Quantitative expression proteomics and phosphoproteomics profile of brain from PINK1 knockout mice: insights into mechanisms of familial Parkinson's disease
Abstract
Parkinson's disease (PD) is an age-related, neurodegenerative motor disorder characterized by progressive degeneration of dopaminergic neurons in the substantia nigra pars compacta and presence of α-synuclein-containing protein aggregates. Mutations in the mitochondrial Ser/Thr kinase PTEN-induced kinase 1 (PINK1) are associated with an autosomal recessive familial form of early-onset PD. Recent studies have suggested that PINK1 plays important neuroprotective roles against mitochondrial dysfunction by phosphorylating and recruiting Parkin, a cytosolic E3 ubiquitin ligase, to facilitate elimination of damaged mitochondria via autophagy-lysosomal pathways. Loss of PINK1 in cells and animals leads to various mitochondrial impairments and oxidative stress, culminating in dopaminergic neuronal death in humans. Using a 2-D polyacrylamide gel electrophoresis proteomics approach, the differences in expressed brain proteome and phosphoproteome between 6-month-old PINK1-deficient mice and wild-type mice were identified. The observed changes in the brain proteome and phosphoproteome of mice lacking PINK1 suggest that defects in signaling networks, energy metabolism, cellular proteostasis, and neuronal structure and plasticity are involved in the pathogenesis of familial PD. Mutations in PINK1 are associated with an early-onset form of Parkinson's disease (PD). This study examines changes in the proteome and phosphoproteome of the PINK1 knockout mouse brain. Alterations were noted in several key proteins associated with: increased oxidative stress, aberrant cellular signaling, altered neuronal structure, decreased synaptic plasticity, reduced neurotransmission, diminished proteostasis networks, and altered metabolism. 14-3-3ε, 14-3-3 protein epsilon; 3-PGDH, phosphoglycerate dehydrogenase; ALDOA, aldolase A; APT1, acyl-protein thioesterase 1; CaM, calmodulin; CBR3, carbonyl reductase [NADPH] 3; ENO2, gamma-enolase; HPRT, hypoxanthine-guanine phosphoribosyltransferase; HSP70, heat-shock-related 70 kDa protein 2; IDHc, cytoplasmic isocitrate dehydrogenase [NADP+]; MAPK1, mitogen-activated protein kinase 1; MEK1, MAP kinase kinase 1; MDHc, cytoplasmic malate dehydrogenase; NFM, neurofilament medium polypeptide; NSF, N-ethylmaleimide-sensitive fusion protein; PHB, prohibitin; PINK1, PTEN-induced putative kinase 1; PPIaseA, peptidyl-prolyl cis-trans isomerase A; PSA2, proteasome subunit alpha type-2; TK, transketolase; VDAC-2, voltage-dependent anion-selective channel protein 2.
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Reduced mitophagy via Pink1/Parkin-regulated ubiquitination in aged neurons contributes to greater ROS accumulation.
“Reduced mitophagy associated Pink1- and Parkin-regulated ubiquitination of the outer mitochondrial membrane of damaged mitochondria in aged neurons (79, 99, 140) contribute to a greater accumulation of ROS (81).”
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Self-citationRegulation of mitochondrial permeability transition pore by PINK1
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Self-citationPINK1 enhances insulin-like growth factor-1-dependent Akt signaling and protection against apoptosis
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Ubiquitin proteasome system in Parkinson's disease: A keeper or a witness?
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GSK ‐3α/β‐mediated phosphorylation of CRMP ‐2 regulates activity‐dependent dendritic growth
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Metabolic Control Analysis in a Cellular Model of Elevated MAO-B: Relevance to Parkinson’s Disease
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PINK1 as a Molecular Checkpoint in the Maintenance of Mitochondrial Function and Integrity
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“Previous research has suggested that VDACs are probably factors in PD-associated neurodegeneration (Sun et al., 2012) (Triplett et al., 2015).”
Oligodendrocytes support axonal transport and maintenance via exosome secretion
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BackgroundMitochondria initiate and regulate sarcopenia
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“However, mitochondrial damage and modifications also may occur by posttranslational modifications such as ubiquitination (67,99,140,148), acetylation (9,21,28), succinylation (114,150), and phosphorylation (51,73,79).”
BackgroundInteractions between iron and α-synuclein pathology in Parkinson's disease
Chen, B., Wen, X., Jiang, H. F., Wang, J., Song, N., & Xie, J. (2019) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2019.06.024 · Cited by 103 · see citing works
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“Another target of SIRT3 is FOXO3a, where, specifically, the deacetylation of FOXO3a at K271 and K290 results in the up-regulation of proteins such as previously mentioned PGC-1α and TFAM (Tseng et al., 2013).”
BackgroundInfluentialGene networks in neurodegenerative disorders
Recabarren, D. A., & Alarcón, M. A. (2017) · Life Sciences · doi:10.1016/j.lfs.2017.06.009 · Cited by 65 · see citing works
PARK2 Mutation Causes Metabolic Disturbances and Impaired Survival of Human iPSC-Derived Neurons
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“Such methods have been applied to cell and animal models of parkin and PINK1 dysfunction revealing changes in proteins involved in oxidative stress, synaptic plasticity, protein folding, and energy metabolism (Ozgul et al., 2015; Triplett et al., 2015).”
MethodPhosphoregulation on mitochondria: Integration of cell and organelle responses
Lucero, M., Suarez, A. E., & Chambers, J. W. (2019) · CNS Neuroscience & Therapeutics · doi:10.1111/cns.13141 · Cited by 58 · see citing works
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Proteasome Subunits Involved in Neurodegenerative Diseases
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“of several neurodegenerative diseases [22, 30, 31].”
Self-citationAnalysis of neuronal phosphoproteome reveals PINK1 regulation of BAD function and cell death
Wan, H., Tang, B., Liao, X., Zeng, Q., Zhang, Z., & Liao, L. (2017) · Cell Death and Differentiation · doi:10.1038/s41418-017-0027-x · Cited by 39 · see citing works
Self-citationLu, X., Liu, Q., Zhang, J., Zhou, D., Yang, G., Li, M., Qiu, Y., Chen, Q., Zheng, H., & Dai, J. (2020) · Cancer Management and Research · doi:10.2147/cmar.s262466 · Cited by 36 · see citing works
Mitochondrial Protein PINK1 Positively Regulates RLR Signaling
Zhou, J., Yang, R., Zhang, Z., Liu, Q., Zhang, Y., Wang, Q., & Yuan, H. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.01069 · Cited by 33 · see citing works
“PINK1 plays neuroprotective roles against dysfunctional mitochondria by recruiting Parkin, a cytosolic E3 ubiquitin ligase (27).”
BackgroundSelf-citationZhang, L., Wang, J.-Z., Liu, Q., Xiao, Z., & Dai, Q.-D. (2020) · NeuroToxicology · doi:10.1016/j.neuro.2020.02.004 · Cited by 33 · see citing works
Involvement of heat shock proteins on Mn-induced toxicity in Caenorhabditis elegans
Ávila, D. S., Benedetto, A., Au, C., Bornhorst, J., & Aschner, M. (2016) · BMC Pharmacology and Toxicology · doi:10.1186/s40360-016-0097-2 · Cited by 32 · see citing works
Ren, X., Hinchie, A., Swomley, A., Powell, D. K., & Butterfield, D. A. (2019) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2019.08.008 · Cited by 29 · see citing works
“Oxidative damage, inflammation, dysfunction of brain mitochondria, and altered proteostasis also are thought to be associated with the pathophysiology and progression of PD [3].”
BackgroundChaanine, A. H. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms221910579 · Cited by 30 · see citing works
PINK1 deficiency enhances autophagy and mitophagy induction
Gómez‐Sánchez, R., Yakhine-Diop, S. M. S., Pedro, J. M. B., Pizarro‐Estrella, E., Rodríguez‐Arribas, M., Climent, V. E., Martín‐Cano, F. E., González-Soltero, M. E., Tandon, A., Fuentes, J. M., et al. (2015) · Molecular & Cellular Oncology · doi:10.1080/23723556.2015.1046579 · Cited by 29 · see citing works
“In summary, PINK1 is involved in several signaling networks that are essential for cellular homeostasis, thus increasing the risk of developing separate disorders.(50) Because of its dual role, PINK1 is a promising therapeutic strategy for PD and cancer, but further information about its function is required in order…”
BackgroundArndt, D. A., Oostveen, E. K., Triplett, J. C., Butterfield, D. A., Tsyusko, O. V., Collin, B., Starnes, D. L., Cai, J., Klein, J. B., Nass, R., et al. (2017) · Comparative Biochemistry and Physiology Part C Toxicology & Pharmacology · doi:10.1016/j.cbpc.2017.08.009 · Cited by 27 · see citing works
“Immunoprecipitation was performed with 100 µg of C. elegans protein, and immunoprecipitation and western blotting validation were performed following methods from a previously described protocol (Triplett et al., 2015).”
MethodInfluentialSelf-citationDJ-1 mutation decreases astroglial release of inflammatory mediators
Ashley, A. K., Hinds, A., Hanneman, W. H., Tjalkens, R. B., & Legare, M. E. (2015) · NeuroToxicology · doi:10.1016/j.neuro.2015.12.007 · Cited by 27 · see citing works
Khan, A., Kuriachan, G., & Mahalakshmi, R. (2021) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.1c00429 · Cited by 25 · see citing works
Butterfield, D. A., Palmieri, E. M., & Castegna, A. (2016) · Expert Review of Proteomics · doi:10.1586/14789450.2016.1149470 · Cited by 25 · see citing works
Self-citationNetwork Analysis Identifies Disease-Specific Pathways for Parkinson’s Disease
Monti, C., Colugnat, I., Lopiano, L., Chiò, A., & Alberio, T. (2016) · Molecular Neurobiology · doi:10.1007/s12035-016-0326-0 · Cited by 25 · see citing works
Chithra, Y., Dey, G., Ghose, V., Chandramohan, V., Gowthami, N., Vasudev, V., & Bharath, M. M. S. (2023) · Neurochemical Research · doi:10.1007/s11064-023-03907-x · Cited by 24 · see citing works
“Proteomics in the Rot model revealed altered expression of proteins implicated in mitochondrial, endoplasmic reticulum, autophagy, cytokinesis, cell cycle and cytoskeleton functions [34, 35].”
MethodWang, Y. A., Kammenga, J. E., & Harvey, S. C. (2017) · Human Genomics · doi:10.1186/s40246-017-0108-4 · Cited by 22 · see citing works
“In PD, mutations in PINK and Parkin (related to EOPD) or α-synuclein mutations (LOPD) lead to the inhibition of α-synuclein degradation as well as accumulation of autophagic vacuoles, which result in neuronal death [16, 96].”
BackgroundCompeting endogenous RNA (ceRNA) networks in Parkinson's disease: A systematic review
Asadi, M. R., Abed, S., Kouchakali, G., Fattahi, F., Sabaie, H., Moslehian, M. S., Sharifi‐Bonab, M., Hussen, B. M., Taheri, M. N., Ghafouri‐Fard, S., et al. (2023) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2023.1044634 · Cited by 22 · see citing works
“Previous research has shown a link between MAPK1 and the progression of PD (Triplett et al., 2015).”
BackgroundIdentification of Potential Core Genes in Parkinson’s Disease Using Bioinformatics Analysis
Quan, W., Li, J., Jin, X., Liu, L., Zhang, Q., Qin, Y., Pei, X., & Chen, J. (2021) · Parkinson s Disease · doi:10.1155/2021/1690341 · Cited by 21 · see citing works
“Previous studies have shown that MAPK1 is associated with the progression of PD [36].”
BackgroundHe, F., Qi, G., Zhang, Q., Cai, H., Li, T., Li, M., Zhang, Q., Chen, J., Ming, J., Tian, B., et al. (2020) · Cellular and Molecular Neurobiology · doi:10.1007/s10571-019-00780-7 · Cited by 20 · see citing works
Proteomic studies associated with Parkinson’s disease
Kasap, M., Akpınar, G., & Kanlı, A. (2017) · Expert Review of Proteomics · doi:10.1080/14789450.2017.1291344 · Cited by 20 · see citing works
Metabolic clues to salubrious longevity in the brain of the longest‐lived rodent: the naked mole‐rat
Triplett, J. C., Swomley, A. M., Kirk, J. M., Hardell, K. N. L., Orr, M. E., Rodriguez, K. A., Cai, J., Klein, J. B., Buffenstein, R., & Butterfield, D. A. (2015) · Journal of Neurochemistry · doi:10.1111/jnc.13149 · Cited by 18 · see citing works
“Gel staining to detect proteins and phosphoproteins was carried out according to manufacturer’s directions and as previously described (Triplett et al. 2015).”
MethodSelf-citationTahir, W., Zafar, S., Llorens, F., Arora, A. S., Thüne, K., Schmitz, M., Gotzmann, N., Kruse, N., Mollenhauer, B., Torres, J. M., et al. (2016) · Molecular Neurobiology · doi:10.1007/s12035-016-0294-4 · Cited by 16 · see citing works
“been implicated in PINK1 (KO) mouse brain [76], whereas transforming protein RhoA is reported to have a role in polymerization of actin filaments in sCJD patients [19],”
BackgroundParkin Coordinates Platelet Stress Response in Diabetes Mellitus: A Big Role in a Small Cell
Lee, S. H., Du, J., Hwa, J., & Kim, W. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21165869 · Cited by 15 · see citing works
“It has also been associated with neuronal diseases [36,45,46];”
BackgroundAuburger, G. W. J., Gispert, S., & Brehm, N. (2016) · Parkinson s Disease · doi:10.1155/2016/4686185 · Cited by 15 · see citing works
“It is a component of Lewy bodies in Parkinson’s disease brains [111] and a reduction of phospho-NFM levels was already observed in PINK1-KO mouse brains [112].”
BackgroundRen, X., & Butterfield, D. A. (2020) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2020.12.004 · Cited by 15 · see citing works
Self-citationDomenico, F. D., Zuliani, I., & Tramutola, A. (2019) · Expert Review of Proteomics · doi:10.1080/14789450.2019.1691919 · Cited by 14 · see citing works
“In a different study, Triplett and coworkers performed the proteomic analysis of PINK1 KO mice brain, a further model of PD, showing that two subunits of V0-type proton ATPase were found to be altered in either phosphorylation or expression: V0-ATPase A and V0-ATPase F [124].”
BackgroundRecent advances in applying mass spectrometry and systems biology to determine brain dynamics
Scifo, E., Calza, G., Fuhrmann, M., Soliymani, R., Baumann, M., & Lalowski, M. M. (2017) · Expert Review of Proteomics · doi:10.1080/14789450.2017.1335200 · Cited by 13 · see citing works
Proteomic Investigation of Murine Neuronal α7-Nicotinic Acetylcholine Receptor Interacting Proteins
Mulcahy, M. J., Paulo, J. A., & Hawrot, E. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00618 · Cited by 12 · see citing works
Gel‐Based and Gel‐Free Phosphoproteomics to Measure and Characterize Mitochondrial Phosphoproteins
Thongboonkerd, V., & Chaiyarit, S. (2022) · Current Protocols · doi:10.1002/cpz1.390 · Cited by 10 · see citing works
Eroglu, B., Jin, X., Deane, S., Öztürk, B., Ross, O. A., Moskophidis, D., & Mivechi, N. F. (2022) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-022-04162-z · Cited by 9 · see citing works
Prohibitins in neurodegeneration and mitochondrial homeostasis
Fernandez-Abascal, J., & Artal‐Sanz, M. (2022) · Frontiers in Aging · doi:10.3389/fragi.2022.1043300 · Cited by 10 · see citing works
“464-fold) as compared with control animals (Triplett et al., 2015).”
Smith, A. D. T., Moreno, N. M., Rodrı́guez, J. A., Marín-Loaiza, J. C., & Bustos, G. A. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26125688 · Cited by 6 · see citing works
Bernstein, H., Smalla, K., Keilhoff, G., Dobrowolny, H., Kreutz, M. R., & Steiner, J. H. (2023) · Journal of Chemical Neuroanatomy · doi:10.1016/j.jchemneu.2023.102321 · Cited by 4 · see citing works
Age-Related Changes of 14-3-3 Isoforms in Midbrain of A53T-SNCA Overexpressing Mice
Brehm, N., Rau, K., Kurz, A., Gispert, S., & Auburger, G. W. J. (2015) · Journal of Parkinson s Disease · doi:10.3233/jpd-150606 · Cited by 5 · see citing works
“The relevance of the 14-3-3 family is also underlined by recent observations that they are implicated in the pathogenesis of PD caused by LRRK2, Parkin and PINK1 mutations [41, 55–58].”
BackgroundAntioxidants and Polyphenols Mediate Mitochondrial Mediated Muscle Death Signaling in Sarcopenia
Alway, S. E. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-810422-4.00026-9 · Cited by 6 · see citing works
Mitochondrial Proteins in the Development of Parkinson’s Disease
Zilocchi, M., Fasano, M., & Alberio, T. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-981-13-8367-0_2 · Cited by 5 · see citing works
What if? Mouse proteomics after gene inactivation
Gianazza, E., Miller, I., Guerrini, U., Palazzolo, L., Laurenzi, T., Parravicini, C., & Eberini, I. (2019) · Journal of Proteomics · doi:10.1016/j.jprot.2019.03.008 · Cited by 4 · see citing works
Du, X., Song, S., Wang, J., Zhang, H., Ma, Y., Wang, Z., Mo, Q., Ji, M., Liu, S., Wang, Z., et al. (2025) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2025.10.001 · Cited by 2 · see citing works
Uncovering systems-level molecular similarities between Alzheimer’s and Parkinson’s diseases
Fallahi, H., Radak, M., & Yadegari, Z. S. (2023) · Neuroscience and Behavioral Physiology · doi:10.1007/s11055-023-01484-8 · Cited by 2 · see citing works
“In the literature, TAGLN2 had no direct relationship with PD, but, its close paralog, TAGLN3, has a role in the mouse model for PD [54].”
Le, J., Hu, X., Jiang, Y., Wang, Q., Ma, Q., & Cui, W. (2026) · Journal of Alzheimer s Disease · doi:10.1177/13872877251411546 · Cited by 1 · see citing works
Segura‐Aguilar, J. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-822120-4.00009-5 · Cited by 1 · see citing works
Ren, X. (2020) · UKnowledge (University of Kentucky) · doi:10.13023/etd.2020.024
“…metal ions and metalloids in the environment are suspected to play a role in the development of PD. Oxidative damage, inflammation, dysfunction of brain mitochondria, and altered proteostasis also are thought to be associated with the pathophysiology and progression of PD (Triplett et al., 2015).”
BackgroundInfluentialRecapitulating Parkinson’s disease pathology in a three-dimensional neural cell culture model
Taylor-Whiteley, T. R. (2019) · Sheffield Hallam University · doi:10.7190/shu-thesis-00321
Tytell, M., & Robinson, M. (2021) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.739254713.793583741
Hegde, A., Upadhyay, S. S., Prasad, T. S. K., & Modi, P. K. (2023) · Elsevier eBooks · doi:10.1016/b978-0-443-19084-1.00007-7
Sharma, K., Kaushal, P., & Kumar, V. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-3969-6_10
- Authors
- Triplett, J. C., Zhang, Z., Sultana, R., Cai, J., Klein, J. B., Büeler, H., & Butterfield, D. A.
- Affiliations
- University of Kentucky (US)
- Department of Chemistry University of Kentucky Lexington Kentucky USA
- University of Louisville (US)
- Corresponding author
- Butterfield, David Allan
- Venue
- Journal of Neurochemistry
- Publisher
- Wiley
- Published
- 2015-03
- Volume
- 133
- Issue
- 5
- Pages
- 750-765
- ISSN
- 0022-3042 (ISSN-L)
- 1471-4159
- OpenAlex
- W1974069592
- Cited by
- 58
- References
- 138
- Citations by year
- 2026: 1 · 2025: 2 · 2024: 1 · 2023: 6 · 2022: 3 · 2021: 5 · 2020: 9 · 2019: 10 · 2018: 2 · 2017: 7 · 2016: 6 · 2015: 6
- FWCI
- 4.94
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Neurochemistry (publishedVersion)
- PubMed (publishedVersion)
- Funders
- University of Kentucky Research Challenge Trust Fund
- Topics
- Health Sciences › Medicine › Neurology › Parkinson's Disease Mechanisms and Treatments
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Nuclear Receptors and Signaling
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Keywords
- Parkinson's disease, PINK1, Parkin, PINK1 knockout mice, brain proteome, phosphoproteome, mitochondrial dysfunction, oxidative stress, dopaminergic neurons, synaptic plasticity, energy metabolism, proteostasis, MAPK signaling, 14-3-3 proteins, mitophagy, neurodegeneration, protein phosphorylation
- MeSH terms
- Prohibitins, PTEN-Induced Putative Kinase, Animals, Brain Chemistry, Male, Parkinson Disease, Peptides, Phosphoproteins, Protein Kinases, Trypsin, Blotting, Western, Mice, Knockout, Proteomics, Proteasome Endopeptidase Complex, Immunoprecipitation, Mice
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