and −log10 (adjusted p value). (D) BN-PAGE western blot showing reduced levels of the AsnRS1 dimer in individuals P26 and P29 and fathers compared to control, but not for individual P10. (E) Quantification of BN-PAGE western blot AsnRS1 dimer formation, showing significantly (∗∗∗p < 0.001) reduced levels of the AsnRS1 in individuals P26 and P29 and fathers compared to control but not change for P10. P26 = homozygous c.50C>T (p.Thr17Met), P29 = c.203dupA (p.Met69Aspfs4), c.1067A>C (p.Asp356Ala), P10 = c.1633C>T (p.Arh545Cys), father of P26 = heterozygous c.50C>T (p.Thr17Met), father of P29 = c.1067A>C (p.Asp356Ala).
Figure 6
Figure 6
Molecular Modeling of the NARS1 p.Arg545Cys Homozygous Variant The crystal structure is based on B.malayi AsnRS1. AsnRS1 is a homodimer; one AsnRS1 monomer is given in yellow and one in orange. Analog of the transition state presented in the surface representation, C terminus in dark blue, Asp230 and Asp226 in cyan, Arg545 and Arg545Cys in magenta. (A) Interaction between AsnRS1 and tRNA with residues on the helical linker. (B–E) Zoom in on the C terminus helical linker region, (B) and (E) show loss of molecular interaction and folding of the p.Arg545Cys variant ().
Figure 7
Figure 7
Reduced Asparaginyl-tRNA Synthetase Activity in Individuals with Homozygous NARS1 Variants c.1600C>T (p.Arg534) (P2), c.1633C>T (p.Arg545Cys) (P9 and P20), c.32G>C (p.Arg11Pro) (P24), c.50C>T (p.Thr17Met) (P26), and c.1067A>C (p.Asp356Ala)/c.203dupA (p.M69Aspfs4) (P29) NARS1 variants in comparison to the average of three unrelated fibroblast cell lines. (All cell lines are fibroblast except P2, which is a lymphoblast cell line. Control values for lymphoblast are similar to fibroblasts.) n = 9, p value FDR < 0.01.

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