Abstract
Dominant optic atrophy (DOA)1,2 and axonal peripheral neuropathy (Charcot-Marie-Tooth type 2, or CMT2)3 are hereditary neurodegenerative disorders most commonly caused by mutations in the canonical mitochondrial fusion genes OPA1 and MFN2, respectively4. In yeast, homologs of OPA1 (Mgm1) and MFN2 (Fzo1)5,6 work in concert with Ugo1, for which no human equivalent has been identified thus far7. By whole-exome sequencing of patients with optic atrophy and CMT2, we identified four families with recessive mutations in SLC25A46. We demonstrate that SLC25A46, like Ugo1, is a modified carrier protein that has been recruited to the outer mitochondrial membrane and interacts with the inner membrane remodeling protein mitofilin (Fcj1). Loss of function in cultured cells and in zebrafish unexpectedly leads to increased mitochondrial connectivity, while severely affecting the development and maintenance of neurons in the fish. The discovery of SLC25A46 strengthens the genetic overlap between optic atrophy and CMT2 while exemplifying a new class of modified solute transporters linked to mitochondrial dynamics.
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Acknowledgements
We would like to thank all families for participating in this study. We thank A. Torroni and A. Olivieri for their kind help with the control population samples from Sardinia. From the University of Miami, we are thankful to R. Cepeda for his excellent care and maintenance of the zebrafish facility, the transmission electron microscopy class of J. Prince, and to R. Duncan, W. Browne and P. Tsouflas for advice concerning phylogenic analysis. We are thankful to F. Poulain from the University of Utah for providing the Islet2-b fish and B. Schmid from the German Center for Neurodegenerative Diseases (DZNE) for donating the mitofish construct. This study was supported by US National Institutes of Health (NIH) grants R01NS075764, 5R01NS072248 and U54NS065712 (to S.Z.) and by the CMT Association and the Muscular Dystrophy Association. A.J.A. received additional support from the Lois Pope Life Foundation development award. This study was partially supported by the Cincinnati Children's Hospital Medical Center (CCHMC) Research Foundation and the Division of Human Genetics (to T.H.), US NIH grant R01DC012564 (to Z.M.A.) and ERMION, the E-RARE European consortium on optic atrophies (to V.C.). A.H.N. and S.M.D. were funded by the UK Oxford Partnership Comprehensive Biomedical Research Centre with funding from the UK Department of Health's National Institute for Health Research (NIHR) Biomedical Research Centres funding scheme. R.S. was funded by the European Union (E-RARE JTC grants 'NEUROLIPID' 01GM1408B and 'HSP/CMT genetics' PIOF-GA-2012-326681) and the Interdisciplinary Center for Clinical Research (IZKF) Tübingen (grant 1970-0-0). A.A. is supported by the National Institute of Neurological Disorders and Stroke, and L.B.G. is supported by US NIH Cellular and Molecular Biology Training Grant T32GM007315, US NIH Medical Scientist Training Grant T32GM07863 and US NIH grant F30 NRSA NS092238. A.B. is supported by US NIH grants RO1GM071775, GM105781 and GM112179. F.F. is supported by a Development grant from the American Heart Association.
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A.H.N., S.Z. and J.E.D. initiated the project, which was subsequently developed and led jointly by J.E.D., S.Z., T.H. and V.C. Experiments were conceived and carried out by A.J.A., A.R., C.Z., N.P., A.V.S., F.T., F.F., A.B., R.B.H., L.B.G., A.M. and R.S., with financial support from S.Z., T.H., A.A. and J.P. Zebrafish experiments were carried out by A.J.A., I.J.C. and S.G., with financial support from S.Z. and J.E.D. Patient recruitment, collection and analysis of human DNA, and genetic data analysis were carried out by M.A.G., F.S., L.A., S.M.D., L.C., C.L.M., R. Liguori, Z.M.A., K.L.S., X.W., L.A.K., Y.P., C.E.P., C.A.P., E.K.S., H.H.Z., O.A.A.-R. and Y.Y. Functional MRI-MRS data were generated by R. Lodi and Z.M.A. A.J.A. wrote the manuscript with critical input from S.Z. and J.E.D.
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Integrated supplementary information
Supplementary Figure 1 Sanger sequence traces and Clustal alignments of identified mutations.
(a) Sequence traces of the probands and one unaffected family member of all four pedigrees. Heterozygous mutations are marked by standard FASTA ambiguity code (R = A or G; Y = C or T; W = A or T). For frameshifts, inserted sequences are shown in red. (b) Clustal alignments show that all affected residues are conserved in vertebrates, with the exception of the residue affect by frameshift p.N296fs*297.
Supplementary Figure 2 Magnetic resonance imaging and spectroscopy (MRI-MRS) data.
(a) Midsagittal MRIs showing significant cerebellar atrophy in three of the probands. (b) MRS data indicating decreased NAA and increased lactate peaks in affected patients, typical of metabolic disorders.
Supplementary Figure 3 Maximum-likelihood phylogenetic tree containing all predicted mitochondrial carriers of H. sapiens, C. elegans, S. cerevisiae and S. pombe.
(a) Full tree drawn with 1,000 bootstraps. The red arrow indicates the node at which the SLC25A46 and Ugo1 orthologs bifurcate. (b) Collapsed tree depicting the node with calculated branch support values out of 1,000 and respective branch lengths (blue). SLC25A46 is orthologous to Y40B1B.8 in C. elegans, while Ugo1 is orthologous to Ugo1p in S. pombe; however, the branch support value between Ugo1 and SLC25A46 is under 700 and is therefore insufficient evidence for orthology between these proteins.
Supplementary Figure 4 Unrooted neighbor-joining trees of the mitochondrial solute carrier families of S. cerevisiae and H. sapiens with branch lengths drawn to scale.
Typical transporters are 30–40% identical to the family consensus sequence, while SLC25A46 and Ugo1 are both less than 20% identical to their respective families, as represented by longer branch lengths. Mitochondrial carrier homologs (MTCH1 and MTCH2) are also highly divergent.
Supplementary Figure 5 Colocalization patterns of additional outer and inner membrane proteins and endogenous mitofilin immunoprecipitation.
(a) Immunostaining patterns of SLC25A46, ANT2, mitofilin and TOM20 in COS-7 cells (scale bars, 1 µm). Linear profiles represent fluorescence intensity along the 2-µm white line in the merged image. Outer membrane proteins (SLC25A46 and TOM20) colocalize more with each other than with the inner membrane proteins (ANT2 and mitofilin). (b) Coimmunoprecipitation assay in mitochondrial extracts from HEK293T cells cotransfected with SLC25A46-HA. Immunoprecipitations were performed either by antibody to HA conjugated to Sepharose beads or protein G–conjugated seahorse beads plus a monoclonal antibody against mitofilin. The bound and unbound material were collected and probed by immunostaining with antibodies against HA, mitofilin and MFN2. M, total mitochondria.
Supplementary Figure 6 Validation of gene knockdown and assorted negative results.
(a) RT-PCR from COS-7 cells transfected with siRNA against SLC25A46 48 h post-transfection (h.p.t.). (b) Real-time PCR of HeLa cells transfected with siRNA 48 h.p.t. (c) RT-PCR used to validate morpholino (MO)-mediated knockdown in zebrafish at 48 h.p.f. The 508-bp amplicon was confirmed to be the result of exon 3 skipping, leading to a frameshift and protein truncation. (d) Whole-cell lysates from COS-7 cells show no significant changes in ATP levels. (e) Total mitochondrial DNA amount was not significantly different in HeLa cells. (f) ATP assay in whole zebrafish embryos at 24 h.p.f. shows no significant differences.
Supplementary Figure 7 Mitochondrial fusion assay by the extinction of mitochondrial-targeted photoactivated GFP (Mito PA-GFP).
Mito PA-GFP was activated in an ROI (white circle in the preactivated image), and images were acquired up to 90 min after activation. There was no significant difference between the extinction rates of control and knockdown cells by two-tailed t test, suggesting that there is neither an increase nor decrease in the mitochondrial fusion rate. Scale bars, 10 µm.
Supplementary Figure 8 The expression of slc25a46 in zebrafish retina and effects of morpholino knockdown.
(a–d) RNA In situ hybridization of zebrafish larvae at 72 h.p.f. (a) Control, sense probe shows background staining. (b–d) The antisense probe shows that the slc25a46 transcript is highly enriched in the neuronal processes of retinal ganglion cells (RGCs), including those of the optic nerve (ON), optic tectum (OT) and inner plexiform layer (IPL). The slc25a46 transcript is also enriched in a portion of the inner nuclear layer (INL). (e) Retinal ganglion cell staining using antibody to ZN5 with DAB in embryos injected with 0.45 pmol of either scrambled control MO or slc25a46 MO at 96 h.p.f. (f) Quantification of the staining intensity of the inner plexiform layer (IPL) suggests that fewer dendrites are present in the knockdown. The 8-bit gray scale numbers 0 = white and 256 = black were converted to percentages whereby 0 = white and 100 = black. One-tailed Student’s t test was used to determine significance. Control MO, n = 6; 0.45 pmol slc25a46 MO, n = 6. Scale bars, 50 μm in a–e. (g) Representative images of the gross morphology at 48 h.p.f. Scale bar, 1 mm. (h) Quantification of morphology: the curly phenotype was predominantly observed at the 0.45-pmol dosage. 0.45 pmol of control MO, n = 220; 0.45 pmol of slc25a46 MO, n = 223; 0.3 pmol of slc25a46 MO, n = 181. (i) Swim traces from three different larvae illustrating the angle of body curvature at 96 h.p.f.
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Abrams, A., Hufnagel, R., Rebelo, A. et al. Mutations in SLC25A46, encoding a UGO1-like protein, cause an optic atrophy spectrum disorder. Nat Genet 47, 926–932 (2015). https://doi.org/10.1038/ng.3354
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DOI: https://doi.org/10.1038/ng.3354
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