Abstract
Elevated iron in the SNpc may play a key role in Parkinson’s disease (PD) neurodegeneration, yet the underlying mechanism accounting for this iron accumulation is unclear. Although iron is an essential element, excessive amounts produce toxicity. Here, we focused on the role of iron and ATP13A2, the causative gene of PARK9 neurodegeneration with brain iron accumulation, using a cellular model. ATP13A2 deficiency resulted in impaired lysosomal function and iron accumulation in cell organelles. Further, we found dysfunction of mitophagy, which is involved in managing mitochondrial quality, as well as mitochondrial damage. Furthermore, we confirmed a decreased heme synthesis capacity, which is important to maintain intracellular iron homeostasis. Overall, our study indicates that lysosome-derived mitochondrial impairment can disrupt intracellular iron homeostasis in a cell model of PD pathology. This could help better understand the mechanisms underlying PD.
Similar content being viewed by others
Data availability
The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.
Abbreviations
- PD:
-
Parkinson’s disease
- α-Syn:
-
α-synuclein
- ATP13A2:
-
ATPase cation transporting 13A2
- NBIA:
-
neurodegeneration with brain iron accumulation
- IRP2:
-
Iron regulatory protein 2
- SDS:
-
sodium dodecyl sulfate
- PBS:
-
phosphate-buffered saline
- KD:
-
knockdown
- α-Syn-SH cells:
-
human wild-type α-Syn in SH-SY5Y cells
- DFO:
-
deferoxamine mesylate
- TfR:
-
transferrin receptor
- DMT1:
-
divalent metal transporter 1
- FPN:
-
ferroportin
- apo-Tf apo:
-
Transferrin
- GBD:
-
glibenclamide
- 5-ALA:
-
5-aminolevulinic acid
- FAC:
-
ferric ammonium citrate
- naïve-SH:
-
cells naïve SH-SY5Y cells
- siATP:
-
siRNA targeting ATP13A2
- NC:
-
siRNA of negative control
References
Braak, H. et al. Staging of brain pathology related to sporadic parkinson’s disease. Neurobiol. Aging. 24, 197–211. https://doi.org/10.1016/s0197-4580(02)00065-9 (2003).
Charvin, D., Medori, R., Hauser, R. A. & Rascol, O. Therapeutic strategies for Parkinson disease: beyond dopaminergic drugs. Nat. Rev. Drug Discov. 17, 804–822. https://doi.org/10.1038/nrd.2018.136 (2018).
Ding, X. S. et al. Ferroptosis in parkinson’s disease: molecular mechanisms and therapeutic potential. Ageing Res. Rev. 91, 102077. https://doi.org/10.1016/j.arr.2023.102077 (2023).
Wise, R. M. et al. Interactions of dopamine, iron, and alpha-synuclein linked to dopaminergic neuron vulnerability in parkinson’s disease and neurodegeneration with brain iron accumulation disorders. Neurobiol. Dis. 175, 105920. https://doi.org/10.1016/j.nbd.2022.105920 (2022).
Zeng, X. S., Geng, W. S., Jia, J. J., Chen, L. & Zhang, P. P. Cellular and molecular basis of neurodegeneration in Parkinson disease. Front. Aging Neurosci. 10, 109. https://doi.org/10.3389/fnagi.2018.00109 (2018).
Perinan, M. T. et al. Effect modification between genes and environment and parkinson’s disease risk. Ann. Neurol. 92, 715–724. https://doi.org/10.1002/ana.26467 (2022).
Bandres-Ciga, S., Diez-Fairen, M., Kim, J. J. & Singleton, A. B. Genetics of parkinson’s disease: an introspection of its journey towards precision medicine. Neurobiol. Dis. 137, 104782. https://doi.org/10.1016/j.nbd.2020.104782 (2020).
Gialluisi, A. et al. Identification of sixteen novel candidate genes for late onset Parkinson’s disease. Mol. Neurodegener. 16 https://doi.org/10.1186/s13024-021-00455-2 (2021).
Matsui, H. et al. Cytosolic DsDNA of mitochondrial origin induces cytotoxicity and neurodegeneration in cellular and zebrafish models of parkinson’s disease. Nat. Commun. 12, 3101. https://doi.org/10.1038/s41467-021-23452-x (2021).
Meng, Y. et al. Putaminal Recombinant glucocerebrosidase delivery with magnetic Resonance-Guided focused ultrasound in parkinson’s disease: A phase I study. Mov. Disord. 37, 2134–2139. https://doi.org/10.1002/mds.29190 (2022).
Henrich, M. T., Oertel, W. H., Surmeier, D. J. & Geibl, F. F. Mitochondrial dysfunction in parkinson’s disease - a key disease hallmark with therapeutic potential. Mol. Neurodegener. 18, 83. https://doi.org/10.1186/s13024-023-00676-7 (2023).
Clark, E. H., de la Torre, V., Hoshikawa, A., Briston, T. & T. & Targeting mitophagy in parkinson’s disease. J. Biol. Chem. 296, 100209. https://doi.org/10.1074/jbc.REV120.014294 (2021).
Lin, M. K. & Farrer, M. J. Genetics and genomics of parkinson’s disease. Genome Med. 6, 48. https://doi.org/10.1186/gm566 (2014).
Li, H. et al. Mitochondrial dysfunction and mitophagy defect triggered by heterozygous GBA mutations. Autophagy 15, 113–130. https://doi.org/10.1080/15548627.2018.1509818 (2019).
Bloem, B. R., Okun, M. S. & Klein, C. Parkinson’s disease. Lancet 397, 2284–2303. https://doi.org/10.1016/S0140-6736(21)00218-X (2021).
Tian, Y. et al. Iron metabolism in aging and Age-Related diseases. Int. J. Mol. Sci. 23 https://doi.org/10.3390/ijms23073612 (2022).
Ramirez, A. et al. Hereditary parkinsonism with dementia is caused by mutations in ATP13A2, encoding a lysosomal type 5 P-type ATPase. Nat. Genet. 38, 1184–1191. https://doi.org/10.1038/ng1884 (2006).
Schneider, S. A. et al. ATP13A2 mutations (PARK9) cause neurodegeneration with brain iron accumulation. Mov. Disord. 25, 979–984. https://doi.org/10.1002/mds.22947 (2010).
Dehay, B. et al. Loss of P-type ATPase ATP13A2/PARK9 function induces general lysosomal deficiency and leads to Parkinson disease neurodegeneration. Proc. Natl. Acad. Sci. U S A. 109, 9611–9616. https://doi.org/10.1073/pnas.1112368109 (2012).
van Veen, S. et al. ATP13A2 deficiency disrupts lysosomal polyamine export. Nature 578, 419–424. https://doi.org/10.1038/s41586-020-1968-7 (2020).
Fujii, T. et al. Parkinson’s disease-associated ATP13A2/PARK9 functions as a lysosomal H(+),K(+)-ATPase. Nat. Commun. 14, 2174. https://doi.org/10.1038/s41467-023-37815-z (2023).
Rinaldi, D. E., Corradi, G. R., Cuesta, L. M. & Adamo, H. P. Tezanos Pinto, F. The Parkinson-associated human P5B-ATPase ATP13A2 protects against the iron-induced cytotoxicity. Biochim. Biophys. Acta. 1848, 1646–1655. https://doi.org/10.1016/j.bbamem.2015.04.008 (2015). de.
Ryan, B. J., Hoek, S., Fon, E. A. & Wade-Martins, R. Mitochondrial dysfunction and mitophagy in parkinson’s: from Familial to sporadic disease. Trends Biochem. Sci. 40, 200–210. https://doi.org/10.1016/j.tibs.2015.02.003 (2015).
Hsieh, C. H. et al. Functional impairment in Miro degradation and mitophagy is a shared feature in Familial and sporadic parkinson’s disease. Cell. Stem Cell. 19, 709–724. https://doi.org/10.1016/j.stem.2016.08.002 (2016).
Costas, M., Mehn, M. P., Jensen, M. P. & Que, L. Jr. Dioxygen activation at mononuclear nonheme iron active sites: enzymes, models, and intermediates. Chem. Rev. 104, 939–986. https://doi.org/10.1021/cr020628n (2004).
Enami, S., Sakamoto, Y. & Colussi, A. J. Fenton chemistry at aqueous interfaces. Proc. Natl. Acad. Sci. U S A. 111, 623–628. https://doi.org/10.1073/pnas.1314885111 (2014).
Lee, J. & Hyun, D. H. The interplay between intracellular iron homeostasis and neuroinflammation in neurodegenerative diseases. Antioxid. (Basel). 12 https://doi.org/10.3390/antiox12040918 (2023).
Zecca, L., Youdim, M. B., Riederer, P., Connor, J. R. & Crichton, R. R. Iron, brain ageing and neurodegenerative disorders. Nat. Rev. Neurosci. 5, 863–873. https://doi.org/10.1038/nrn1537 (2004).
Ishikawa, H. et al. Involvement of Heme regulatory motif in Heme-mediated ubiquitination and degradation of IRP2. Mol. Cell. 19, 171–181. https://doi.org/10.1016/j.molcel.2005.05.027 (2005).
Hirayama, T., Niwa, M., Hirosawa, S. & Nagasawa, H. High-Throughput screening for the discovery of iron homeostasis modulators using an extremely sensitive fluorescent probe. ACS Sens. 5, 2950–2958. https://doi.org/10.1021/acssensors.0c01445 (2020).
Hirayama, T., Kadota, S., Niwa, M. & Nagasawa, H. A mitochondria-targeted fluorescent probe for selective detection of mitochondrial labile Fe(ii). Metallomics 10, 794–801. https://doi.org/10.1039/c8mt00049b (2018).
Niwa, M., Hirayama, T., Okuda, K. & Nagasawa, H. A new class of high-contrast Fe(II) selective fluorescent probes based on spirocyclized scaffolds for visualization of intracellular labile iron delivered by transferrin. Org. Biomol. Chem. 12, 6590–6597. https://doi.org/10.1039/c4ob00935e (2014).
Hirayama, T. et al. A Golgi-targeting fluorescent probe for labile Fe(ii) to reveal an abnormal cellular iron distribution induced by dysfunction of VPS35. Chem. Sci. 10, 1514–1521. https://doi.org/10.1039/c8sc04386h (2019).
Kawai, K. et al. Molecular imaging of labile Heme in living cells using a small molecule fluorescent probe. J. Am. Chem. Soc. 144, 3793–3803. https://doi.org/10.1021/jacs.1c08485 (2022).
Xie, Y. X. et al. Lysosomal exocytosis releases pathogenic alpha-synuclein species from neurons in synucleinopathy models. Nat. Commun. 13, 4918. https://doi.org/10.1038/s41467-022-32625-1 (2022).
Rivero-Rios, P., Madero-Perez, J., Fernandez, B. & Hilfiker, S. Targeting the Autophagy/Lysosomal degradation pathway in parkinson’s disease. Curr. Neuropharmacol. 14, 238–249. https://doi.org/10.2174/1570159x13666151030103027 (2016).
Krishna, A. et al. Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for parkinson’s disease. BMC Genom. 15, 1154. https://doi.org/10.1186/1471-2164-15-1154 (2014).
Usenovic, M., Tresse, E., Mazzulli, J. R., Taylor, J. P. & Krainc, D. Deficiency of ATP13A2 leads to lysosomal dysfunction, alpha-synuclein accumulation, and neurotoxicity. J. Neurosci. 32, 4240–4246. https://doi.org/10.1523/JNEUROSCI.5575-11.2012 (2012).
Erb, M. L., Sipple, K., Levine, N., Chen, X. & Moore, D. J. Adult-onset deletion of ATP13A2 in mice induces progressive nigrostriatal pathway dopaminergic degeneration and lysosomal abnormalities. NPJ Parkinsons Dis. 10, 133. https://doi.org/10.1038/s41531-024-00748-5 (2024).
Wang, R. et al. ATP13A2 facilitates HDAC6 recruitment to lysosome to promote autophagosome-lysosome fusion. J. Cell. Biol. 218, 267–284. https://doi.org/10.1083/jcb.201804165 (2019).
Kolnagou, A., Kontoghiorghe, C. N. & Kontoghiorghes, G. J. New targeted therapies and diagnostic methods for iron overload diseases. Front. Biosci. (Schol Ed). 10, 1–20. https://doi.org/10.2741/s498 (2018).
Terzi, E. M., Sviderskiy, V. O., Alvarez, S. W., Whiten, G. C. & Possemato, R. Iron-sulfur cluster deficiency can be sensed by IRP2 and regulates iron homeostasis and sensitivity to ferroptosis independent of IRP1 and FBXL5. Sci. Adv. 7 https://doi.org/10.1126/sciadv.abg4302 (2021).
Muckenthaler, M. U., Galy, B. & Hentze, M. W. Systemic iron homeostasis and the iron-responsive element/iron-regulatory protein (IRE/IRP) regulatory network. Annu. Rev. Nutr. 28, 197–213. https://doi.org/10.1146/annurev.nutr.28.061807.155521 (2008).
Klausner, R. D., Ashwell, G., van Renswoude, J., Harford, J. B. & Bridges, K. R. Binding of apotransferrin to K562 cells: explanation of the transferrin cycle. Proc. Natl. Acad. Sci. U S A. 80, 2263–2266. https://doi.org/10.1073/pnas.80.8.2263 (1983).
Du, X. et al. Activation of ATP-sensitive potassium channels enhances DMT1-mediated iron uptake in SK-N-SH cells in vitro. Sci. Rep. 6, 33674. https://doi.org/10.1038/srep33674 (2016).
Zhang, Q. et al. Deletion of Kir6.2/SUR1 potassium channels rescues diminishing of DA neurons via decreasing iron accumulation in PD. Mol. Cell. Neurosci. 92, 164–176. https://doi.org/10.1016/j.mcn.2018.08.006 (2018).
Kim, J. et al. miR-27a and miR-27b regulate autophagic clearance of damaged mitochondria by targeting PTEN-induced putative kinase 1 (PINK1). Mol. Neurodegener. 11, 55. https://doi.org/10.1186/s13024-016-0121-4 (2016).
Rajagopalan, S., Rane, A., Chinta, S. J. & Andersen, J. K. Regulation of ATP13A2 via PHD2-HIF1alpha signaling is critical for cellular iron homeostasis: implications for parkinson’s disease. J. Neurosci. 36, 1086–1095. https://doi.org/10.1523/JNEUROSCI.3117-15.2016 (2016).
Mochizuki, H. & Yasuda, T. Iron accumulation in parkinson’s disease. J. Neural Transm (Vienna). 119, 1511–1514. https://doi.org/10.1007/s00702-012-0905-9 (2012).
Borie, C. et al. Association study between iron-related genes polymorphisms and parkinson’s disease. J. Neurol. 249, 801–804. https://doi.org/10.1007/s00415-002-0704-6 (2002).
Salazar, J. et al. Divalent metal transporter 1 (DMT1) contributes to neurodegeneration in animal models of parkinson’s disease. Proc. Natl. Acad. Sci. U S A. 105, 18578–18583. https://doi.org/10.1073/pnas.0804373105 (2008).
Devos, D. et al. Trial of deferiprone in parkinson’s disease. N Engl. J. Med. 387, 2045–2055. https://doi.org/10.1056/NEJMoa2209254 (2022).
Acknowledgements
We thank the members of Inden’s lab for helpful discussions. This work was supported by the Japan Society for the Promotion of Science (JSPS) KAKENHI (Grant No. 22K06744 to MI), a Grant-in-Aid for Scientific Research on Innovative Areas JSPS KAKENHI (JP19H05767A02 to IH) a grant from the Smoking Research Foundation (Grant No. 2021G021) to MI, JST SPRING (Grant No. JPMJSP2142 to TM), and a grant from the Takeda Science Foundation to MI.
Funding
This work was supported by the Japan Society for the Promotion of Science (JSPS) KAKENHI (Grant No. 22K06744 to MI), a Grant-in-Aid for Scientific Research on Innovative Areas JSPS KAKENHI (JP19H05767A02 to IH), a grant from the Smoking Research Foundation (Grant No. 2021G021) to MI, JST SPRING (Grant No. JPMJSP2142 to TM) and a grant from the Takeda Science Foundation to MI.
Author information
Authors and Affiliations
Contributions
TM, KO and MI. designed the experiments. TM, KO, MK, HK, KK, RK, and ZW performed the experiments. TM, KO, HK, TH, ZW and MI analyzed the data. TM, KO and MI wrote and edited the manuscript. HN, YM and IH supervised the project. IH and MI acquired funding.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
About this article
Cite this article
Murakami, T., Ohuchi, K., Kiuchi, M. et al. Disruption of intracellular iron homeostasis through mitochondrial dysfunction associated with suppression of ATP 13A2 expression. Sci Rep (2026). https://doi.org/10.1038/s41598-026-35368-x
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s41598-026-35368-x


