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Chun KY, Kim SN. Integrative analysis of plasma and substantia nigra in Parkinson's disease: unraveling biomarkers and insights from the lncRNA-miRNA-mRNA ceRNA network. Front Aging Neurosci 2024; 16:1388655. [PMID: 38784444 PMCID: PMC11112011 DOI: 10.3389/fnagi.2024.1388655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction Parkinson's disease (PD) is a rapidly growing neurological disorder characterized by diverse movement symptoms. However, the underlying causes have not been clearly identified, and accurate diagnosis is challenging. This study aimed to identify potential biomarkers suitable for PD diagnosis and present an integrative perspective on the disease. Methods We screened the GSE7621, GSE8397-GPL96, GSE8397-GPL97, GSE20163, and GSE20164 datasets in the NCBI GEO database to identify differentially expressed (DE) mRNAs in the substantia nigra (SN). We also screened the GSE160299 dataset from the NCBI GEO database to identify DE lncRNAs and miRNAs in plasma. We then constructed 2 lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) regulatory networks based on the ceRNA hypothesis. To understand the biological function, we performed Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology analyses for each ceRNA network. The receiver operating characteristic analyses (ROC) was used to assess ceRNA results. Results We identified 7 upregulated and 29 downregulated mRNAs as common DE mRNAs in the 5 SN datasets. In the blood dataset, we identified 31 DE miRNAs (9 upregulated and 22 downregulated) and 332 DE lncRNAs (69 upregulated and 263 downregulated). Based on the determined interactions, 5 genes (P2RX7, HSPA1, SLCO4A1, RAD52, and SIRT4) appeared to be upregulated as a result of 10 lncRNAs sponging 4 miRNAs (miR-411, miR-1193, miR-301b, and miR-514a-2/3). Competing with 9 genes (ANK1, CBLN1, RGS4, SLC6A3, SYNGR3, VSNL1, DDC, KCNJ6, and SV2C) for miR-671, a total of 26 lncRNAs seemed to function as ceRNAs, influencing genes to be downregulated. Discussion In this study, we successfully constructed 2 novel ceRNA regulatory networks in patients with PD, including 36 lncRNAs, 5 miRNAs, and 14 mRNAs. Our results suggest that these plasma lncRNAs are involved in the pathogenesis of PD by sponging miRNAs and regulating gene expression in the SN of the brain. We propose that the upregulated and downregulated lncRNA-mediated ceRNA networks represent mechanisms of neuroinflammation and dopamine neurotransmission, respectively. Our ceRNA network, which was associated with PD, suggests the potential use of DE miRNAs and lncRNAs as body fluid diagnostic biomarkers. These findings provide an integrated view of the mechanisms underlying gene regulation and interactions in PD.
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Affiliation(s)
| | - Seung-Nam Kim
- College of Korean Medicine, Dongguk University, Goyang, Republic of Korea
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2
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Phan BN, Ray MH, Xue X, Fu C, Fenster RJ, Kohut SJ, Bergman J, Haber SN, McCullough KM, Fish MK, Glausier JR, Su Q, Tipton AE, Lewis DA, Freyberg Z, Tseng GC, Russek SJ, Alekseyev Y, Ressler KJ, Seney ML, Pfenning AR, Logan RW. Single nuclei transcriptomics in human and non-human primate striatum in opioid use disorder. Nat Commun 2024; 15:878. [PMID: 38296993 PMCID: PMC10831093 DOI: 10.1038/s41467-024-45165-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/12/2024] [Indexed: 02/02/2024] Open
Abstract
In brain, the striatum is a heterogenous region involved in reward and goal-directed behaviors. Striatal dysfunction is linked to psychiatric disorders, including opioid use disorder (OUD). Striatal subregions are divided based on neuroanatomy, each with unique roles in OUD. In OUD, the dorsal striatum is involved in altered reward processing, formation of habits, and development of negative affect during withdrawal. Using single nuclei RNA-sequencing, we identified both canonical (e.g., dopamine receptor subtype) and less abundant cell populations (e.g., interneurons) in human dorsal striatum. Pathways related to neurodegeneration, interferon response, and DNA damage were significantly enriched in striatal neurons of individuals with OUD. DNA damage markers were also elevated in striatal neurons of opioid-exposed rhesus macaques. Sex-specific molecular differences in glial cell subtypes associated with chronic stress were found in OUD, particularly female individuals. Together, we describe different cell types in human dorsal striatum and identify cell type-specific alterations in OUD.
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Affiliation(s)
- BaDoi N Phan
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Madelyn H Ray
- Department of Pharmacology, Physiology & Biophysics, Boston University School of Medicine, Boston, MA, 02118, USA
- Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Xiangning Xue
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Chen Fu
- Department of Psychiatry, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Robert J Fenster
- Department of Psychiatry, Harvard Medical School, Boston, MA, 02115, USA
- Division of Depression and Anxiety, McLean Hospital, Department of Psychiatry, Harvard Medical School, Belmont, MA, 02478, USA
| | - Stephen J Kohut
- Department of Psychiatry, Harvard Medical School, Boston, MA, 02115, USA
- Behavioral Biology Program, McLean Hospital, Belmont, MA, 02478, USA
| | - Jack Bergman
- Department of Psychiatry, Harvard Medical School, Boston, MA, 02115, USA
- Behavioral Biology Program, McLean Hospital, Belmont, MA, 02478, USA
| | - Suzanne N Haber
- Department of Psychiatry, Harvard Medical School, Boston, MA, 02115, USA
- Department of Pharmacology and Physiology, University of Rochester, School of Medicine, Rochester, NY, 14642, USA
| | - Kenneth M McCullough
- Basic Neuroscience Division, Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, MA, 02478, USA
| | - Madeline K Fish
- Center for Systems Neuroscience, Boston University, Boston, MA, 02118, USA
- Graduate Program for Neuroscience, Boston University, Boston, MA, 02118, USA
| | - Jill R Glausier
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - Qiao Su
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Allison E Tipton
- Center for Systems Neuroscience, Boston University, Boston, MA, 02118, USA
- Graduate Program for Neuroscience, Boston University, Boston, MA, 02118, USA
| | - David A Lewis
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - Zachary Freyberg
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Shelley J Russek
- Department of Pharmacology, Physiology & Biophysics, Boston University School of Medicine, Boston, MA, 02118, USA
- Center for Systems Neuroscience, Boston University, Boston, MA, 02118, USA
- Graduate Program for Neuroscience, Boston University, Boston, MA, 02118, USA
| | - Yuriy Alekseyev
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Kerry J Ressler
- Department of Psychiatry, Harvard Medical School, Boston, MA, 02115, USA
- Division of Depression and Anxiety, McLean Hospital, Department of Psychiatry, Harvard Medical School, Belmont, MA, 02478, USA
| | - Marianne L Seney
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - Andreas R Pfenning
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
| | - Ryan W Logan
- Department of Pharmacology, Physiology & Biophysics, Boston University School of Medicine, Boston, MA, 02118, USA.
- Department of Psychiatry, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
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Zimmer J, Mueller L, Frank-Herrmann P, Rehnitz J, Dietrich JE, Bettendorf M, Strowitzki T, Krivega M. Low androgen signaling rescues genome integrity with innate immune response by reducing fertility in humans. Cell Death Dis 2024; 15:30. [PMID: 38212646 PMCID: PMC10784536 DOI: 10.1038/s41419-023-06397-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/13/2024]
Abstract
Development of the gonads under complex androgen regulation is critical for germ cells specification. In this work we addressed the relationship between androgens and genomic integrity determining human fertility. We used different study groups: individuals with Differences of Sex Development (DSD), including Complete Androgen Insensitivity Syndrome (CAIS) due to mutated androgen receptor (AR), and men with idiopathic nonobstructive azoospermia. Both showed genome integrity status influenced by androgen signaling via innate immune response activation in blood and gonads. Whole proteome analysis connected low AR to interleukin-specific gene expression, while compromised genome stability and tumorigenesis were also supported by interferons. AR expression was associated with predominant DNA damage phenotype, that eliminated AR-positive Sertoli cells as the degeneration of gonads increased. Low AR contributed to resistance from the inhibition of DNA repair in primary leukocytes. Downregulation of androgen promoted apoptosis and specific innate immune response with higher susceptibility in cells carrying genomic instability.
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Affiliation(s)
- J Zimmer
- Research Group of Gonadal Differentiation and Embryonic Development, Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - L Mueller
- Research Group of Gonadal Differentiation and Embryonic Development, Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - P Frank-Herrmann
- Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - J Rehnitz
- Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - J E Dietrich
- Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - M Bettendorf
- Division of Pediatric Endocrinology, Children's Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - T Strowitzki
- Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - M Krivega
- Research Group of Gonadal Differentiation and Embryonic Development, Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany.
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Pradhan SH, Liu JY, Sayes CM. Evaluating Manganese, Zinc, and Copper Metal Toxicity on SH-SY5Y Cells in Establishing an Idiopathic Parkinson's Disease Model. Int J Mol Sci 2023; 24:16129. [PMID: 38003318 PMCID: PMC10671677 DOI: 10.3390/ijms242216129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative condition marked by loss of motor coordination and cognitive impairment. According to global estimates, the worldwide prevalence of PD will likely exceed 12 million cases by 2040. PD is primarily associated with genetic factors, while clinically, cases are attributed to idiopathic factors such as environmental or occupational exposure. The heavy metals linked to PD and other neurodegenerative disorders include copper, manganese, and zinc. Chronic exposure to metals induces elevated oxidative stress and disrupts homeostasis, resulting in neuronal death. These metals are suggested to induce idiopathic PD in the literature. This study measures the effects of lethal concentration at 10% cell death (LC10) and lethal concentration at 50% cell death (LC50) concentrations of copper, manganese, and zinc chlorides on SH-SY5Y cells via markers for dopamine, reactive oxygen species (ROS) generation, DNA damage, and mitochondrial dysfunction after a 24 h exposure. These measurements were compared to a known neurotoxin to induce PD, 100 µM 6-hydroxydopamine (6-ODHA). Between the three metal chlorides, zinc was statistically different in all parameters from all other treatments and induced significant dopaminergic loss, DNA damage, and mitochondrial dysfunction. The LC50 of manganese and copper had the most similar response to 6-ODHA in all parameters, while LC10 of manganese and copper responded most like untreated cells. This study suggests that these metal chlorides respond differently from 6-ODHA and each other, suggesting that idiopathic PD utilizes a different mechanism from the classic PD model.
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Affiliation(s)
| | | | - Christie M. Sayes
- Department of Environmental Science, Baylor University, Waco, TX 76798, USA; (S.H.P.)
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Wysocki R, Rodrigues JI, Litwin I, Tamás MJ. Mechanisms of genotoxicity and proteotoxicity induced by the metalloids arsenic and antimony. Cell Mol Life Sci 2023; 80:342. [PMID: 37904059 PMCID: PMC10616229 DOI: 10.1007/s00018-023-04992-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/12/2023] [Accepted: 09/29/2023] [Indexed: 11/01/2023]
Abstract
Arsenic and antimony are metalloids with profound effects on biological systems and human health. Both elements are toxic to cells and organisms, and exposure is associated with several pathological conditions including cancer and neurodegenerative disorders. At the same time, arsenic- and antimony-containing compounds are used in the treatment of multiple diseases. Although these metalloids can both cause and cure disease, their modes of molecular action are incompletely understood. The past decades have seen major advances in our understanding of arsenic and antimony toxicity, emphasizing genotoxicity and proteotoxicity as key contributors to pathogenesis. In this review, we highlight mechanisms by which arsenic and antimony cause toxicity, focusing on their genotoxic and proteotoxic effects. The mechanisms used by cells to maintain proteostasis during metalloid exposure are also described. Furthermore, we address how metalloid-induced proteotoxicity may promote neurodegenerative disease and how genotoxicity and proteotoxicity may be interrelated and together contribute to proteinopathies. A deeper understanding of cellular toxicity and response mechanisms and their links to pathogenesis may promote the development of strategies for both disease prevention and treatment.
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Affiliation(s)
- Robert Wysocki
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328, Wroclaw, Poland.
| | - Joana I Rodrigues
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30, Göteborg, Sweden
| | - Ireneusz Litwin
- Academic Excellence Hub - Research Centre for DNA Repair and Replication, Faculty of Biological Sciences, University of Wroclaw, 50-328, Wroclaw, Poland
| | - Markus J Tamás
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30, Göteborg, Sweden.
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Cordeiro Y, Freire MHO, Wiecikowski AF, do Amaral MJ. (Dys)functional insights into nucleic acids and RNA-binding proteins modulation of the prion protein and α-synuclein phase separation. Biophys Rev 2023; 15:577-589. [PMID: 37681103 PMCID: PMC10480379 DOI: 10.1007/s12551-023-01067-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/22/2023] [Indexed: 09/09/2023] Open
Abstract
Prion diseases are prototype of infectious diseases transmitted by a protein, the prion protein (PrP), and are still not understandable at the molecular level. Heterogenous species of aggregated PrP can be generated from its monomer. α-synuclein (αSyn), related to Parkinson's disease, has also shown a prion-like pathogenic character, and likewise PrP interacts with nucleic acids (NAs), which in turn modulate their aggregation. Recently, our group and others have characterized that NAs and/or RNA-binding proteins (RBPs) modulate recombinant PrP and/or αSyn condensates formation, and uncontrolled condensation might precede pathological aggregation. Tackling abnormal phase separation of neurodegenerative disease-related proteins has been proposed as a promising therapeutic target. Therefore, understanding the mechanism by which polyanions, like NAs, modulate phase transitions intracellularly, is key to assess their role on toxicity promotion and neuronal death. Herein we discuss data on the nucleic acids binding properties and phase separation ability of PrP and αSyn with a special focus on their modulation by NAs and RBPs. Furthermore, we provide insights into condensation of PrP and/or αSyn in the light of non-trivial subcellular locations such as the nuclear and cytosolic environments.
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Affiliation(s)
- Yraima Cordeiro
- Faculty of Pharmacy, Universidade Federal do Rio de Janeiro, Av Carlos Chagas Filho 373, bloco B, subsolo Sala 36, Rio de Janeiro, RJ 21941-902 Brazil
| | - Maria Heloisa O. Freire
- Faculty of Pharmacy, Universidade Federal do Rio de Janeiro, Av Carlos Chagas Filho 373, bloco B, subsolo Sala 36, Rio de Janeiro, RJ 21941-902 Brazil
| | - Adalgisa Felippe Wiecikowski
- Faculty of Pharmacy, Universidade Federal do Rio de Janeiro, Av Carlos Chagas Filho 373, bloco B, subsolo Sala 36, Rio de Janeiro, RJ 21941-902 Brazil
| | - Mariana Juliani do Amaral
- Faculty of Pharmacy, Universidade Federal do Rio de Janeiro, Av Carlos Chagas Filho 373, bloco B, subsolo Sala 36, Rio de Janeiro, RJ 21941-902 Brazil
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Wang ZX, Liu Y, Li YL, Wei Q, Lin RR, Kang R, Ruan Y, Lin ZH, Xue NJ, Zhang BR, Pu JL. Nuclear DJ-1 Regulates DNA Damage Repair via the Regulation of PARP1 Activity. Int J Mol Sci 2023; 24:ijms24108651. [PMID: 37239999 DOI: 10.3390/ijms24108651] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 05/28/2023] Open
Abstract
DNA damage and defective DNA repair are extensively linked to neurodegeneration in Parkinson's disease (PD), but the underlying molecular mechanisms remain poorly understood. Here, we determined that the PD-associated protein DJ-1 plays an essential role in modulating DNA double-strand break (DSB) repair. Specifically, DJ-1 is a DNA damage response (DDR) protein that can be recruited to DNA damage sites, where it promotes DSB repair through both homologous recombination and nonhomologous end joining. Mechanistically, DJ-1 interacts directly with PARP1, a nuclear enzyme essential for genomic stability, and stimulates its enzymatic activity during DNA repair. Importantly, cells from PD patients with the DJ-1 mutation also have defective PARP1 activity and impaired repair of DSBs. In summary, our findings uncover a novel function of nuclear DJ-1 in DNA repair and genome stability maintenance, and suggest that defective DNA repair may contribute to the pathogenesis of PD linked to DJ-1 mutations.
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Affiliation(s)
- Zhong-Xuan Wang
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Yi Liu
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Yao-Lin Li
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Qiao Wei
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Rong-Rong Lin
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Ruiqing Kang
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Yang Ruan
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Zhi-Hao Lin
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Nai-Jia Xue
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Bao-Rong Zhang
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Jia-Li Pu
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
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