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L.G. Riley et al.
in cluster 1. YARS2 (p.Ser203Ile) led to a reduced affinity for tRNATyr, resulting in a 17-fold loss in catalytic efficien- cy (Figure 1C). Patient 10 has no lactic acidosis or myopa- thy, and presented with isolated normocytic anemia and asthenia, and has not required transfusion.
Patient 7 presented with anemia in infancy requiring two transfusions within the first 16 months of life and then became transfusion independent. She has moderate myopathy and no lactic acidosis and a compound het- erozygous genotype: a missense variant, p.(Gly244Ala), occurring in cis with p.(Gly191Val) and in trans with the p.(Asp311Glu) variant. Gly244 is a critical residue for tyro- syl-adenylate binding.19 YARS2 p.(Gly244Ala) only affect- ed the kcat indicating that, as predicted, this variant hinders binding of the tyrosyl-adenylate in the active site (Figure 1C). YARS2 Asp311 is involved in the recognition of anti- codon residue G34 of tRNATyr.19 The p.(Asp311Glu) vari- ant is respiratory deficient in a yeast model, and patients homozygous for this allele also have transfusion-depen- dent sideroblastic anemia in the first year of life; however, in contrast to patient 7, they have lactic acidosis but no myopathy.8 Further phenotypic variability for the p.(Asp311Glu) variant was observed in Patient 11 who was homozygous for p.(Asp311Glu), with transfusion- dependent MLASA2.
In two families in this study (Families 6 and 8), affected patients have the common p.(Gly191Val) allele (MAF = 0.1259) in trans of a predicted null allele. Importantly, all of the unaffected carriers of predicted null alleles in these and other families, where probands had the ancestral p.Gly191 variant in trans, were asymptomatic (data not shown). Patient 6 presented in infancy with CSA requir- ing transfusions every three weeks. She has mild lactic acidosis, no myopathy and intermittent neutropenia. She has a c.590_645del variant resulting in a 12 amino acid deletion in the catalytic domain (Figure 1A), which would almost certainly lead to a completely dysfunction- al protein, in trans with p.(Gly191Val). Individuals 8a and 8b also carry p.(Gly191Val) in trans with a predicted null or severe loss-of-function allele, c.1360_1360insG, p.(Ile454Serfs*10). This variant truncates the S4-like domain which is thought to stabilize the interaction with tRNATyr, and the deletion of the YARS2 S4-like domain leads to a 100-fold reduced amino-acylation activity in vitro.20 Patient 8a had sideroblastic anemia and edema. Lactate was elevated only on exertion and the patient did not have myopathy. Her sister (P8b) is asymptomatic. Patient 8a also had a somatic mutation in SF3B1 p.(Lys700Glu) that is strongly associated with myelodysplastic syndromes with ringed sideroblasts.26 Based on the childhood presentation of her anemia and exercise intolerance that was exacerbated significantly decades later, and the fact that a mutation in SF3B1 would be exceptional in a patient under 30 years of age, we infer the YARS2 mutations to be the primary cause of her anemia with the SF3B1 mutation occurring as a sec- ondary somatic event, which exacerbated her anemia, bringing her to clinical attention. In addition to the reduced activity in vitro,5 support of the notion that YARS2 p.(Gly191Val) contributes to the disease pheno- type in these patients comes from the observation that this variant is a disease modifier in Leber Hereditary Optic Neuropathy (LHON); the three common LHON
mitochondrial DNA mutations have incomplete pene- trance. However, all patients who carry both the LHON m.11778G>A mtDNA disease-associated variant in com- bination with a homozygous YARS2 p.(Gly191Val) geno- type were symptomatic.11
Patients 9a and 9b carried the YARS2 c.98C>A, p.(Ser33*) nonsense variant, which would result in a null allele, and the p.(Tyr236Cys) variant (Figure 1A and B) that did not alter amino-acylation activity in vitro. In addition, in silico analysis using Alamut did not predict that this vari- ant would lead to alteration of an exonic splicing enhancer site. Patient 9a presented in infancy with sideroblastic ane- mia that has come and gone throughout his life. He has no lactic acidosis or myopathy. He and his unaffected brother have some dysmorphic features, which have not previ- ously been reported in association with YARS2 variants, but are typical of MLASA1 patients with pseudouridine synthase 1 (PUS1) mutations.17,27 His genotypically concor- dant fraternal twin (P9b) has only mild anemia and similar facial dysmorphology, once again highlighting the poten- tial for decreased penetrance and/or expressivity of the disorder.
Interestingly, some YARS2 patients with myopathy, but no sideroblastic anemia, have recently been reported by Sommerville et al.9 They report siblings with a homozy- gous YARS2 p.(Leu392Ser) variant who had MLASA2, while another individual homozygous for the same vari- ant had myopathy without sideroblastic anemia or lactic acidosis.
To summarize, the inter- and intra-familial phenotypic variability, intermittent transfusion dependence of some YARS2 cases, and the association of a common variant with disease, suggest that all MLASA2 phenotypes may be susceptible to subtle changes in YARS2 function, which may in turn be influenced by genetic and/or environmen- tal modifiers. This study shows that YARS2 variants can result in CSA in the absence of clinically significant myopathy or lactic acidosis. Thus, we recommend that YARS2 variants be considered as a cause of isolated sider- oblastic anemia as well as MLASA2 or mitochondrial myopathy.
Funding
This research was supported by Australian NHMRC grant 1026891 to JC, NIH DK087992 to MDF, and grants SAF2015-70412-R from the Spanish Secretary of Research, Development and Innovation (MINECO), DJCLS R14/04 from Deutsche José Carreras Leukämie Stiftung, 2014 SGR225 (GRE) from Generalitat de Catalunya and economical support from Fundació Internacional Josep Carreras and from Obra Social “la Caixa” Spain to MS.
Acknowledgments
We thank Katinka Redert for her help in data collection. We thank Beatriz Cadenas from Josep Carreras Leukaemia Research Institute (IJC) and Whole Genix, S.L. for excellent tech- nical and bioinformatic assistance, and Dr. Carme Pedro and Dr. Sara Montesdeoca from IMIM Hospital del Mar for medical assistance for P10. We also gratefully acknowledge donations to JC by the Crane and Perkins families as well as the participation of the research subjects. The research conducted at the Murdoch Children’s Research Institute was supported by the Victorian Government's Operational Infrastructure Support Program.
2014
haematologica | 2018; 103(12)