Variants in Mitochondrial ATP Synthase Cause Variable Neurologic Phenotypes

Abstract

Objective ATP synthase (ATPase) is responsible for the majority of ATP production. Nevertheless, disease phenotypes associated with mutations in ATPase subunits are extremely rare. We aimed at expanding the spectrum of ATPase‐related diseases. Methods Whole‐exome sequencing in cohorts with 2,962 patients diagnosed with mitochondrial disease and/or dystonia and international collaboration were used to identify deleterious variants in ATPase‐encoding genes. Findings were complemented by transcriptional and proteomic profiling of patient fibroblasts. ATPase integrity and activity were assayed using cells and tissues from 5 patients. Results We present 10 total individuals with biallelic or de novo monoallelic variants in nuclear ATPase subunit genes. Three unrelated patients showed the same homozygous missense ATP5F1E mutation (including one published case). An intronic splice‐disrupting alteration in compound heterozygosity with a nonsense variant in ATP5PO was found in one patient. Three patients had de novo heterozygous missense variants in ATP5F1A, whereas another 3 were heterozygous for ATP5MC3 de novo missense changes. Bioinformatics methods and populational data supported the variants’ pathogenicity. Immunohistochemistry, proteomics, and/or immunoblotting revealed significantly reduced ATPase amounts in association to ATP5F1E and ATP5PO mutations. Diminished activity and/or defective assembly of ATPase was demonstrated by enzymatic assays and/or immunoblotting in patient samples bearing ATP5F1A‐p.Arg207His, ATP5MC3‐p.Gly79Val, and ATP5MC3‐p.Asn106Lys. The associated clinical profiles were heterogeneous, ranging from hypotonia with spontaneous resolution (1/10) to epilepsy with early death (1/10) or variable persistent abnormalities, including movement disorders, developmental delay, intellectual disability, hyperlactatemia, and other neurologic and systemic features. Although potentially reflecting an ascertainment bias, dystonia was common (7/10). Interpretation Our results establish evidence for a previously unrecognized role of ATPase nuclear‐gene defects in phenotypes characterized by neurodevelopmental and neurodegenerative features. ANN NEUROL 2022;91:225–237

A homozygous splice variant in ATP5PO, disrupts mitochondrial complex V function and causes Leigh syndrome in two unrelated families

“…The presence of the residual wild‐type ATP5PO transcript likely resulted in the residual ATP5PO protein, the small amount of holocomplex V assembly and the residual complex V hydrolytic activity. This is similar to the recent report of an affected individual with bi‐allelic ATP5PO variants, including a splice variant which also retained some normal splicing and residual activity 4 . Given these observations, we hypothesize that complete loss of function of ATP5PO is likely not compatible with life.…”

“…15 In contrast, partial downregulation of ATP5PO/OSCP with a shRNA did not change the expression of other subunits of ATPase or its structure, 16 indicating that profound loss of ATP5PO/OSCP expression is likely needed before it starts to affect the complex V assembly. Both the previously reported and our affected individuals lack proteins of the matrix part of the peripheral stalk (reflected in family 2, II.4, by the absence of subunits ATP5PO/OSCP, b and d, and in the reported individual in Zech et al, 2022, 4 with the decrease in subunits d and f), and the membrane bound part of the peripheral stalk (in the reported individual in Zech et al, 2022 4 with the decrease in subunit e) , showing that these variants profoundly impair complex V assembly. Thus, pathogenic variants in the critical subunits for early complex V assembly result in instability and loss of the peripheral stalk V resulting in its dysfunction.…”

“…There were increased levels of 3‐methylglutaconic acid (3‐MGA) in the urine of individual II.4 (family 2), which has been noted in cases of complex V deficiency caused by defects of nuclear encoded genes such as TMEM70 and ATP5FD1 , likely related to the essential function of complex V in maintaining the structure and cristae formation of the mitochondrial inner membrane. Notably the recently reported individual with biallelic ATP5PO variants did not show elevated 3‐MGA 4 . The elevation of C3 and 5‐hydroxy‐acylcarnitines described in individuals with MT‐ATP6 pathogenic variants was not observed in our study, but a transient increase in butyryl/isobutyrylcarnitine was seen in the two affected individuals of family 2 (II.1 and II.4), without any corresponding abnormalities in urine organic acids.…”

“…The BN‐PAGE analysis with in‐gel activity staining confirmed a pathological pattern of lower molecular weight F 1 subunits with sharply reduced holocomplex activity. This is different from what has been observed in individuals with other complex V disorders but is similar to that reported for the individual with the biallelic ATP5PO variants 4 . In contrast, in individuals with MT‐ATP6 and TMEM70 variants, active complex V assembly intermediates are present in addition to normal holocomplex enzyme 17,18 whereas in individuals harboring ATP5F1D 19 and ATPAF2 20 variants, a severe reduction in active complex V holocomplex was observed, as well as the presence of inactive lower molecular weight F 1 subunits.…”

“…Until recently, pathogenic variants that result in complex V deficiency were only reported in 7 of the 18 genes encoding the complex V subunits ( ATP5F1A , ATP5F1D , ATP5F1E , ATP5MK , ATP5MC3 , MT‐ATP6 , and MT‐ATP8 ) and in two assembly factors ( TMEM70 and ATPAF2) . A recent report described a single individual with compound heterozygous variants in ATP5PO (c.34C>T (p.Gln12Ter) and c.329‐20A>G), who had seizures, hypotonia, elevated lactate in cerebrospinal fluid, acquired microcephaly, dystonia, global developmental delay, and progressive brain atrophy 4 . Here, we report three additional individuals from two unrelated families in whom we identified a rare, homozygous splice variant in ATP5PO .…”