nakamura lab

Liao SC*, Kano K*, Phanse S*, Margolis E, Nguyen MK, Moutaoufik MT, Meng J, Simms J, Sei YJ, McAvoy K, Manfredi G, Halliday G, Babu M and Nakamura K. (2024) CHCHD2 mutant mice display mitochondrial protein accumulation and disrupted energy metabolism. bioRxiv. [preprint] doi: 10.1101/2024.08.30.610586. PMCID: PMC11384018. *equal contribution

Rademacher K*, Doric Z*, Haddad D*, Mamaligas A, Liao SC, Creed RB, Kano K, Chatterton Z, Fu Y, Garcia JH, Vance V, Sei YJ, Kreitzer A, Halliday GM, Nelson AB, Margolis EB, and Nakamura K. (2024) Chronic hyperactivation of midbrain dopamine neurons causes preferential dopamine neuron degeneration. bioRxiv. [preprint] doi: 10.1101/2024.04.05.588321. PMCID: PMC11030348. *equal contribution

Rademacher K, Nakamura K. (2024) Role of dopamine neuron activity in Parkinson’s disease pathophysiology. Exp Neurol. 373:114645. PMID: 38092187.

Bennett NK, Lee M, Orr AL, Nakamura K. (2024) Systems-level analyses dissociate genetic regulators of reactive oxygen species and energy production. PNAS 10.1073/pnas.2307904121. PMID: 38207075.

Ehinger Y, Laguesse S, Phamluong K, Salvi A, Hoisington ZW, Sonja D, Sei YJ, Nakamura K and Ron D. (2023) Paradoxical mTORC1-Dependent microRNA-mediated translation repression in the nucleus accumbens of mice consuming alcohol attenuates glycolysis. bioRxiv. [preprint] doi: 10.1101/2023.11.29.569312. PMCID: PMC10705386.

Furthmann N, Angersbach L, Bader V, Blusch A, Goel S, Sánchez-Vicente A, Krause LJ, Grover P, Trinkaus VA, van Well EM, Jaugstetter M, Tschulik K, Damgaard RB, Saft C, Ellrichmann G, Gold R, Koch A, Englert B, Glatzel M, Hartl U, Nakamura K, Christine CW, Huang EJ, Tatzelt J and Winklhofer KF. (2023) NEMO reshapes the protein aggregate interface and promotes aggrephagy by co-condensation with p62. Nat. Commun. 14(1):8368. PMCID: PMC10730909.

Sei YJ, Chaumeil MM, Nakamura K. (2023) Protocol to combine brain sections from multiple mice into a single block for spatial transcriptomic analyses. STAR Protoc 4(4):102617. PMCID: PMC10523026.

Li H*, Guglielmetti C*, Sei YJ*, Zilberter M, Le Page LM, Shields L, Yang J, Nguyen K, Tiret B, Gao X, Bennett N, Lo I, Dayton TL, Kampmann M, Huang Y, Rathmell JC, Vander Heiden M, Chaumeil MM, Nakamura K. (2023) Neurons Require Glucose Uptake and Glycolysis In Vivo. Cell Rep. 42(4):112335, PMID: 37027294. *equal contribution

Goel S, Oliva R, Jeganathan S, Kriegler S, Stender ID, Christine CW, Nakamura K, Hoffmann J, Winter R, Tatzelt J and Winklhofer KF. (2023) Linear ubiquitination induces NEMO phase separation to activate NF-κB signaling. Life Sci. Alliance. 6(4):e202201607. PMCID: PMC9889916.

Crouch EE, Bhaduri A, Andrews MG, Cebrian-Silla A, Diafos LN, Birrueta JO, Wedderburn-Pugh K, Valenzuela EJ, Bennett NK, Eze UC, Sandoval-Espinosa C, Chen J, Mora CN, Ross JM, Howard CE, Gonzalez-Granero S, Lozano JF, Vento M, Haeussler M, Paredes MF, Nakamura K, Garcia-Verdugo JM, Alvarez-Buylla A, Kriegstein AR, Huang EJ. (2022) Ensembles of endothelial and mural cells promote angiogenesis in prenatal human brain. Cell. 185(20):3753-3769.e18. PMID: 36179668.

Bennett NK*, Nakaoka HJ*, Laurent D, Okomoto RA, Sei Y, Horvai AE, Bivona TG, ten Hoeve J, Graeber TG, Nakamura K, Nakamura JL. (2022) Primary and metastatic tumors exhibit systems-level differences in dependence on mitochondrial respiratory function. PLoS Biol. 20(9):e3001753. PMID: 36137002. *equal contribution

Rius R*, Bennett NK*, Bhattacharya K, Yueksel Z, Formosa LE, Compton AG, Dale RC, Cowley MJ, Gayevskiy V, Al Tala SM, Almehery AA, Ryan MT, Thorburn DR, Nakamura K**, Christodoulou J**. (2022) Biallelic pathogenic variants in COX11 are associated with an infantile-onset mitochondrial encephalopathy. Hum Mutat. PMID 36030551. *equal contribution, **co-last authors

Kang UJ, Nakamura K, Zhuang X. (2022) Reader Response: Safety of AADC Gene Therapy for Moderately Advanced Parkinson Disease: Three-Year Outcomes From the PD-1101 Trial. Neurology. 99(6):258-259. PMID: 35940895.

Jung S, Zimin PI, Woods CB, Kayser EB, Haddad D, Reczek CR, Nakamura K, Ramirez JM, Sedensky MM, Morgan PG. (2022) Isoflurane inhibition of endocytosis is an anesthetic mechanism of action. Curr Biol. 32(14):3016-3032, PMID 35688155.

Doric Z, Li H, Nakamura K. (2022) The PINK1 advantage: recycling mitochondria in times of trouble? Autophagy 18(1): 231-232, PMID 34812108.

Nguyen MK*, McAvoy K*, Liao SC, Doric Z, Lo I, Li H, Manfredi G, Nakamura K. (2022) Mouse midbrain dopaminergic neurons survive loss of the PD-associated mitochondrial protein CHCHD2. Hum Mol Genet. 31(9):1500-1518, PMID 34791217.

Doric, Z, Nakamura K. (2021) Mice with disrupted mitochondria used to model Parkinson’s disease. Nature. 599(7886):558-560.

Linsley JW, Shah K, Castello N, Chan M, Haddad D, Doric Z, Wang S, Leks W, Mancini J, Oza V, Javaherian A, Nakamura K, Kokel D, Finkbeiner S. (2021) Genetically encoded cell-death indicators (GEDI) to detect an early irreversible commitment to neurodegeneration. Nat Commun. 12(1):5284.

Li H*, Doric Z*, Berthet A*, Jorgens DM, Nguyen MK, Hsieh I, Margulis J, Fang R, Debnath J, Sesaki H, Finkbeiner S, Huang E and Nakamura K. (2021) Longitudinal tracking of neuronal mitochondria delineates PINK1/Parkin-dependent mechanisms of mitochondrial recycling and degradation. Science Advances. 7(32): eabf6580.

Perez-Bermejo JA*, Kang S*, Rockwood SJ*, Simoneau CR*, Joy DA, Silva AC, Ramadoss GN, Flanigan WR, Fozouni P, Li H, Chen PY, Nakamura K, Whitman JD, Hanson PJ, McManus BM, Ott M, Conklin BR, McDevitt TC. (2021) SARS-CoV-2 infection of human iPSC-derived cardiac cells reflects cytopathic features in hearts of patients with COVID-19. Sci Transl Med. 13(590).

Shields LY, Li H, Nguyen K, Kim H, Doric Z, Garcia JH, Gill TM, Haddad D, Vossel K, Calvert M, Nakamura K. (2021) Mitochondrial fission is a critical modulator of mutant APP-induced neural toxicity. J Biol Chem. 296:100469.

Klionsky DJ, …, Finkbeiner S, …, Nakamura K, …, Tong CK. (2021) Guidelines for the use and interpretation of assays for monitoring autophagy. (4th edition)1. Autophagy. 17(1):1-382.

Bennett NK, Nguyen MK, Darch M, Nakaoka HJ, Cousineau D, Hoeve JT, Graeber T, Schuelke M, Maltepe E, Kampmann M, Mendelsohn BA, Nakamura JL, Nakamura K. (2020) Defining the ATPome reveals cross-optimization of metabolic pathways. Nat Commun. 11, 4319.

Zhang J, Shang Y, Kamiya S, Kotowski SJ, Nakamura K, Huang E. (2019) Loss of HIPK2 protects neurons from mitochondrial toxins by regulating Parkin protein turnover. J Neurosci. 40(3):557-568.

de Haas R, Heltzel LCMW, Tax D, van den Broek P, Steenbreker H, Verheij MMM, Russel FGM, Orr AL, Nakamura K, and Smeitink JAM. (2019) To be or not to be Pink(1): contradictory findings in an animal model for Parkinson’s Disease. Brain Communications. 2019;1(1).

Mendelsohn BA, Bennett NK, Darch MA, Yu K, Nguyen MK, Pucciarelli D, Nelson M, Horlbeck MA, Gilbert LA, Hyun W, Kampmann M, Nakamura JL, and Nakamura K. (2018) A high throughput screen of real-time ATP levels in individual cells reveals mechanisms of energy failure. PLoS Biol. 16(8): e2004624.

Horlbeck MA, Xu A, Wang M, Bennett NK, Park CY, Bogdanoff D, Adamson B, Chow ED, Kampmann M, Peterson TR,Nakamura K, Fischback MA, Weissman JS*, Gilbert LA*. (2018) Mapping the genetic landscape of human cells. Cell. 174(4):953-967.

Malty RH, Aoki H, Kumar A, Phanse S, Amin S, Zhang Q, Minic Z, Goebels F, Musso G, Wu Z, Abou-tok H, Meyer M, Deineko V, Kassir S, Sidhu V, Jessulat M, Scott NE, Xiong X, Vlasbom J, Prasad B, Foster LJ, Alberio T, Garavaglia B, Yu H, Bader GD, Nakamura K, Parkinson J, Babu M. (2017) A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling. Cell Syst. 5(6):564-577.

Pathak D, Berthet A, Bendor JT, Yu K, Sellnow RC, Orr AL, Nguyen MK, Edwards RH, Manfredsson FP and Nakamura K. (2017) Loss of α-synuclein does not affect mitochondrial bioenergetics in rodent neurons. eNeuro. 4(2).

Haddad D, Nakamura K. (2017) PINK1-based screen shines light on autophagy enhancers for Parkinson’s disease. Cell Chem Biol. 24(4), 429-30.

Orr AL, Rutaganira FU, de Roulet D, Huang EJ, Hertz NT, Shokat KM, Nakamura K. (2017) Long-term oral kinetin does not protect against α-synuclein induced neurodegeneration in rodent models of Parkinson's disease. Neurochem Int.

Shields LY, Mendelsohn BA, Nakamura K. (2017) Measuring ATP in axons with FRET. In: Techniques to Investigate Mitochondrial Functions in Neurons, Neuromethods (eds Stefan Strack and Yuriy Usachev), Humana Press, Springer Science + Business Media LLC, New York, NY, Chapter 6, 115-131.

Haddad D, Nakamura K. (2015) Understanding the susceptibility of dopamine neurons to mitochondrial stressors in Parkinson's disease. FEBS Lett. 2015 Dec 21; 589(24 Pt A):3702-13.

Pathak D, Shields L, Mendelsohn BA, Haddad D, Lin W, Gerencser AA, Kim H, Brand MD, Edwards RH, Nakamura K. (2015) The role of mitochondrially derived ATP in synapatic vesicle recycling. J Biol Chem. 290(37):22325-36. (selected by JBC editors as one of the 16 “Best of JBC Papers of the Week,” top paper from Bioenergetics in 2015)

Shields LY*, Kim H*, Zhu L, Haddad D, Berthet A, Pathak D, Lam M, Ponnusamy R, Diaz-Ramirez LG, Gill TM, Sesaki H, Mucke L, Nakamura K.  (2015) Dynamin-related protein 1 (Drp1) is required for normal mitochondrial bioenergetic and synaptic function in CA1 hippocampal neurons. Cell Death Dis. 6:e1725.

Berthet A, Margolis EB, Zhang J, Hsieh I, Zhang J, Hnasko T, Ahmad J, Edwards RH, Sesaki H, Huang EJ, Nakamura K. (2014) Loss of mitochondrial fission depletes axonal mitochondria in midbrain dopamine neurons. J Neuroscience. 34(43):14304-14317

Skibinski G, Nakamura K, Cookson MR, Finkbeiner S. (2014) Mutant LRRK2 Toxicity in Neurons Depends on LRRK2 Levels and Synuclein But Not Kinase Activity or Inclusion Bodies. J Neuroscience. 34(2), 418-33

Ho, L, Titus AS, Bannerjee KK, George S, Lin W, Saha AK, Nakamura K, Gut P, Verdin E, Kolthur U. (2013) SIRT4 Regulates ATP homeostasis and mediates a retrograde signaling via AMPK. Aging. 5(11), 835-849

Pathak D, Berthet A, Nakamura K. (2013) Energy failure- does it contribute to neurodegeneration? Ann Neurol. 74(4), 506-516

Manzanillo PS, Ayres JS, Watson RO, Collins AC, Souza G, Rae CS, Schneider DS, Nakamura K, Shiloh MU, Cox JS. (2013) The ubiquitin ligase PARKIN is required for autophagy and host resistance to intracellular pathogens. Nature. 501 (7468):512-6

Hertz NT, Berthet A, Sos ML, Thorn KS, Burlingame AL, Nakamura K, Shokat KM. (2013) A neo-substrate that amplifies catalytic activity of Parkinson's disease related kinase PINK1. Cell. 154 (737-747).

Yoshida S, Tsutsumi S, Muhlebach G, Sourbier C, Lee MJ, Lee S, Vartholomaiou E, Tatakoro M, Beebe K, Miyajima N, Mohney RP, Chen Y, Hasumi H, Xu W, Fukushima H, Nakamura K, Koga F, Kihara K, Trepel J, Picard D, Neckers L. (2013) Molecular chaperone TRAP1 regulates a metabolicswitch between mitochondrial respiration and aerobic glycolysis. Proc Natl Acad Sci USA. 110(17), E1604-12

Nakamura, K. (2013) α-Synuclein and mitochondria: partners in crime? Neurotherapeutics. 10(3), 391-9.

Itoh K, Nakamura K, Iijima M, Sesaki H. Mitochondrial Dynamics in Neurodegeneration. (2013) Trends Cell Biol. 23(2), 64-71

Nakamura K, Nemani VM, Azarbal F, Skibinski G, Levy JM, Egami K, Munishkina L, Zhang J, Gardner B, Wakabayashi J, Sesaki H, Cheng Y, Finkbeiner S, Nussbaum RL, Edwards RH. (2011) Direct membrane association drives mitochondrial fission by the Parkinson’s disease-associated protein α-synuclein. J Biol Chem. 286(23), 20710-26. (selected by JBC editors as one of the 20 “Best of 2011,” top paper from Neurobiology in 2011)

Nemani VM, Lu W, Berge V, Nakamura K, Ono V, Lee MK, Chaudhry FA, Nicoll RA, Edwards RH. (2010) Increased expression of alpha-synuclein reduces neurotransmitter release by inhibiting synaptic vesicle reclustering after endocytosis. Neuron 65(1), 66-79.

Fortin DL, Nemani VM, Nakamura K, Edwards RH. (2010) The behavior of alpha-synuclein in neurons. Mov Disord. 25 Suppl 1: S21-6.

Nakamura K, Nemani VM, Wallender EK, Kaehlcke K, Ott M, Edwards RH. (2008) Optical reporters for the conformation of alpha-synuclein reveal a specific interaction with mitochondria. J Neurosc i28(47), 12305-17.

Nakamura K, Christine CW, Starr PA, Marks WJ. (2007) Effects of unilateral subthalamic and pallidal deep brain stimulation on fine motor functions in Parkinson's disease. Mov Disord. 22(5), 619-26.

Nakamura K, Edwards RH. (2007) Physiology versus pathology in Parkinson's disease. Proc Natl Acad Sci USA. 104(29), 11867-8.

Nakamura K, Aminoff MJ. (2007) Huntington's disease: clinical characteristics, pathogenesis and therapies. Drugs Today. 43(2), 97-116.

Nakamura K. (2006) Medical management of Parkinson's disease. Harrison's Online. McGraw-Hill, www.accessmedicine.com.

Nakamura K, Kang UJ. (2006) Trophic factor delivery by gene therapy. In: Textbook of neural repair and rehabilitation (eds Selzer ME, Cohen L, Gage FH, Clarke S and Duncan PW), Cambridge University Press, Cambridge, UK, Chapter 29, pp 532-547.

Fortin DL, Troyer MD, Nakamura K, Kubo S, Anthony MD, Edwards RH. (2004) Lipid rafts mediate the synaptic localization of α-synuclein. J Neurosci. 24(30), 6715-6723.

Nakamura K, Mukherjee P, Swanson RA. (2004) Vitamin B12 deficiency. Arch Neurol. 61(6), 960.

Nakamura K, Roberson ED, Reilly LG, Tsao JW. (2003) Polyneuropathy following gastric bypass surgery. Am J Med. 115(8), 679-680.

Kang UJ, Nakamura K. (2003) Potential of gene therapy for pediatric neurotransmitter diseases: lessons from Parkinson's disease. Ann Neurol. 54 Suppl 6, S103-9.

Nakamura K, Bindokas VP, Kowlessur D, Elas M, Milstien S, Marks JD, Halpern HJ, Kang UJ. (2001) Tetrahydrobiopterin scavenges superoxide in dopaminergic neurons. J Biol Chem. 276(37), 34402-7.

Nakamura K, Ahmed M, Barr E, Leiden J, Kang UJ. (2000) The localization and functional contribution of striatal aromatic L-amino acid decarboxylase to L-3,4-dihydroxyphenylalanine decarboxylation in rodent parkinsonian models. Cell Transplantation. 9(5), 567-576.

Nakamura K, Won L, Heller A, Kang UJ. (2000) Preferential resistance of dopaminergic neurons to glutathione depletion in a reconstituted nigrostriatal system. Brain Res. 873(2), 203-211.

Nakamura K, Bindokas VP, Marks JD, Wright DA, Frim DM, Miller RJ, Kang UJ. (2000) The selective toxicity of 1-methyl-4-phenylpyridinium to dopaminergic neurons: the role of mitochondrial complex I and reactive oxygen species revisited. Mol Pharmacol. 58(2), 271-278.

Nakamura K, Wright DA, Wiatr T, Kowlessur D, Milstien S, Lei XG, Kang UJ. (2000) Preferential resistance of dopaminergic neurons to glutathione depletion is independent of cellular glutathione peroxidase and is mediated by tetrahydrobiopterin. J Neurochem. 74(6), 2305-2314.

Nakamura K, Wang W, and Kang UJ. (1997) The role of glutathione in dopaminergic neuronal survival. J Neurochem. 69, 1850-1858.