IDENTIFICATION OF CORE GENES IN SCHIZOPHRENIATHROUGH BIOINFORMATICS ANALYSIS OF THE GSE21138DATASET
Main Article Content
Keywords
Schizophrenia, GSE21138, Hub genes, DEGs
Abstract
Schizophrenia is a complex psychiatric disorder with elusive molecular mechanisms. This study analyzes the GSE21138 dataset to identify differentially expressed genes (DEGs) and construct a protein-protein interaction (PPI) network. Among the top 250 DEGs, several key genes, including DCP2, SPCS2, ATP2A1, and SSTR5, emerged as central hub genes. These hub genes are highly connected within the network, suggesting their pivotal roles in schizophrenia-related pathways. The network organization reveals distinct functional modules, implicating processes like immune response, cell cycle regulation, and signal transduction in the disorder's pathology. Gene enrichment analysis highlights significant associations with cancer-related pathways, such as "Chronic myeloid leukemia" and "P53 signaling pathway," further underscoring the relevance of these DEGs in critical regulatory processes. The identification of these hub genes not only provides new insights into the molecular mechanisms underlying schizophrenia but also suggests potential therapeutic targets and biomarkers. These findings offer a comprehensive view of the disrupted biological processes in schizophrenia, emphasizing the need for further research to explore the functional roles of these hub genes in the context of the disorder.
References
[2] Popa ȘP, Susanu C, Nistor OL, Matei N, Zaharescu AM, Buruiană DL, Palivan CCM and Budacu CC. PLANNING THE COMPLEX ORAL REHABILITATION OF PATIENTS ON A PSYCHIATRIC PATHOLOGY-SCHIZOPHRENIA. Romanian Journal of Oral Rehabilitation 2021; 13:
[3] Hameed A, Condò C, Tauseef I, Idrees M, Ghazanfar S, Farid A, Muzammal M, Al Mohaini M, Alsalman AJ and Al Hawaj MA. Isolation and characterization of a cholesterol-lowering bacteria from Bubalus bubalis raw milk. Fermentation 2022; 8: 163.
[4] Arciniegas DB. Psychosis. CONTINUUM: lifelong learning in neurology 2015; 21: 715-736.
[5] Orsolini L, Pompili S and Volpe U. Schizophrenia: a narrative review of etiopathogenetic, diagnostic and treatment aspects. Journal of Clinical Medicine 2022; 11: 5040.
[6] Usman M, Hameed Y, Ahmad M, Iqbal MJ, Maryam A, Mazhar A, Naz S, Tanveer R, Saeed H and Ashraf A. SHMT2 is associated with tumor purity, CD8+ T immune cells infiltration, and a novel therapeutic target in four different human cancers. Current Molecular Medicine 2023; 23: 161-176.
[7] Udhaya Kumar S, Thirumal Kumar D, Bithia R, Sankar S, Magesh R, Sidenna M, George Priya Doss C and Zayed H. Analysis of differentially expressed genes and molecular pathways in familial hypercholesterolemia involved in atherosclerosis: a systematic and bioinformatics approach. Frontiers in Genetics 2020; 11: 734.
[8] Khalil T, Okla M, Al-Qahtani W, Ali F, Zahra M, Shakeela Q, Ahmed S, Akhtar N, AbdElgawad H and Asif R. Tracing probiotic producing bacterial species from gut of buffalo (Bubalus bubalis), South-East-Asia. Brazilian Journal of Biology 2022; 84: e259094.
[9] Khatun MT, Rana HK, Hossain MA, Lakshmanna K, Rahman MM, Parvin A and Rahman MH. Bioinformatics and systems biology approaches to identify molecular targets and pathways shared between Schizophrenia and Bipolar Disorder. Informatics in Medicine Unlocked 2024; 101556.
[10] Bryzgalov LO, Korbolina EE, Brusentsov II, Leberfarb EY, Bondar NP and Merkulova TI. Novel functional variants at the GWAS-implicated loci might confer risk to major depressive disorder, bipolar affective disorder and schizophrenia. BMC neuroscience 2018; 19: 41-56.
[11] Sial N, Rehman JU, Saeed S, Ahmad M, Hameed Y, Atif M, Rehman A, Asif R, Ahmed H and Hussain MS. Integrative analysis reveals methylenetetrahydrofolate dehydrogenase 1-like as an independent shared diagnostic and prognostic biomarker in five different human cancers. Bioscience Reports 2022; 42: BSR20211783.
[12] Khan MW, Shams Malick RA and Cherifi H. Discovering Disease Genes in PPI Networks: A Bridge from Centrality to Communities. bioRxiv 2023; 2023.2009. 2008.556873.
[13] Jayaswamy PK, Gollapalli P, Vijaykrishnaraj M, Alexander LM, Patil P and Shetty P. Identification of network-based differential gene expression signatures and their transcriptional factors to develop progressive blood biomarkers for Alzheimer's disease. Human Gene 2023; 37: 201202.
[14] Zhang L, Sahar A, Li C, Chaudhary A, Yousaf I, Saeedah M, Mubarak A, Haris M, Nawaz M and Reem M. A detailed multi-omics analysis of GNB2 gene in human cancers. Brazilian Journal of Biology 2022; 84: e260169.
[15] Mao J, Huang X, Okla MK, Abdel-Maksoud MA, Mubarak A, Hameed Z, Noreen R, Chaudhary A, Ghazanfar S and Liao Y. [Retracted] Risk Factors for TERT Promoter Mutations with Papillary Thyroid Carcinoma Patients: A Meta‐Analysis and Systematic Review. Computational and Mathematical Methods in Medicine 2022; 2022: 1721526.
[16] McCutcheon RA, Marques TR and Howes OD. Schizophrenia—an overview. JAMA psychiatry 2020; 77: 201-210.
[17] Ordieres MGL. Schizophrenia: A Complex Mental Illness. Psychiatry and Neuroscience Update: From Translational Research to a Humanistic Approach-Volume III 2019; 417-426.
[18] Baloyianni N and Tsangaris GT. The audacity of proteomics: a chance to overcome current challenges in schizophrenia research. Expert Review of Proteomics 2009; 6: 661-674.
[19] J Brand S, Moller M and H Harvey B. A review of biomarkers in mood and psychotic disorders: a dissection of clinical vs. preclinical correlates. Current neuropharmacology 2015; 13: 324-368.
[20] Gillis J and Pavlidis P. Gene Ontology matrices (with descriptions, IDs, etc) from" Guilt by Association" Is the Exception Rather Than the Rule in Gene Networks. Gillis, J. and Pavlidis, P.(2012) PLoS Computational Biology, 8 (3). 2012;
[21] Gillis J and Pavlidis P. Exceptional Edges matrices from" Guilt by Association" Is the Exception Rather Than the Rule in Gene Networks Gillis, J. and Pavlidis, P.(2012) PLoS Computational Biology, 8 (3). 2012;
[22] Arnold SE, Talbot K and Hahn C-G. Neurodevelopment, neuroplasticity, and new genes for schizophrenia. Progress in brain research 2005; 147: 319-345.
[23] Balu DT and Coyle JT. Neuroplasticity signaling pathways linked to the pathophysiology of schizophrenia. Neuroscience & Biobehavioral Reviews 2011; 35: 848-870.
[24] Lang UE, Puls I, Müller DJ, Strutz-Seebohm N and Gallinat J. Molecular mechanisms of schizophrenia. Cellular Physiology and Biochemistry 2007; 20: 687-702.
[25] Hall J, Trent S, Thomas KL, O’Donovan MC and Owen MJ. Genetic risk for schizophrenia: convergence on synaptic pathways involved in plasticity. Biological psychiatry 2015; 77: 52-58.
[26] Moretto E, Murru L, Martano G, Sassone J and Passafaro M. Glutamatergic synapses in neurodevelopmental disorders. Progress in Neuro-Psychopharmacology and Biological Psychiatry 2018; 84: 328-342.
Article Sidebar
Article Details
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
All articles published in JPTCP are licensed under Copyright Creative Commons Attribution-NonCommercial 4.0 International License.
Feroz Usmani
Department of Social Work, University of the Punjab, New Campus Lahore, Pakistan.
Ali Maaz
Department of Medicine, King Edward Medical University, Lahore, Pakistan.
Tehseen Raza
Department of Medicine, King Edward Medical University, Lahore, Pakistan.
Muhammad Usman Khan
Department of Neurology, King Edward Medical University, Lahore, Pakistan.
Amir Sohail
Department of Medicine, King Edward Medical University, Lahore, Pakistan.
Talha Aziz Dhillon
Department of Medicine, King Edward Medical University, Lahore, Pakistan.
Abdul Haseeb
Department of Medicine, King Edward Medical University, Lahore, Pakistan.
Abdul Manaf
Department of Medicine, Quetta Institute of Medical Sciences, Quetta, Pakistan.
Muhammad Zohaib Rehman
Department of Medicine, Khyber Medical College, Peshawar, Pakistan.
Maria Ghafoor
Wapda Teaching Hospital Complex, Lahore, Pakistan.