1
|
Zhang J, Ma X, Li Z, Liu H, Tian M, Wen Y, Wang S, Wang L. Identification of key genes and diagnostic model associated with circadian rhythms and Parkinson's disease by bioinformatics analysis. Front Aging Neurosci 2024; 16:1458476. [PMID: 39478700 PMCID: PMC11523131 DOI: 10.3389/fnagi.2024.1458476] [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: 07/02/2024] [Accepted: 10/02/2024] [Indexed: 11/02/2024] Open
Abstract
Background Circadian rhythm disruption is typical in Parkinson's disease (PD) early stage, and it plays an important role in the prognosis of the treatment effect in the advanced stage of PD. There is growing evidence that circadian rhythm genes can influence development of PD. Therefore, this study explored specific regulatory mechanism of circadian genes (C-genes) in PD through bioinformatic approaches. Methods Differentially expressed genes (DEGs) between PD and control samples were identified from GSE22491 using differential expression analysis. The key model showing the highest correlation with PD was derived through WGCNA analysis. Then, DEGs, 1,288 C-genes and genes in key module were overlapped for yielding differentially expressed C-genes (DECGs), and they were analyzed for LASSO and SVM-RFE for yielding critical genes. Meanwhile, from GSE22491 and GSE100054, receiver operating characteristic (ROC) was implemented on critical genes to identify biomarkers, and Gene Set Enrichment Analysis (GSEA) was applied for the purpose of exploring pathways involved in biomarkers. Eventually, immune infiltrative analysis was applied for understanding effect of biomarkers on immune microenvironment, and therapeutic drugs which could affect biomarkers expressions were also predicted. Finally, we verified the expression of the genes by q-PCR. Results Totally 634 DEGs were yielded between PD and control samples, and MEgreen module had the highest correlation with PD, thus it was defined as key model. Four critical genes (AK3, RTN3, CYP4F2, and LEPR) were identified after performing LASSO and SVM-RFE on 18 DECGs. Through ROC analysis, AK3, RTN3, and LEPR were identified as biomarkers due to their excellent ability to distinguish PD from control samples. Besides, biomarkers were associated with Parkinson's disease and other functional pathways. Conclusion Through bioinformatic analysis, the circadian rhythm related biomarkers were identified (AK3, RTN3 and LEPR) in PD, contributing to studies related to PD treatment.
Collapse
Affiliation(s)
- Jiyuan Zhang
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- School of Basic Medicine, Hebei Medical University, Shijiazhuang, China
| | - Xiaopeng Ma
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- School of Basic Medicine, Hebei Medical University, Shijiazhuang, China
| | | | - Hu Liu
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- The Key Laboratory of Neurology, Hebei Medical University, Ministry of Education, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Mei Tian
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- The Key Laboratory of Neurology, Hebei Medical University, Ministry of Education, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Ya Wen
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- The Key Laboratory of Neurology, Hebei Medical University, Ministry of Education, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Shan Wang
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- The Key Laboratory of Neurology, Hebei Medical University, Ministry of Education, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Liang Wang
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- The Key Laboratory of Neurology, Hebei Medical University, Ministry of Education, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| |
Collapse
|
2
|
Desai D, Majrashi M, Pathak S, Almaghrabi M, Liu K, Pondugula SR, Tiwari AK, Babu RJ, Deruiter J, Dhanasekaran M. Evaluate the in vitro effect of anthracycline and alkylating cytophosphane chemotherapeutics on dopaminergic neurons. Cancer Rep (Hoboken) 2024; 7:e2074. [PMID: 38627904 PMCID: PMC11021631 DOI: 10.1002/cnr2.2074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Iatrogenesis is an inevitable global threat to healthcare that drastically increases morbidity and mortality. Cancer is a fatal pathological condition that affects people of different ages, sexes, and races around the world. In addition to the detrimental cancer pathology, one of the most common contraindications and challenges observed in cancer patients is severe adverse drug effects and hypersensitivity reactions induced by chemotherapy. Chemotherapy-induced cognitive neurotoxicity is clinically referred to as Chemotherapy-induced cognitive impairment (CICI), chemobrain, or chemofog. In addition to CICI, chemotherapy also causes neuropsychiatric issues, mental disorders, hyperarousal states, and movement disorders. A synergistic chemotherapy regimen of Doxorubicin (Anthracycline-DOX) and Cyclophosphamide (Alkylating Cytophosphane-CPS) is indicated for the management of various cancers (breast cancer, lymphoma, and leukemia). Nevertheless, there are limited research studies on Doxorubicin and Cyclophosphamide's pharmacodynamic and toxicological effects on dopaminergic neuronal function. AIM This study evaluated the dopaminergic neurotoxic effects of Doxorubicin and Cyclophosphamide. METHODS AND RESULTS Doxorubicin and Cyclophosphamide were incubated with dopaminergic (N27) neurons. Neuronal viability was assessed using an MTT assay. The effect of Doxorubicin and Cyclophosphamide on various prooxidants, antioxidants, mitochondrial Complex-I & IV activities, and BAX expression were evaluated by Spectroscopic, Fluorometric, and RT-PCR methods, respectively. Prism-V software (La Jolla, CA, USA) was used for statistical analysis. Chemotherapeutics dose-dependently inhibited the proliferation of the dopaminergic neurons. The dopaminergic neurotoxic mechanism of Doxorubicin and Cyclophosphamide was attributed to a significant increase in prooxidants, a decrease in antioxidants, and augmented apoptosis without affecting mitochondrial function. CONCLUSION This is one of the first reports that reveal Doxorubicin and Cyclophosphamide induce significant dopaminergic neurotoxicity. Thus, Chemotherapy-induced adverse drug reaction issues substantially persist during and after treatment and sometimes never be completely resolved clinically. Consequently, failure to adopt adequate patient care measures for cancer patients treated with certain chemotherapeutics might substantially raise the incidence of numerous movement disorders.
Collapse
Affiliation(s)
- Darshini Desai
- Department of Drug Discovery and DevelopmentHarrison College of Pharmacy, Auburn UniversityAuburnAlabamaUSA
| | - Mohammed Majrashi
- Department of Drug Discovery and DevelopmentHarrison College of Pharmacy, Auburn UniversityAuburnAlabamaUSA
- Department of PharmacologyFaculty of Medicine, University of JeddahJeddahSaudi Arabia
| | - Suhrud Pathak
- Department of Drug Discovery and DevelopmentHarrison College of Pharmacy, Auburn UniversityAuburnAlabamaUSA
| | - Mohammed Almaghrabi
- Department of Drug Discovery and DevelopmentHarrison College of Pharmacy, Auburn UniversityAuburnAlabamaUSA
- Department of Medicinal ChemistryFaculty of Pharmacy, Taibah UniversityAl‐MedinaSaudi Arabia
| | - Keyi Liu
- Department of Drug Discovery and DevelopmentHarrison College of Pharmacy, Auburn UniversityAuburnAlabamaUSA
| | - Satyanarayana R. Pondugula
- Department of AnatomyPhysiology and Pharmacology, College of Veterinary Medicine, Auburn UniversityAuburnAlabamaUSA
| | - Amit K. Tiwari
- Department of Pharmaceutical SciencesCollege of Pharmacy, University of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - R. Jayachandra Babu
- Department of Drug Discovery and DevelopmentHarrison College of Pharmacy, Auburn UniversityAuburnAlabamaUSA
| | - Jack Deruiter
- Department of Drug Discovery and DevelopmentHarrison College of Pharmacy, Auburn UniversityAuburnAlabamaUSA
| | | |
Collapse
|
3
|
Garg A, Kumar G, Singh V, Sinha S. Doxorubicin catalyses self-assembly of p53 by phase separation. Curr Res Struct Biol 2024; 7:100133. [PMID: 38435052 PMCID: PMC10906149 DOI: 10.1016/j.crstbi.2024.100133] [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: 10/03/2023] [Revised: 01/29/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024] Open
Abstract
Liquid-liquid phase separation plays a crucial role in cellular physiology, as it leads to the formation of membrane-less organelles in response to various internal stimuli, contributing to various cellular functions. However, the influence of exogenous stimuli on this process in the context of disease intervention remains unexplored. In this current investigation, we explore the impact of doxorubicin on the abnormal self-assembly of p53 using a combination of biophysical and imaging techniques. Additionally, we shed light on the potential mechanisms behind chemoresistance in cancer cells carrying mutant p53. Our findings reveal that doxorubicin co-localizes with both wild-type p53 (WTp53) and its mutant variants. Our in vitro experiments indicate that doxorubicin interacts with the N-terminal-deleted form of WTp53 (WTp53ΔNterm), inducing liquid-liquid phase separation, ultimately leading to protein aggregation. Notably, the p53 variants at the R273 position exhibit a propensity for phase separation even in the absence of doxorubicin, highlighting the destabilizing effects of point mutations at this position. The strong interaction between doxorubicin and p53 variants, along with its localization within the protein condensates, provides a potential explanation for the development of chemotherapy resistance. Collectively, our cellular and in vitro studies emphasize the role of exogenous agents in driving phase separation-mediated p53 aggregation.
Collapse
Affiliation(s)
- Ankush Garg
- Chemical Biology Unit, Institute of Nano Science and Technology, Sector- 81, Mohali (SAS Nagar), Punjab, 140306, India
| | - Gaurav Kumar
- Chemical Biology Unit, Institute of Nano Science and Technology, Sector- 81, Mohali (SAS Nagar), Punjab, 140306, India
| | - Varinder Singh
- Indian Institute of Science Education and Research, Sector- 81, Mohali (SAS Nagar), Punjab, 140306, India
| | - Sharmistha Sinha
- Chemical Biology Unit, Institute of Nano Science and Technology, Sector- 81, Mohali (SAS Nagar), Punjab, 140306, India
| |
Collapse
|
4
|
Quesnel A, Martin LD, Tarzi C, Lenis VP, Coles N, Islam M, Angione C, Outeiro TF, Khundakar AA, Filippou PS. Uncovering potential diagnostic and pathophysiological roles of α-synuclein and DJ-1 in melanoma. Cancer Med 2024; 13:e6900. [PMID: 38189631 PMCID: PMC10807602 DOI: 10.1002/cam4.6900] [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: 08/30/2023] [Revised: 11/20/2023] [Accepted: 12/19/2023] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND Melanoma, the most lethal skin cancer type, occurs more frequently in Parkinson's disease (PD), and PD is more frequent in melanoma patients, suggesting disease mechanisms overlap. α-synuclein, a protein that accumulates in PD brain, and the oncogene DJ-1, which is associated with PD autosomal recessive forms, are both elevated in melanoma cells. Whether this indicates melanoma progression or constitutes a protective response remains unclear. We hereby investigated the molecular mechanisms through which α-synuclein and DJ-1 interact, suggesting novel biomarkers and targets in melanoma. METHODS The Cancer Genome Atlas (TCGA) expression profiles derived from UCSC Xena were used to obtain α-synuclein and DJ-1 expression and correlated with survival in skin cutaneous melanoma (SKCM). Immunohistochemistry determined the expression in metastatic melanoma lymph nodes. Protein-protein interactions (PPIs) and molecular docking assessed protein binding and affinity with chemotherapeutic drugs. Further validation was performed using in vitro cellular models and ELISA immunoassays. RESULTS α-synuclein and DJ-1 were upregulated in primary and metastatic SKCM. Aggregated α-synuclein was selectively detected in metastatic melanoma lymph nodes. α-synuclein overexpression in SK-MEL-28 cells induced the expression of DJ-1, supporting PPI and a positive correlation in melanoma patients. Molecular docking revealed a stable protein complex, with differential binding to chemotherapy drugs such as temozolomide, dacarbazine, and doxorubicin. Parallel reduction of both proteins in temozolomide-treated SK-MEL-28 spheroids suggests drug binding may affect protein interaction and/or stability. CONCLUSION α-synuclein, together with DJ-1, may play a role in melanoma progression and chemosensitivity, constituting novel targets for therapeutic intervention, and possible biomarkers for melanoma.
Collapse
Affiliation(s)
- Agathe Quesnel
- School of Health & Life SciencesTeesside UniversityMiddlesbroughUK
- National Horizons CentreTeesside UniversityDarlingtonUK
| | - Leya Danielle Martin
- School of Health & Life SciencesTeesside UniversityMiddlesbroughUK
- National Horizons CentreTeesside UniversityDarlingtonUK
| | - Chaimaa Tarzi
- School of Computing, Engineering & Digital TechnologiesTeesside UniversityMiddlesbroughUK
- Centre for Digital InnovationTeesside UniversityMiddlesbroughUK
| | - Vasileios P. Lenis
- School of Health & Life SciencesTeesside UniversityMiddlesbroughUK
- National Horizons CentreTeesside UniversityDarlingtonUK
| | - Nathan Coles
- School of Health & Life SciencesTeesside UniversityMiddlesbroughUK
- National Horizons CentreTeesside UniversityDarlingtonUK
| | - Meez Islam
- School of Health & Life SciencesTeesside UniversityMiddlesbroughUK
- National Horizons CentreTeesside UniversityDarlingtonUK
| | - Claudio Angione
- National Horizons CentreTeesside UniversityDarlingtonUK
- School of Computing, Engineering & Digital TechnologiesTeesside UniversityMiddlesbroughUK
- Centre for Digital InnovationTeesside UniversityMiddlesbroughUK
| | - Tiago F. Outeiro
- Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of NeurodegenerationUniversity Medical CenterGöttingenGermany
- Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE)GöttingenGermany
| | - Ahmad A. Khundakar
- School of Health & Life SciencesTeesside UniversityMiddlesbroughUK
- National Horizons CentreTeesside UniversityDarlingtonUK
- Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Panagiota S. Filippou
- School of Health & Life SciencesTeesside UniversityMiddlesbroughUK
- National Horizons CentreTeesside UniversityDarlingtonUK
| |
Collapse
|