A systematic exploration of unexploited genes for oxidative stress in Parkinson’s disease

Rehm, H. L. et al. ClinGen — the clinical genome resource. N. Engl. J. Med. 372, 2235–2242 (2015).PubMed 
PubMed Central 

Google Scholar 
Sollis, E. et al. The NHGRI-EBI GWAS catalog: knowledgebase and deposition resource. Nucleic Acids Res. 51, D977–D985 (2023).PubMed 

Google Scholar 
Ochoa, D. et al. The next-generation open targets platform: reimagined, redesigned, rebuilt. Nucleic Acids Res. 51, D1353–D1359 (2023).PubMed 

Google Scholar 
Tian, R. et al. Genome-wide CRISPRi/a screens in human neurons link lysosomal failure to ferroptosis. Nat. Neurosci. 24, 1020–1034 (2021).PubMed 
PubMed Central 

Google Scholar 
Ghoussaini, M. et al. Open targets genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics. Nucleic Acids Res. 49, D1311–D1320 (2021).PubMed 

Google Scholar 
Dhindsa, R. S. et al. Rare variant associations with plasma protein levels in the UK Biobank. Nature 622, 339–347 (2023).PubMed 
PubMed Central 

Google Scholar 
Karczewski, K. J. et al. Systematic single-variant and gene-based association testing of thousands of phenotypes in 394,841 UK Biobank exomes. Cell Genomics 2, 100168 (2022).PubMed 
PubMed Central 

Google Scholar 
The Europe PMC Consortium. Europe PMC: a full-text literature database for the life sciences and platform for innovation. Nucleic Acids Res. 43, D1042–D1048 (2015).
Google Scholar 
Kafkas, Ş., Dunham, I. & McEntyre, J. Literature evidence in open targets – a target validation platform. J. Biomed. Semant. 8, 20 (2017).
Google Scholar 
Piñero, J. et al. DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. Nucleic Acids Res. 45, D833–D839 (2017).PubMed 

Google Scholar 
Li, G. et al. miRTex: a text mining system for miRNA-gene relation extraction. PLOS Comput. Biol. 11, e1004391 (2015).PubMed 
PubMed Central 

Google Scholar 
Chen, J. et al. RNADisease v4.0: an updated resource of RNA-associated diseases, providing RNA-disease analysis, enrichment and prediction. Nucleic Acids Res. 51, D1397–D1404 (2023).PubMed 

Google Scholar 
Li, Q., Kim, S., Zaslavsky, L., Cheng, T. & Yu, B. Resource description framework (RDF) modeling of named entity co-occurrences derived from biomedical literature in the PubChemRDF https://ceur-ws.org/Vol-3415/paper-4.pdf (2023).Esaki, T. & Ikeda, K. Difficulties and prospects of data curation for ADME in silico modeling. CBIJ 23, 1–6 (2023).
Google Scholar 
Suzuki, T., Ono, Y. & Bono, H. Comparison of oxidative and hypoxic stress responsive genes from meta-analysis of public transcriptomes. Biomedicines 9, 1830 (2021).PubMed 
PubMed Central 

Google Scholar 
Bono, H. Meta-analysis of oxidative transcriptomes in insects. Antioxidants 10, 345 (2021).PubMed 
PubMed Central 

Google Scholar 
Dorsey, E. R. et al. Global, regional, and national burden of Parkinson’s disease, 1990–2016: a systematic analysis for the global burden of disease study 2016. Lancet Neurol. 17, 939–953 (2018).
Google Scholar 
Davie, C. A. A review of Parkinson’s disease. Br. Med. Bull. 86, 109–127 (2008).PubMed 

Google Scholar 
Obeso, J. A. et al. Missing pieces in the Parkinson’s disease puzzle. Nat. Med 16, 653–661 (2010).PubMed 

Google Scholar 
Wiecki, T. V. & Frank, M. J. Chapter 14 – Neurocomputational models of motor and cognitive deficits in Parkinson’s disease. In: Progress in Brain Research (eds. Björklund, A. & Cenci, M. A.) vol. 183, 275–297 (Elsevier, 2010).Sahoo, S., Padhy, A. A., Kumari, V. & Mishra, P. Role of ubiquitin–proteasome and autophagy-lysosome pathways in α-synuclein aggregate clearance. Mol. Neurobiol. 59, 5379–5407 (2022).PubMed 

Google Scholar 
Zhou, Z. D., Yi, L. X., Wang, D. Q., Lim, T. M. & Tan, E. K. Role of dopamine in the pathophysiology of Parkinson’s disease. Transl. Neurodegener. 12, 44 (2023).PubMed 
PubMed Central 

Google Scholar 
Ramesh, S., Arachchige, A. S. P. M., Ramesh, S. & Arachchige, A. S. P. M. Depletion of dopamine in Parkinson’s disease and relevant therapeutic options: a review of the literature. AIMSN 10, 200–231 (2023).
Google Scholar 
Dias, V., Junn, E. & Mouradian, M. M. The role of oxidative stress in Parkinson’s disease. J. Parkinson’s Dis. 3, 461–491 (2013).
Google Scholar 
Klinkovskij, A., Shepelev, M., Isaakyan, Y., Aniskin, D. & Ulasov, I. Advances of genome editing with CRISPR/Cas9 in neurodegeneration: the right path towards therapy. Biomedicines 11, 3333 (2023).PubMed 
PubMed Central 

Google Scholar 
Simmnacher, K. et al. Unique signatures of stress-induced senescent human astrocytes. Exp. Neurol. 334, 113466 (2020).PubMed 

Google Scholar 
Krauskopf, J. et al. Transcriptomics analysis of human iPSC-derived dopaminergic neurons reveals a novel model for sporadic Parkinson’s disease. Mol. Psychiatry 27, 4355–4367 (2022).PubMed 

Google Scholar 
Tong, Z.-B., Braisted, J., Chu, P.-H. & Gerhold, D. The MT1G Gene in LUHMES neurons is a sensitive biomarker of neurotoxicity. Neurotox. Res. 38, 967–978 (2020).PubMed 
PubMed Central 

Google Scholar 
The irradiated brain microenvironment supports glioma stemness and survival via astrocyte-derived transglutaminase 2 | Cancer Research | American Association for Cancer Research. https://aacrjournals.org/cancerres/article/81/8/2101/670586/The-Irradiated-Brain-Microenvironment-Supports (2021).Shimada, M., Tsukada, K., Kagawa, N. & Matsumoto, Y. Reprogramming and differentiation-dependent transcriptional alteration of DNA damage response and apoptosis genes in human induced pluripotent stem cells. J. Radiat. Res. 60, 719–728 (2019).PubMed 
PubMed Central 

Google Scholar 
Loeliger, B. W. et al. Effect of ionizing radiation on transcriptome during neural differentiation of human embryonic stem cells. Rare 193, 460–470 (2020).
Google Scholar 
Murotomi, K. et al. Cyclo-glycylproline attenuates hydrogen peroxide-induced cellular damage mediated by the MDM2-p53 pathway in human neural stem cells. J. Cell. Physiol. 238, 434–446 (2023).PubMed 

Google Scholar 
Crowe, E. P. et al. Changes in the transcriptome of human astrocytes accompanying oxidative stress-induced senescence. Front. Aging Neurosci. 8, 208 (2016).Suzuki, T. A systematic exploration of unexploited disease-related genes. https://doi.org/10.6084/m9.figshare.c.7114075.v2 (2024).Barrett, T. et al. NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids Res. 41, D991–D995 (2013).PubMed 

Google Scholar 
Mariani, E. et al. Meta-analysis of Parkinson’s disease transcriptome data using TRAM software: whole substantia nigra tissue and single dopamine neuron differential gene expression. PLoS One 11, e0161567 (2016).PubMed 
PubMed Central 

Google Scholar 
Phung, D. M. et al. Meta-analysis of differentially expressed genes in the substantia nigra in Parkinson’s disease supports phenotype-specific transcriptome changes. Front. Neurosci. 14, (2020).Cappelletti, C. et al. Transcriptomic profiling of Parkinson’s disease brains reveals disease stage specific gene expression changes. Acta Neuropathol. 146, 227–244 (2023).PubMed 
PubMed Central 

Google Scholar 
Lu, M. et al. TWAS Atlas: a curated knowledgebase of transcriptome-wide association studies. Nucleic Acids Res. 51, D1179–D1187 (2023).PubMed 

Google Scholar 
szktkyk. szktkyk/gene-disease-linker (2024).Index of /gene/DATA. https://ftp.ncbi.nlm.nih.gov/gene/DATA/.Kia, D. A. et al. Identification of candidate Parkinson disease genes by integrating genome-wide association study, expression, and epigenetic data sets. JAMA Neurol. 78, 464–472 (2021).PubMed 

Google Scholar 
Li, Y. I., Wong, G., Humphrey, J. & Raj, T. Prioritizing Parkinson’s disease genes using population-scale transcriptomic data. Nat. Commun. 10, 994 (2019).PubMed 
PubMed Central 

Google Scholar 
Chen, L. et al. Study of molecular patterns associated with ferroptosis in Parkinson’s disease and its immune signature. PLoS One 18, e0295699 (2023).PubMed 
PubMed Central 

Google Scholar 
Chung, S.-K. & Lee, S.-Y. Advances in gene therapy techniques to treat LRRK2 gene mutation. Biomolecules 12, 1814 (2022).PubMed 
PubMed Central 

Google Scholar 
Lei, J., Aimaier, G., Aisha, Z., Zhang, Y. & Ma, J. eEF1A1 regulates the expression and alternative splicing of genes associated with Parkinson’s disease in U251 cells. Genes Genom. 46, 817–829 (2024).Zhang, X., Hu, D., Shang, Y. & Qi, X. Using induced pluripotent stem cell neuronal models to study neurodegenerative diseases. Biochim. Biophys. Acta Mol. Basis Dis. 1866, 165431 (2020).PubMed 

Google Scholar 
Liu, J. et al. NUPR1 is a critical repressor of ferroptosis. Nat. Commun. 12, 647 (2021).PubMed 
PubMed Central 

Google Scholar 
Wang, X. et al. UHRF2 regulates cell cycle, epigenetics and gene expression to control the timing of retinal progenitor and ganglion cell differentiation. Development 149, dev195644 (2022).PubMed 
PubMed Central 

Google Scholar 
Bucher, M. L. et al. Acquired dysregulation of dopamine homeostasis reproduces features of Parkinson’s disease. npj Parkinsons Dis. 6, 1–13 (2020).
Google Scholar 
Choi, W.-S., Kim, H.-W. & Xia, Z. JNK inhibition of VMAT2 contributes to rotenone-induced oxidative stress and dopamine neuron death. Toxicology 328, 75–81 (2015).PubMed 

Google Scholar 
Su, C.-J. et al. Thioredoxin-interacting protein induced α-synuclein accumulation via inhibition of autophagic flux: Implications for Parkinson’s disease. CNS Neurosci. Ther. 23, 717–723 (2017).PubMed 
PubMed Central 

Google Scholar 
Yang, D. et al. Neurofilament light chain as a mediator between LRRK2 mutation and dementia in Parkinson’s disease. npj Parkinsons Dis. 9, 1–6 (2023).
Google Scholar 
Gong, L. et al. Neurofilament light chain (NF-L) stimulates lipid peroxidation to neuronal membrane through microglia-derived ferritin heavy chain (FTH) secretion. Oxid. Med. Cell. Longev. 2022, e3938940 (2022).
Google Scholar 
Gellhaar, S., Sunnemark, D., Eriksson, H., Olson, L. & Galter, D. Myeloperoxidase-immunoreactive cells are significantly increased in brain areas affected by neurodegeneration in Parkinson’s and Alzheimer’s disease. Cell Tissue Res. 369, 445–454 (2017).PubMed 
PubMed Central 

Google Scholar 
Maki, R. A. et al. Human myeloperoxidase (hMPO) is expressed in neurons in the substantia nigra in Parkinson’s disease and in the hMPO-α-synuclein-A53T mouse model, correlating with increased nitration and aggregation of α-synuclein and exacerbation of motor impairment. Free Radic. Biol. Med. 141, 115–140 (2019).PubMed 
PubMed Central 

Google Scholar 
Verdiperstat | ALZFORUM https://www.alzforum.org/therapeutics/verdiperstat.Chang, C. Y., Choi, D.-K., Lee, D. K., Hong, Y. J. & Park, E. J. Resveratrol confers protection against rotenone-induced neurotoxicity by modulating myeloperoxidase levels in glial cells. PLoS One 8, e60654 (2013).PubMed 
PubMed Central 

Google Scholar 
Zhao, J. et al. LINC00938 alleviates hypoxia ischemia encephalopathy induced neonatal brain injury by regulating oxidative stress and inhibiting JNK/p38 MAPK signaling pathway. Exp. Neurol. 367, 114449 (2023).PubMed 

Google Scholar 
Yousefi, M., Peymani, M., Ghaedi, K., Irani, S. & Etemadifar, M. Significant modulations of linc001128 and linc0938 with miR-24-3p and miR-30c-5p in Parkinson disease. Sci. Rep. 12, 2569 (2022).PubMed 
PubMed Central 

Google Scholar 
Liu, C., Fang, J. & Liu, W. Superoxide dismutase coding of gene polymorphisms associated with susceptibility to Parkinson’s disease. J. Integr. Neurosci. 18, 299–303 (2019).PubMed 

Google Scholar 
Yu, H. et al. yyoshiaki/ikra: ikra v2.0.1. Zenodo https://doi.org/10.5281/zenodo.5541399 (2021).The NCBI SRA (Sequence Read Archive); NCBI—National Center for Biotechnology Information/NLM/NIH: Bethesda, MD, USA, 2021.Babraham Bioinformatics – Trim Galore! https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/.Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14, 417–419 (2017).PubMed 
PubMed Central 

Google Scholar 
Zhou, Y. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10, 1523 (2019).PubMed 
PubMed Central 

Google Scholar 

Hot Topics

Related Articles