Identification of molecular signatures and pathways common to blood cells and brain tissue based RNA-Seq datasets of bipolar disorder: Insights from comprehensive bioinformatics approach

Vieta, 2018, Bipolar disorders, Nat Rev Dis Prim, 4, 1 Harvey, 2015, Interventions for sleep disturbance in bipolar disorder, Sleep medicine clinics, 10, 101, 10.1016/j.jsmc.2014.11.005 You, 2020, Does single gene expression omnibus data mining analysis apply for only tumors and not mental illness? a preliminary study on bipolar disorder based on bioinformatics methodology, Medicine, 99, 10.1097/MD.0000000000021989 Grande, 2016, Bipolar disorder, Lancet, 387, 1561, 10.1016/S0140-6736(15)00241-X Merikangas, 2007, Lifetime and 12-month prevalence of bipolar spectrum disorder in the national comorbidity survey replication, Arch Gen Psychiatr, 64, 543, 10.1001/archpsyc.64.5.543 Pini, 2005, Prevalence and burden of bipolar disorders in european countries, Eur Neuropsychopharmacol, 15, 425, 10.1016/j.euroneuro.2005.04.011 Scott, 2006, Cognitive–behavioural therapy for severe and recurrent bipolar disorders: randomised controlled trial, Br J Psychiatr, 188, 313, 10.1192/bjp.188.4.313 Apps, 2008, Bipolar disorders: symptoms and treatment in children and adolescents, Pediatr Nurs, 34, 84 Lopresti, 2015, Diet and bipolar disorder: a review of its relationship and potential therapeutic mechanisms of action, J Alternative Compl Med, 21, 733, 10.1089/acm.2015.0125 Husson, 2018, Identification of potential genetic risk factors for bipolar disorder by whole-exome sequencing, Transl Psychiatry, 8, 1, 10.1038/s41398-018-0291-7 Lima, 2018, Cognitive deficits in bipolar disorders: implications for emotion, Clin Psychol Rev, 59, 126, 10.1016/j.cpr.2017.11.006 Tidemalm, 2014, Attempted suicide in bipolar disorder: risk factors in a cohort of 6086 patients, PLoS One, 9, e94097, 10.1371/journal.pone.0094097 McClellan, 2007, Practice parameter for the assessment and treatment of children and adolescents with bipolar disorder, J Am Acad Child Adolesc Psychiatry, 46, 107, 10.1097/01.chi.0000242240.69678.c4 Kim, 2017, Molecular mechanisms of bipolar disorder: progress made and future challenges, Front Cell Neurosci, 11, 30, 10.3389/fncel.2017.00030 Geddes, 2013, Treatment of bipolar disorder, The lancet, 381, 1672, 10.1016/S0140-6736(13)60857-0 Huxley, 2007, Disability and its treatment in bipolar disorder patients, Bipolar Disord, 9, 183, 10.1111/j.1399-5618.2007.00430.x Hlastala, 2010, Interpersonal and social rhythm therapy for adolescents with bipolar disorder: treatment development and results from an open trial, Depress Anxiety, 27, 457, 10.1002/da.20668 Kanba, 2013, Guideline for treatment of bipolar disorder by the j apanese s ociety of m ood d isorders, 2012, Psychiatr Clin Neurosci, 67, 285, 10.1111/pcn.12060 Su, 2004, Lithium, a common drug for bipolar disorder treatment, regulates amyloid-β precursor protein processing, Biochemistry, 43, 6899, 10.1021/bi035627j Fountoulakis, 2007, Treatment of bipolar disorder: a complex treatment for a multi-faceted disorder, Ann Gen Psychiatr, 6, 1, 10.1186/1744-859X-6-27 Association, 2002 O'Connell, 1991, Outcome of bipolar disorder on long-term treatment with lithium, Br J Psychiatr, 159, 123, 10.1192/bjp.159.1.123 Squassina, 2013, Insulin-like growth factor 1 (igf-1) expression is upregulated in lymphoblastoid cell lines of lithium responsive bipolar disorder patients, Pharmacol Res, 73, 1, 10.1016/j.phrs.2013.04.004 Kraemer, 2012, Determining gene moderation of environmental risk factors for a mental disorder: a “perfect storm” of methodological problems, Int J Methods Psychiatr Res, 21, 185, 10.1002/mpr.1360 Fergusson, 2011, Life stress, 5-httlpr and mental disorder: findings from a 30-year longitudinal study, Br J Psychiatr, 198, 129, 10.1192/bjp.bp.110.085993 Hunsberger, 2015, Novel integrative genomic tool for interrogating lithium response in bipolar disorder, Transl Psychiatry, 5, 10.1038/tp.2014.139 Hasan, 2021, Systems biology and bioinformatics approach to identify blood based signatures molecules and drug targets of patient with covid-19,, Informatics in Medicine Unlocked, 100840 Akula, 2014, Rna-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and gtpase binding in bipolar disorder, Mol Psychiatr, 19, 1179, 10.1038/mp.2013.170 MacMullen, 2017, Novel pde10a transcript diversity in the human striatum: insights into gene complexity, conservation and regulation, Gene, 606, 17, 10.1016/j.gene.2016.12.033 C. L. Schoch, S. Ciufo, M. Domrachev, C. L. Hotton, S. Kannan, R. Khovanskaya, D. Leipe, R. Mcveigh, K. O'Neill, B. Robbertse et al., “Ncbi taxonomy: a comprehensive update on curation, resources and tools,” Database, vol. 2020, 2020. Rahman, 2021, Bioinformatics and system biology approaches to identify pathophysiological impact of covid-19 to the progression and severity of neurological diseases, Comput Biol Med, 104859, 10.1016/j.compbiomed.2021.104859 Rahman, 2021, bbaa365 Al Mahi, 2019, Grein: an interactive web platform for re-analyzing geo rna-seq data, Sci Rep, 9, 1 Heberle, 2015, Interactivenn: a web-based tool for the analysis of sets through venn diagrams, BMC Bioinf, 16, 1, 10.1186/s12859-015-0611-3 Rahman, 2020, A network-based bioinformatics approach to identify molecular biomarkers for type 2 diabetes that are linked to the progression of neurological diseases, Int J Environ Res Publ Health, 17, 1035, 10.3390/ijerph17031035 Subramanian, 2005, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc Natl Acad Sci Unit States Am, 102, 15545, 10.1073/pnas.0506580102 Rahman, 2019, Bioinformatics methodologies to identify interactions between type 2 diabetes and neurological comorbidities, IEEE Access, 7, 183948, 10.1109/ACCESS.2019.2960037 Jiao, 2012, David-ws: a stateful web service to facilitate gene/protein list analysis, Bioinformatics, 28, 1805, 10.1093/bioinformatics/bts251 Gene, 2015, Gene ontology consortium: going forward, Nucleic Acids Res, 43, D1049, 10.1093/nar/gku1179 Consortium, 2019, The gene ontology resource: 20 years and still going strong, Nucleic Acids Res, 47, D330, 10.1093/nar/gky1055 Kanehisa, 2017, Kegg: new perspectives on genomes, pathways, diseases and drugs, Nucleic Acids Res, 45, D353, 10.1093/nar/gkw1092 Fabregat, 2018, The reactome pathway knowledgebase, Nucleic Acids Res, 46, D649, 10.1093/nar/gkx1132 Rahman, 2018, 480400 V. S. Rao, K. Srinivas, G. Sujini, and G. Kumar, “Protein-protein interaction detection: methods and analysis,” International journal of proteomics, vol. 2014, 2014. Mahmud, 2021, Bioinformatics and system biology approach to identify the influences of sars-cov-2 infections to idiopathic pulmonary fibrosis and chronic obstructive pulmonary disease patients, Briefings Bioinf, 22 Zhou, 2019, Networkanalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis, Nucleic Acids Res, 47, W234, 10.1093/nar/gkz240 Szklarczyk, 2016, gkw937 Xia, 2015, Networkanalyst for statistical, visual and network-based meta-analysis of gene expression data, Nat Protoc, 10, 823, 10.1038/nprot.2015.052 Chin, 2014, cytohubba: identifying hub objects and sub-networks from complex interactome, BMC Syst Biol, 8, 1 Shannon, 2003, Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res, 13, 2498, 10.1101/gr.1239303 Mitsis, 2020, Transcription factors and evolution: an integral part of gene expression, World Academy of Sciences Journal, 2, 3 Fornes, 2020, Jaspar 2020: update of the open-access database of transcription factor binding profiles, Nucleic Acids Res, 48 Rahman, 2020, Discovering biomarkers and pathways shared by alzheimer's disease and Parkinson's disease to identify novel therapeutic targets, Int J Eng Res Technol, 6 Chou, 2018, Mirtarbase update 2018: a resource for experimentally validated microrna-target interactions, Nucleic Acids Res, 46, D296, 10.1093/nar/gkx1067 Huang, 2020, Mirtarbase 2020: updates to the experimentally validated microrna–target interaction database, Nucleic Acids Res, 48, D148 Hsu, 2014, Mirtarbase update 2014: an information resource for experimentally validated mirna-target interactions, Nucleic Acids Res, 42, D78, 10.1093/nar/gkt1266 Yoo, 2015, Dsigdb: drug signatures database for gene set analysis, Bioinformatics, 31, 3069, 10.1093/bioinformatics/btv313 Mahmud, 2021, Predtis: prediction of drug–target interactions based on multiple feature information using gradient boosting framework with data balancing and feature selection techniques, Briefings Bioinf, 22, 10.1093/bib/bbab046 Pinero, 2015, Disgenet: a discovery platform for~ the dynamical exploration of human diseases and their genes, Database, 2015, 10.1093/database/bav028 Podder, 2020, A system biological approach to investigate the genetic profiling and comorbidities of type 2 diabetes, Gene Reports, 21, 100830, 10.1016/j.genrep.2020.100830 Satagopan, 2004, Two-stage designs for gene–disease association studies with sample size constraints, Biometrics, 60, 589, 10.1111/j.0006-341X.2004.00207.x Califf, 2018, Biomarker definitions and their applications, Exp Biol Med, 243, 213, 10.1177/1535370217750088 Consortium, 2017, Expansion of the gene ontology knowledgebase and resources, Nucleic Acids Res, 45, D331, 10.1093/nar/gkw1108 Khatri, 2012, Ten years of pathway analysis: current approaches and outstanding challenges, PLoS Comput Biol, 8, e1002375, 10.1371/journal.pcbi.1002375 Al-Mustanjid, 2020, Detection of molecular signatures and pathways shared in inflammatory bowel disease and colorectal cancer: a bioinformatics and systems biology approach, Genomics, 112, 3416, 10.1016/j.ygeno.2020.06.001 Moni, 2014, comor: a software for disease comorbidity risk assessment, J Clin Bioinf, 4, 1, 10.1186/2043-9113-4-8 Sinclair, 2013, Dysregulation of glucocorticoid receptor co-factors fkbp5, bag1 and ptges3 in prefrontal cortex in psychotic illness, Sci Rep, 3, 1, 10.1038/srep03539 Pinho, 2016, Gene expression differences in peripheral blood of Parkinson's disease patients with distinct progression profiles, PLoS One, 11, e0157852, 10.1371/journal.pone.0157852 Plasil, 2019, The major histocompatibility complex of old world camelids: class i and class i-related genes, Hla, 93, 203, 10.1111/tan.13510 Abe, 2007, Nmda-receptor activation induces calpain-mediated β-catenin cleavages for triggering gene expression, Neuron, 53, 387, 10.1016/j.neuron.2007.01.016 Schott, 2021, Mhc class iii rna binding proteins and immunity, RNA Biol, 18, 640, 10.1080/15476286.2020.1860388 Frederiksen, 2019, 801563 Sturner, 2017, The role of the multifunctional bag3 protein in cellular protein quality control and in disease, Front Mol Neurosci, 10, 177, 10.3389/fnmol.2017.00177 Oliverio, 2018, Functional characterization of natural variants found on the major stress inducible 70-kda heat shock gene, hspa1a, in humans, Biochem Biophys Res Commun, 506, 799, 10.1016/j.bbrc.2018.10.148 Chen, 2013, Gene expression alterations in bipolar disorder postmortem brains, Bipolar Disord, 15, 177, 10.1111/bdi.12039 Pilaz, 2020 Wu, 2019, A novel m 6 a reader prrc2a controls oligodendroglial specification and myelination, Cell Res, 29, 23, 10.1038/s41422-018-0113-8 Toncheva, 2015 Bhat, 2018, Comprehensive network map of interferon gamma signaling, Journal of cell communication and signaling, 12, 745, 10.1007/s12079-018-0486-y Habib, 2016, Application of r to investigate common gene regulatory network pathway among bipolar disorder and associate diseases, Network Biology, 6, 86 Tang, 2018, Interferon-gamma-mediated osteoimmunology, Front Immunol, 9, 1508, 10.3389/fimmu.2018.01508 Barbosa, 2014, Cytokines in bipolar disorder: paving the way for neuroprogression, Neural Plast, 2014, 10.1155/2014/360481 Milenkovic, 2019, The role of chemokines in the pathophysiology of major depressive disorder, Int J Mol Sci, 20, 2283, 10.3390/ijms20092283 Figueiredo, 2012, Reconsidering the association between the major histocompatibility complex and bipolar disorder, J Mol Neurosci, 47, 26, 10.1007/s12031-011-9656-6 C. Carter, “Toxoplasmosis and polygenic disease susceptibility genes: extensive toxoplasma gondii host/pathogen interactome enrichment in nine psychiatric or neurological disorders,” Journal of pathogens, vol. 2013, 2013. Reyahi, 2015, Foxf2 is required for brain pericyte differentiation' and development and maintenance of the blood-brain barrier, Dev Cell, 34, 19, 10.1016/j.devcel.2015.05.008 El Wakil, 2006 Rahman, 2019, Networkbased approach to identify molecular signatures and therapeutic agents in alzheimer's disease, Comput Biol Chem, 78, 431, 10.1016/j.compbiolchem.2018.12.011 Rahman, 2020, Comprehensive analysis of rna-seq gene expression profiling of brain transcriptomes reveals novel genes, regulators, and pathways in autism spectrum disorder, Brain Sci, 10, 747, 10.3390/brainsci10100747 Knoll, 2009, Functional versatility of transcription factors in the nervous system: the srf paradigm, Trends Neurosci, 32, 432, 10.1016/j.tins.2009.05.004 Liou, 2012, Genome-wide association study of treatment refractory schizophrenia in han Chinese, PLoS One, 7, e33598, 10.1371/journal.pone.0033598 Cristino, 2014, Neurodevelopmental and neuropsychiatric disorders represent an interconnected molecular system, Mol Psychiatr, 19, 294, 10.1038/mp.2013.16 Mahmood, 2016, Association of egf, igfbp-3 and tp53 gene polymorphisms with major depressive disorder in Slovak population, Cent Eur J Publ Health, 24, 223, 10.21101/cejph.a4301 Hashimoto, 2011, Variants of the rela gene are associated with schizophrenia and their startle responses, Neuropsychopharmacology, 36, 1921, 10.1038/npp.2011.78 De Luna, 2020, Downregulation of mir-335-5p in amyotrophic lateral sclerosis can contribute to neuronal mitochondrial dysfunction and apoptosis, Sci Rep, 10, 1, 10.1038/s41598-020-61246-1 Kutsche, 2018, Combined experimental and system-level analyses reveal the complex regulatory network of mir-124 during human neurogenesis, Cell systems, 7, 438, 10.1016/j.cels.2018.08.011 He, 2019, mir-627-3p inhibits osteosarcoma cell proliferation and metastasis by targeting ptn, Aging (Albany NY), 11, 5744, 10.18632/aging.102157 Gallelli, 2019, Hsa-mir-34a-5p and hsa-mir-375 as biomarkers for monitoring the effects of drug treatment for migraine pain in children and adolescents: a pilot study, J Clin Med, 8, 928, 10.3390/jcm8070928 Faraci, 1993, Beryllium competitively inhibits brain myo-inositol monophosphatase, but unlike lithium does not enhance agonist-induced inositol phosphate accumulation, Biochem J, 291, 369, 10.1042/bj2910369 Beneyto, 2008, Lamina-specific abnormalities of nmda receptor-associated postsynaptic protein transcripts in the prefrontal cortex in schizophrenia and bipolar disorder, Neuropsychopharmacology, 33, 2175, 10.1038/sj.npp.1301604 Tran, 2016, Pm377. role of glutathione peroxidase-1 gene in the phencyclidine-induced schizophrenia-like psychosis in mice, Int J Neuropsychopharmacol, 19 Carta, 2012, Quality of life and psychiatric symptoms in wilson's disease: the relevance of bipolar disorders, Clin Pract Epidemiol Ment Health: CP & EMH, 8, 102, 10.2174/1745017901208010102 Cleymaet, 2019, A review and update on the diagnosis and treatment of neuropsychiatric wilson disease, Expert Rev Neurother, 19, 1117, 10.1080/14737175.2019.1645009