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Wei J, Wang M, Dou Y, Wang Y, Du Y, Zhao L, Ni R, Yang X, Ma X. Dysconnectivity of the brain functional network and abnormally expressed peripheral transcriptional profiles in patients with anxious depression. J Psychiatr Res 2024; 171:316-324. [PMID: 38340698 DOI: 10.1016/j.jpsychires.2024.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/18/2023] [Accepted: 01/15/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Major depressive disorder (MDD) is a heterogeneous mental disorder, and accompanying anxiety symptoms, known as anxious depression (AD), are the most common subtype. However, the pathophysiology of AD may be distinct in depressed patients without anxiety (NAD) and remains unknown. This study aimed to investigate the relationship between functional connectivity and peripheral transcriptional profiles in patients with AD and NAD. METHODS Functional imaging data were collected to identify differences in functional networks among patients with AD (n = 66), patients with NAD (n = 115), and healthy controls (HC, n = 200). The peripheral transcriptional data were clustered as co-expression modules, and their associations with AD, AND, and HC were analyzed. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses of the genes in the significant module were performed. Correlation analysis was performed to identify functional network-associated gene co-expression modules. RESULTS A network was identified which consisted of 23 nodes and 28 edges that were significantly different among three sample groups. The regions of the network were located in temporal and occipital lobe. Two gene co-expression modules were shown to be associated with NAD, and one of which was correlated with the disrupted network in the AD group. The biological function of this module was enriched in immune regulation pathways. CONCLUSION The results suggested that immune-related mechanisms were associated with functional networks in AD.
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Affiliation(s)
- Jinxue Wei
- Mental Health Center and Psychiatric Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Min Wang
- Mental Health Center and Psychiatric Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Yikai Dou
- Mental Health Center and Psychiatric Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Wang
- Mental Health Center and Psychiatric Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Yue Du
- Mental Health Center and Psychiatric Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Liansheng Zhao
- Mental Health Center and Psychiatric Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Rongjun Ni
- Mental Health Center and Psychiatric Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Xiao Yang
- Mental Health Center and Psychiatric Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaohong Ma
- Mental Health Center and Psychiatric Laboratory, West China Hospital, Sichuan University, Chengdu, China.
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Sprissler R, Hammer M, Labiner D, Joshi N, Alan A, Weinand M. Leukocyte differential gene expression prognostic value for high versus low seizure frequency in temporal lobe epilepsy. BMC Neurol 2024; 24:16. [PMID: 38166692 PMCID: PMC10759702 DOI: 10.1186/s12883-023-03459-1] [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: 09/18/2022] [Accepted: 10/26/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND This study was performed to test the hypothesis that systemic leukocyte gene expression has prognostic value differentiating low from high seizure frequency refractory temporal lobe epilepsy (TLE). METHODS A consecutive series of patients with refractory temporal lobe epilepsy was studied. Based on a median baseline seizure frequency of 2.0 seizures per month, low versus high seizure frequency was defined as ≤ 2 seizures/month and > 2 seizures/month, respectively. Systemic leukocyte gene expression was analyzed for prognostic value for TLE seizure frequency. All differentially expressed genes were analyzed, with Ingenuity® Pathway Analysis (IPA®) and Reactome, to identify leukocyte gene expression and biological pathways with prognostic value for seizure frequency. RESULTS There were ten males and six females with a mean age of 39.4 years (range: 16 to 62 years, standard error of mean: 3.6 years). There were five patients in the high and eleven patients in the low seizure frequency cohorts, respectively. Based on a threshold of twofold change (p < 0.001, FC > 2.0, FDR < 0.05) and expression within at least two pathways from both Reactome and Ingenuity® Pathway Analysis (IPA®), 13 differentially expressed leukocyte genes were identified which were all over-expressed in the low when compared to the high seizure frequency groups, including NCF2, HMOX1, RHOB, FCGR2A, PRKCD, RAC2, TLR1, CHP1, TNFRSF1A, IFNGR1, LYN, MYD88, and CASP1. Similar analysis identified four differentially expressed genes which were all over-expressed in the high when compared to the low seizure frequency groups, including AK1, F2R, GNB5, and TYMS. CONCLUSIONS Low and high seizure frequency TLE are predicted by the respective upregulation and downregulation of specific leukocyte genes involved in canonical pathways of neuroinflammation, oxidative stress and lipid peroxidation, GABA (γ-aminobutyric acid) inhibition, and AMPA and NMDA receptor signaling. Furthermore, high seizure frequency-TLE is distinguished prognostically from low seizure frequency-TLE by differentially increased specific leukocyte gene expression involved in GABA inhibition and NMDA receptor signaling. High and low seizure frequency patients appear to represent two mechanistically different forms of temporal lobe epilepsy based on leukocyte gene expression.
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Affiliation(s)
- Ryan Sprissler
- Center for Applied Genetics and Genomic Medicine, RII, University of Arizona, Tucson, AZ, USA.
| | - Michael Hammer
- Department of Neurology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - David Labiner
- Department of Neurology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Neil Joshi
- Department of Neurosurgery, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Albert Alan
- Department of Neurosurgery, University of Arizona College of Medicine, Tucson, AZ, USA
- University of Arizona College of Medicine, Tucson, AZ, USA
| | - Martin Weinand
- Department of Neurosurgery, University of Arizona College of Medicine, Tucson, AZ, USA
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Zhang LM, Chen L, Zhao YF, Duan WM, Zhong LM, Liu MW. Identification of key potassium channel genes of temporal lobe epilepsy by bioinformatics analyses and experimental verification. Front Neurol 2023; 14:1175007. [PMID: 37483435 PMCID: PMC10361730 DOI: 10.3389/fneur.2023.1175007] [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: 02/27/2023] [Accepted: 06/16/2023] [Indexed: 07/25/2023] Open
Abstract
One of the most prevalent types of epilepsy is temporal lobe epilepsy (TLE), which has unknown etiological factors and drug resistance. The detailed mechanisms underlying potassium channels in human TLE have not yet been elucidated. Hence, this study aimed to mine potassium channel genes linked to TLE using a bioinformatic approach. The results found that Four key TLE-related potassium channel genes (TERKPCGs) were identified: potassium voltage-gated channel subfamily E member (KCNA) 1, KCNA2, potassium inwardly rectifying channel, subfamily J, member 11 (KCNJ11), and KCNS1. A protein-protein interaction (PPI) network was constructed to analyze the relationship between TERKPCGs and other key module genes. The results of gene set enrichment analysis (GSEA) for a single gene indicated that the four TERKPCGs were highly linked to the cation channel, potassium channel, respiratory chain, and oxidative phosphorylation. The mRNA-TF network was established using four mRNAs and 113 predicted transcription factors. A ceRNA network containing seven miRNAs, two mRNAs, and 244 lncRNAs was constructed based on the TERKPCGs. Three common small-molecule drugs (enflurane, promethazine, and miconazole) target KCNA1, KCNA2, and KCNS1. Ten small-molecule drugs (glimepiride, diazoxide, levosimendan, and thiamylal et al.) were retrieved for KCNJ11. Compared to normal mice, the expression of KCNA1, KCNA2, KCNJ11, and KCNS1 was downregulated in the brain tissue of the epilepsy mouse model at both the transcriptional and translational levels, which was consistent with the trend of human data from the public database. The results indicated that key potassium channel genes linked to TLE were identified based on bioinformatics analysis to investigate the potential significance of potassium channel genes in the development and treatment of TLE.
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Affiliation(s)
- Lin-ming Zhang
- Department of Neurology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Provincial Clinical Research Center for Neurological Disease, Kunming, Yunnan, China
| | - Ling Chen
- Department of Neurology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Provincial Clinical Research Center for Neurological Disease, Kunming, Yunnan, China
| | - Yi-fei Zhao
- Department of Neurology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Provincial Clinical Research Center for Neurological Disease, Kunming, Yunnan, China
| | - Wei-mei Duan
- Department of Neurology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Provincial Clinical Research Center for Neurological Disease, Kunming, Yunnan, China
| | - Lian-mei Zhong
- Department of Neurology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Provincial Clinical Research Center for Neurological Disease, Kunming, Yunnan, China
| | - Ming-wei Liu
- Department of Emergency, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
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Sforzini L, Cattaneo A, Ferrari C, Turner L, Mariani N, Enache D, Hastings C, Lombardo G, Nettis MA, Nikkheslat N, Worrell C, Zajkowska Z, Kose M, Cattane N, Lopizzo N, Mazzelli M, Pointon L, Cowen PJ, Cavanagh J, Harrison NA, Jones D, Drevets WC, Mondelli V, Bullmore ET, Pariante CM. Higher immune-related gene expression in major depression is independent of CRP levels: results from the BIODEP study. Transl Psychiatry 2023; 13:185. [PMID: 37264010 PMCID: PMC10235092 DOI: 10.1038/s41398-023-02438-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 04/14/2023] [Accepted: 04/19/2023] [Indexed: 06/03/2023] Open
Abstract
Compelling evidence demonstrates that some individuals suffering from major depressive disorder (MDD) exhibit increased levels of inflammation. Most studies focus on inflammation-related proteins, such as serum or plasma C-reactive protein (CRP). However, the immune-related modifications associated with MDD may be not entirely captured by CRP alone. Analysing mRNA gene expression levels, we aimed to identify broader molecular immune-related phenotypes of MDD. We examined 168 individuals from the non-interventional, case-control, BIODEP study, 128 with a diagnosis of MDD and 40 healthy controls. Individuals with MDD were further divided according to serum high-sensitivity (hs)CRP levels (n = 59 with CRP <1, n = 33 with CRP 1-3 and n = 36 with CRP >3 mg/L). We isolated RNA from whole blood and performed gene expression analyses using RT-qPCR. We measured the expression of 16 immune-related candidate genes: A2M, AQP4, CCL2, CXCL12, CRP, FKBP5, IL-1-beta, IL-6, ISG15, MIF, GR, P2RX7, SGK1, STAT1, TNF-alpha and USP18. Nine of the 16 candidate genes were differentially expressed in MDD cases vs. controls, with no differences between CRP-based groups. Only CRP mRNA was clearly associated with serum CRP. In contrast, plasma (proteins) IL-6, IL-7, IL-8, IL-10, IL-12/IL-23p40, IL-16, IL-17A, IFN-gamma and TNF-alpha, and neutrophils counts, were all differentially regulated between CRP-based groups (higher in CRP >3 vs. CRP <1 and/or controls), reflecting the gradient of CRP values. Secondary analyses on MDD individuals and controls with CRP values <1 mg/L (usually interpreted as 'no inflammation') confirmed MDD cases still had significantly different mRNA expression of immune-related genes compared with controls. These findings corroborate an immune-related molecular activation in MDD, which appears to be independent of serum CRP levels. Additional biological mechanisms may then be required to translate this mRNA signature into inflammation at protein and cellular levels. Understanding these mechanisms will help to uncover the true immune abnormalities in depression, opening new paths for diagnosis and treatment.
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Affiliation(s)
- Luca Sforzini
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, London, SE5 9RT, UK.
| | - Annamaria Cattaneo
- Biological Psychiatric Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125, Brescia, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Clarissa Ferrari
- Research and Clinical Trials Service, Fondazione Poliambulanza Istituto Ospedaliero, Brescia, 25124, Italy
| | - Lorinda Turner
- Department of Psychiatry, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SZ, UK
| | - Nicole Mariani
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, London, SE5 9RT, UK
| | - Daniela Enache
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, London, SE5 9RT, UK
| | - Caitlin Hastings
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, London, SE5 9RT, UK
| | - Giulia Lombardo
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, London, SE5 9RT, UK
| | - Maria A Nettis
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, London, SE5 9RT, UK
| | - Naghmeh Nikkheslat
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, London, SE5 9RT, UK
| | - Courtney Worrell
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, London, SE5 9RT, UK
| | - Zuzanna Zajkowska
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, London, SE5 9RT, UK
| | - Melisa Kose
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, London, SE5 9RT, UK
| | - Nadia Cattane
- Biological Psychiatric Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125, Brescia, Italy
| | - Nicola Lopizzo
- Biological Psychiatric Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125, Brescia, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Monica Mazzelli
- Biological Psychiatric Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125, Brescia, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Linda Pointon
- Department of Psychiatry, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SZ, UK
| | - Philip J Cowen
- University of Oxford Department of Psychiatry, Warneford Hospital, Oxford, OX3 7JX, UK
| | - Jonathan Cavanagh
- Centre for Immunobiology, School of Infection & Immunity, University of Glasgow, G12 8TA, Glasgow, Scotland
| | - Neil A Harrison
- School of Medicine, School of Psychology, Cardiff University Brain Research Imaging Centre, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Declan Jones
- Neuroscience External Innovation, Janssen Pharmaceuticals, J&J Innovation Centre, London, W1G 0BG, UK
| | - Wayne C Drevets
- Janssen Research & Development, Neuroscience Therapeutic Area, 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Valeria Mondelli
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, London, SE5 9RT, UK
- National Institute for Health Research (NIHR) Mental Health Biomedical Research Centre at South London and Maudsley NHS Foundation Trust, London, UK
| | - Edward T Bullmore
- Department of Psychiatry, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SZ, UK
| | - Carmine M Pariante
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, London, SE5 9RT, UK
- National Institute for Health Research (NIHR) Mental Health Biomedical Research Centre at South London and Maudsley NHS Foundation Trust, London, UK
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Issler O, van der Zee YY, Ramakrishnan A, Xia S, Zinsmaier AK, Tan C, Li W, Browne CJ, Walker DM, Salery M, Torres-Berrío A, Futamura R, Duffy JE, Labonte B, Girgenti MJ, Tamminga CA, Dupree JL, Dong Y, Murrough JW, Shen L, Nestler EJ. The long noncoding RNA FEDORA is a cell type- and sex-specific regulator of depression. SCIENCE ADVANCES 2022; 8:eabn9494. [PMID: 36449610 PMCID: PMC9710883 DOI: 10.1126/sciadv.abn9494] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 10/12/2022] [Indexed: 05/31/2023]
Abstract
Women suffer from depression at twice the rate of men, but the underlying molecular mechanisms are poorly understood. Here, we identify marked baseline sex differences in the expression of long noncoding RNAs (lncRNAs), a class of regulatory transcripts, in human postmortem brain tissue that are profoundly lost in depression. One such human lncRNA, RP11-298D21.1 (which we termed FEDORA), is enriched in oligodendrocytes and neurons and up-regulated in the prefrontal cortex (PFC) of depressed females only. We found that virally expressing FEDORA selectively either in neurons or in oligodendrocytes of PFC promoted depression-like behavioral abnormalities in female mice only, changes associated with cell type-specific regulation of synaptic properties, myelin thickness, and gene expression. We also found that blood FEDORA levels have diagnostic implications for depressed women and are associated with clinical response to ketamine. These findings demonstrate the important role played by lncRNAs, and FEDORA in particular, in shaping the sex-specific landscape of the brain and contributing to sex differences in depression.
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Affiliation(s)
- Orna Issler
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yentl Y. van der Zee
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sunhui Xia
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Chunfeng Tan
- Department of Psychiatry, UT Southwestern, Dallas, TX, USA
| | - Wei Li
- Department of Psychiatry, UT Southwestern, Dallas, TX, USA
| | - Caleb J. Browne
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Deena M. Walker
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marine Salery
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Angélica Torres-Berrío
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rita Futamura
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Julia E. Duffy
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benoit Labonte
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew J. Girgenti
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Jeffrey L. Dupree
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Yan Dong
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - James W. Murrough
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric J. Nestler
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Li Y(J, Kresock E, Kuplicki R, Savitz J, McKinney BA. Differential expression of MDGA1 in major depressive disorder. Brain Behav Immun Health 2022; 26:100534. [PMID: 36247836 PMCID: PMC9563614 DOI: 10.1016/j.bbih.2022.100534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 09/08/2022] [Accepted: 10/09/2022] [Indexed: 11/09/2022] Open
Abstract
The identification of gene expression-based biomarkers for major depressive disorder (MDD) continues to be an important challenge. In order to identify candidate biomarkers and mechanisms, we apply statistical and machine learning feature selection to an RNA-Seq gene expression dataset of 78 unmedicated individuals with MDD and 79 healthy controls. We identify 49 genes by LASSO penalized logistic regression and 45 genes at the false discovery rate threshold 0.188. The MDGA1 gene has the lowest P-value (4.9e-5) and is expressed in the developing brain, involved in axon guidance, and associated with related mood disorders in previous studies of bipolar disorder (BD) and schizophrenia (SCZ). The expression of MDGA1 is associated with age and sex, but its association with MDD remains significant when adjusted for covariates. MDGA1 is in a co-expression cluster with another top gene, ATXN7L2 (ataxin 7 like 2), which was associated with MDD in a recent GWAS. The LASSO classification model of MDD includes MDGA1, and the model has a cross-validation accuracy of 79%. Another noteworthy top gene, IRF2BPL, is in a close co-expression cluster with MDGA1 and may be related to microglial inflammatory states in MDD. Future exploration of MDGA1 and its gene interactions may provide insights into mechanisms and heterogeneity of MDD. We use penalized regression to select differentially expressed genes and characterize their relationships through clustering. We identify MDGA1 as the most differentially expressed gene between MDD and healthy controls using RNA-Seq. Previous studies have implicated MDGA1 in psychiatric disorders, such as schizophrenia and bipolar disorder, but not in MDD. Different psychiatric disorders have some genetic associations in common due to shared neural pathways between disorders. A top gene, IRF2BPL, in a close co-expression cluster with MDGA1 may be related to microglial inflammatory states in MDD. Future investigation of interactions of MDGA1 and IRF2BPL may provide insights into mechanisms and heterogeneity of MDD.
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Bekhbat M, Ulukaya GB, Bhasin MK, Felger JC, Miller AH. Cellular and immunometabolic mechanisms of inflammation in depression: Preliminary findings from single cell RNA sequencing and a tribute to Bruce McEwen. Neurobiol Stress 2022; 19:100462. [PMID: 35655933 PMCID: PMC9152104 DOI: 10.1016/j.ynstr.2022.100462] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/03/2022] [Accepted: 05/16/2022] [Indexed: 11/04/2022] Open
Abstract
Inflammation is associated with symptoms of anhedonia, a core feature of major depression (MD). We have shown that MD patients with high inflammation as measured by plasma C-reactive protein (CRP) and anhedonia display gene signatures of metabolic reprograming (e.g., shift to glycolysis) necessary to sustain cellular immune activation. To gain preliminary insight into the immune cell subsets and transcriptomic signatures that underlie increased inflammation and its relationship with behavior in MD at the single-cell (sc) level, herein we conducted scRNA-Seq on peripheral blood mononuclear cells from a subset of medically-stable, unmedicated MD outpatients. Three MD patients with high CRP (>3 mg/L) before and two weeks after anti-inflammatory challenge with the tumor necrosis factor antagonist infliximab and three patients with low CRP (≤3 mg/L) were studied. Cell clusters were identified using a Single Cell Wizard pipeline, followed by pathway analysis. CD14+ and CD16+ monocytes were more abundant in MD patients with high CRP and were reduced by 29% and 55% respectively after infliximab treatment. Within CD14+ and CD16+ monocytes, genes upregulated in high CRP patients were enriched for inflammatory (phagocytosis, complement, leukocyte migration) and immunometabolic (hypoxia-inducible factor [HIF]-1, aerobic glycolysis) pathways. Shifts in CD4+ T cell subsets included ∼30% and ∼10% lower abundance of CD4+ central memory (TCM) and naïve cells and ∼50% increase in effector memory-like (TEM-like) cells in high versus low CRP patients. TCM cells of high CRP patients displayed downregulation of the oxidative phosphorylation (OXPHOS) pathway, a main energy source in this cell type. Following infliximab, changes in the number of CD14+ monocytes and CD4+ TEM-like cells predicted improvements in anhedonia scores (r = 1.0, p < 0.001). In sum, monocytes and CD4+ T cells from MD patients with increased inflammation exhibited immunometabolic reprograming in association with symptoms of anhedonia. These findings are the first step toward determining the cellular and molecular immune pathways associated with inflammatory phenotypes in MD, which may lead to novel immunomodulatory treatments of psychiatric illnesses with increased inflammation.
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Baratta AM, Brandner AJ, Plasil SL, Rice RC, Farris SP. Advancements in Genomic and Behavioral Neuroscience Analysis for the Study of Normal and Pathological Brain Function. Front Mol Neurosci 2022; 15:905328. [PMID: 35813067 PMCID: PMC9259865 DOI: 10.3389/fnmol.2022.905328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022] Open
Abstract
Psychiatric and neurological disorders are influenced by an undetermined number of genes and molecular pathways that may differ among afflicted individuals. Functionally testing and characterizing biological systems is essential to discovering the interrelationship among candidate genes and understanding the neurobiology of behavior. Recent advancements in genetic, genomic, and behavioral approaches are revolutionizing modern neuroscience. Although these tools are often used separately for independent experiments, combining these areas of research will provide a viable avenue for multidimensional studies on the brain. Herein we will briefly review some of the available tools that have been developed for characterizing novel cellular and animal models of human disease. A major challenge will be openly sharing resources and datasets to effectively integrate seemingly disparate types of information and how these systems impact human disorders. However, as these emerging technologies continue to be developed and adopted by the scientific community, they will bring about unprecedented opportunities in our understanding of molecular neuroscience and behavior.
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Affiliation(s)
- Annalisa M. Baratta
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Adam J. Brandner
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sonja L. Plasil
- Department of Pharmacology & Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Rachel C. Rice
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sean P. Farris
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Anesthesiology and Perioperative Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Sean P. Farris,
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Ren J, Li C, Wei S, He Y, Huang P, Xu J. Identifying Antidepressant Effects of Brain-Derived Neurotrophic Factor and IDO1 in the Mouse Model Based on RNA-Seq Data. Front Genet 2022; 13:890961. [PMID: 35711916 PMCID: PMC9195421 DOI: 10.3389/fgene.2022.890961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/15/2022] [Indexed: 11/27/2022] Open
Abstract
Deletion of brain-derived neurotrophic factor (BDNF) and upregulation of indoleamine 2,3-dioxygenase 1 (IDO1) are associated with depression severity in animals. The neurotransmitter hypothesis of depression at the transcriptomic level can be tested using BDNF- and IDO1-knockout mouse models and RNA-seq. In this study, BDNF+/−, IDO1−/−, and chronic ultra-mild stress (CUMS)-induced depression mouse models and controls were developed, and the differentially expressed genes were analyzed. Furthermore, the ceRNA package was used to search the lncRNA2Target database for potential lncRNAs. Finally, a protein–protein interaction (PPI) network was constructed using STRINGdb. By comparing the control and CUMS model groups, it was found that pathway enrichment analysis and ceRNA network analysis revealed that most differentially expressed genes (DEGs) were associated with protection of vulnerable neuronal circuits. In addition, we found the enriched pathways were associated with nervous system development and synapse organization when comparing the control and BDNF+/−model groups. When replicating the neurotransmitter disruption features of clinical patients, such comparisons revealed the considerable differences between CUMS and knockdown BDNF models, and the BDNF+/−model may be superior to the classic CUMS model. The data obtained in the present study implicated the potential DEGs and their enriched pathway in three mouse models related to depression and the regulation of the ceRNA network-mediated gene in the progression of depression. Together, our findings may be crucial for uncovering the mechanisms underlying the neurotransmitter hypothesis of depression in animals.
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Affiliation(s)
- Jing Ren
- Department of Neuropharmacology and Novel Drug Discovery, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China.,Students Affairs Division, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Chenyang Li
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Songren Wei
- Department of Neuropharmacology and Novel Drug Discovery, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Yanjun He
- Emergency Department, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, China
| | - Peng Huang
- Women and Children Medical Research Center, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, China
| | - Jiangping Xu
- Department of Neuropharmacology and Novel Drug Discovery, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
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10
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Antidepressant-Like Effect of Traditional Medicinal Plant Carthamus Tinctorius in Mice Model through Neuro-Behavioral Tests and Transcriptomic Approach. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12115594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Major depression disorder (MDD) has become a common life-threatening disorder. Despite the number of studies and the introduced antidepressants, MDD remains a major global health issue. Carthamus tinctorius (safflower) is traditionally used for food and medical purposes. This study investigated the chemical profile and the antidepressant-like effect of the Carthamus tincto-rius hot water extract in male mice and its mechanism using a transcriptomic analysis. The antidepressant effect of hot water extract (50 mg/kg and 150 mg/kg) was investigated in mice versus the untreated group (saline) and positive control group (fluoxetine 10 mg/kg). Hippocampus transcriptome changes were investigated to understand the Carthamus tinctorius mechanism of action. The GC-MS analysis of Carthamus tinctorius showed that hot water extract yielded the highest amount of oleamide as the most active ingredient. Neuro-behavioral tests demonstrated that the safflower treatment significantly reduced immobility time in TST and FST and improved performance in the YMSAT compared to the control group. RNA-seq analysis revealed a significant differential gene expression pattern in several genes such as Ube2j2, Ncor1, Tuba1c, Grik1, Msmo1, and Casp9 related to MDD regulation in 50 mg/kg safflower treatment as compared to untreated and fluoxetine-treated groups. Our findings demonstrated the antidepressant-like effect of safflower hot water extract and its bioactive ingredient oleamide on mice, validated by a significantly shortened immobility time in TST and FST and an increase in the percentage of spontaneous alternation.
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11
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Bai Y, Li Y, Shen Y, Yang M, Zhang W, Cui B. AutoDC: an Automatic Machine Learning Framework for Disease Classification. Bioinformatics 2022; 38:3415-3421. [PMID: 35583303 DOI: 10.1093/bioinformatics/btac334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 04/12/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The emergence of next-generation sequencing techniques opens up tremendous opportunities for researchers to uncover the basic mechanisms of disease at the molecular level. Recently, automatic machine learning (AutoML) frameworks have been employed for genomic and epigenomic data analysis. However, to analyze those high-dimensional data, existing AutoML frameworks suffer from the following issues: 1) they could not effectively filter out the redundant features from the original data, and 2) they usually obey the rule of feature engineering first and algorithm hyper-parameter tuning later to build the machine learning pipeline, which could lead to sub-optimal outcomes. Thus, it is an urgent need to design a new AutoML framework for high-dimensional omics data analysis. RESULTS We introduce a new method: AutoDC, a tailored automatic machine learning framework, for different disease classification based on gene expression data. AutoDC designs two novel optimization strategies to improve the performance. One is that AutoDC designs a novel two-stage feature selection method to select the features with high gene contribution scores. The other is that AutoDC proposes a novel optimization method, based on a two-layer Multi-Armed Bandit framework, to jointly optimize the feature engineering, algorithm selection, and algorithm hyper-parameter tuning. We apply our framework to two public gene expression datasets. Compared with three state-of-the-art AutoML frameworks, AutoDC could effectively classify diseases with higher predictive accuracy. AVAILABILITY The data and codes of AutoDC are available at https://github.com/dingdian110/AutoDC. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yang Bai
- Key Laboratory of High Confidence Software Technologies (MOE), School of CS, Peking University, Beijing, China
| | - Yang Li
- Key Laboratory of High Confidence Software Technologies (MOE), School of CS, Peking University, Beijing, China
| | - Yu Shen
- Key Laboratory of High Confidence Software Technologies (MOE), School of CS, Peking University, Beijing, China
| | - Mingyu Yang
- Key Laboratory of High Confidence Software Technologies (MOE), School of CS, Peking University, Beijing, China
| | - Wentao Zhang
- Key Laboratory of High Confidence Software Technologies (MOE), School of CS, Peking University, Beijing, China
| | - Bin Cui
- Key Laboratory of High Confidence Software Technologies (MOE), School of CS, Peking University, Beijing, China.,Institute of Computational Social Science, Peking University (Qingdao), Qingdao, China
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12
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Identification of Key Modules and Genes Associated with Major Depressive Disorder in Adolescents. Genes (Basel) 2022; 13:genes13030464. [PMID: 35328018 PMCID: PMC8949287 DOI: 10.3390/genes13030464] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/26/2022] [Accepted: 03/02/2022] [Indexed: 12/25/2022] Open
Abstract
Major depressive disorder (MDD) is a leading cause of disability worldwide. Adolescence is a crucial period for the occurrence and development of depression. There are essential distinctions between adolescent and adult depression patients, and the etiology of depressive disorder is unclear. The interactions of multiple genes in a co-expression network are likely to be involved in the physiopathology of MDD. In the present study, RNA-Seq data of mRNA were acquired from the peripheral blood of MDD in adolescents and healthy control (HC) subjects. Co-expression modules were constructed via weighted gene co-expression network analysis (WGCNA) to investigate the relationships between the underlying modules and MDD in adolescents. In the combined MDD and HC groups, the dynamic tree cutting method was utilized to assign genes to modules through hierarchical clustering. Moreover, functional enrichment analysis was conducted on those co-expression genes from interested modules. The results showed that eight modules were constructed by WGCNA. The blue module was significantly associated with MDD after multiple comparison adjustment. Several Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with stress and inflammation were identified in this module, including histone methylation, apoptosis, NF-kappa β signaling pathway, and TNF signaling pathway. Five genes related to inflammation, immunity, and the nervous system were identified as hub genes: CNTNAP3, IL1RAP, MEGF9, UBE2W, and UBE2D1. All of these findings supported that MDD was associated with stress, inflammation, and immune responses, helping us to obtain a better understanding of the internal molecular mechanism and to explore biomarkers for the diagnosis or treatment of depression in adolescents.
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13
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Imbert A, Vialaneix N, Marquis J, Vion J, Charpagne A, Metairon S, Laurens C, Moro C, Boulet N, Walter O, Lefebvre G, Hager J, Langin D, Saris WHM, Astrup A, Viguerie N, Valsesia A. Network Analyses Reveal Negative Link Between Changes in Adipose Tissue GDF15 and BMI During Dietary-induced Weight Loss. J Clin Endocrinol Metab 2022; 107:e130-e142. [PMID: 34415992 DOI: 10.1210/clinem/dgab621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT Adipose tissue (AT) transcriptome studies provide holistic pictures of adaptation to weight and related bioclinical settings changes. OBJECTIVE To implement AT gene expression profiling and investigate the link between changes in bioclinical parameters and AT gene expression during 3 steps of a 2-phase dietary intervention (DI). METHODS AT transcriptome profiling was obtained from sequencing 1051 samples, corresponding to 556 distinct individuals enrolled in a weight loss intervention (8-week low-calorie diet (LCD) at 800 kcal/day) followed with a 6-month ad libitum randomized DI. Transcriptome profiles obtained with QuantSeq sequencing were benchmarked against Illumina RNAseq. Reverse transcription quantitative polymerase chain reaction was used to further confirm associations. Cell specificity was assessed using freshly isolated cells and THP-1 cell line. RESULTS During LCD, 5 modules were found, of which 3 included at least 1 bioclinical variable. Change in body mass index (BMI) connected with changes in mRNA level of genes with inflammatory response signature. In this module, change in BMI was negatively associated with changes in expression of genes encoding secreted protein (GDF15, CCL3, and SPP1). Through all phases of the DI, change in GDF15 was connected to changes in SPP1, CCL3, LIPA and CD68. Further characterization showed that these genes were specific to macrophages (with LIPA, CD68 and GDF15 expressed in anti-inflammatory macrophages) and GDF15 also expressed in preadipocytes. CONCLUSION Network analyses identified a novel AT feature with GDF15 upregulated with calorie restriction induced weight loss, concomitantly to macrophage markers. In AT, GDF15 was expressed in preadipocytes and macrophages where it was a hallmark of anti-inflammatory cells.
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Affiliation(s)
- Alyssa Imbert
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, Institute of Metabolic and Cardiovascular Diseases, Team Metabolic Disorders and Diabesity, 31400, Toulouse, France
- Université de Toulouse, UMR1297, Institute of Metabolic and Cardiovascular Diseases, Paul Sabatier University, 31400, Toulouse, France
- INRAE, UR875 Mathématiques et Informatique Appliquées Toulouse, F-31326 Castanet-Tolosan, France
| | - Nathalie Vialaneix
- INRAE, UR875 Mathématiques et Informatique Appliquées Toulouse, F-31326 Castanet-Tolosan, France
| | - Julien Marquis
- Université de Lausanne, Genomic Technologies Facility, 1015, Lausanne, Switzerland
| | - Julie Vion
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, Institute of Metabolic and Cardiovascular Diseases, Team Metabolic Disorders and Diabesity, 31400, Toulouse, France
- Université de Toulouse, UMR1297, Institute of Metabolic and Cardiovascular Diseases, Paul Sabatier University, 31400, Toulouse, France
| | - Aline Charpagne
- Nestlé Institute of Health Sciences, Metabolic Health Department, 1015, Lausanne, Switzerland
| | - Sylviane Metairon
- Nestlé Institute of Health Sciences, Metabolic Health Department, 1015, Lausanne, Switzerland
| | - Claire Laurens
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, Institute of Metabolic and Cardiovascular Diseases, Team Metabolic Disorders and Diabesity, 31400, Toulouse, France
- Université de Toulouse, UMR1297, Institute of Metabolic and Cardiovascular Diseases, Paul Sabatier University, 31400, Toulouse, France
| | - Cedric Moro
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, Institute of Metabolic and Cardiovascular Diseases, Team Metabolic Disorders and Diabesity, 31400, Toulouse, France
- Université de Toulouse, UMR1297, Institute of Metabolic and Cardiovascular Diseases, Paul Sabatier University, 31400, Toulouse, France
| | - Nathalie Boulet
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, Institute of Metabolic and Cardiovascular Diseases, Team Metabolic Disorders and Diabesity, 31400, Toulouse, France
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, Institute of Metabolic and Cardiovascular Diseases, Team Adipose tissue, microbiota and cardiometabolic flexibility, 31400, Toulouse, France
| | - Ondine Walter
- Nestlé Institute of Health Sciences, Metabolic Health Department, 1015, Lausanne, Switzerland
| | - Grégory Lefebvre
- Nestlé Institute of Health Sciences, Metabolic Health Department, 1015, Lausanne, Switzerland
| | - Jörg Hager
- Nestlé Institute of Health Sciences, Metabolic Health Department, 1015, Lausanne, Switzerland
| | - Dominique Langin
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, Institute of Metabolic and Cardiovascular Diseases, Team Metabolic Disorders and Diabesity, 31400, Toulouse, France
- Université de Toulouse, UMR1297, Institute of Metabolic and Cardiovascular Diseases, Paul Sabatier University, 31400, Toulouse, France
- Franco-Czech Laboratory for Clinical Research on Obesity, Third Faculty of Medicine, Prague and Paul Sabatier University, Toulouse, France
- Toulouse University Hospitals, Laboratory of Clinical Biochemistry, 31000, Toulouse, France
| | - Wim H M Saris
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Arne Astrup
- Department of Nutrition, Exercise and Sports, Faculty of Sciences, University of Copenhagen, Denmark
| | - Nathalie Viguerie
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1297, Institute of Metabolic and Cardiovascular Diseases, Team Metabolic Disorders and Diabesity, 31400, Toulouse, France
- Université de Toulouse, UMR1297, Institute of Metabolic and Cardiovascular Diseases, Paul Sabatier University, 31400, Toulouse, France
- Franco-Czech Laboratory for Clinical Research on Obesity, Third Faculty of Medicine, Prague and Paul Sabatier University, Toulouse, France
| | - Armand Valsesia
- Nestlé Institute of Health Sciences, Metabolic Health Department, 1015, Lausanne, Switzerland
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14
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Zonca V. Preventive strategies for adolescent depression: What are we missing? A focus on biomarkers. Brain Behav Immun Health 2021; 18:100385. [PMID: 34825234 PMCID: PMC8604665 DOI: 10.1016/j.bbih.2021.100385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/21/2021] [Accepted: 10/31/2021] [Indexed: 11/25/2022] Open
Abstract
Adolescent depression is an important global issue with several unmet needs that still must be addressed and, to date, there are only few effective preventive strategies to reduce the burden of this disorder worldwide. In this mini-review, the evidence and potential ways to improve an early detection will be discussed as well as prompt interventions by focusing on a better understanding of the risks underlying the developing of adolescent depression from both a sociodemographic and a biological perspective.
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Affiliation(s)
- Valentina Zonca
- King's College London, Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, London, UK.,Biological Psychiatry Lab, IRCCS Istituto Centro San Giovanni di Dio, Brescia, Italy
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15
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Cole JJ, McColl A, Shaw R, Lynall ME, Cowen PJ, de Boer P, Drevets WC, Harrison N, Pariante C, Pointon L, Goodyear C, Bullmore E, Cavanagh J. No evidence for differential gene expression in major depressive disorder PBMCs, but robust evidence of elevated biological ageing. Transl Psychiatry 2021; 11:404. [PMID: 34294682 PMCID: PMC8298604 DOI: 10.1038/s41398-021-01506-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/20/2021] [Accepted: 06/10/2021] [Indexed: 12/30/2022] Open
Abstract
The increasingly compelling data supporting the involvement of immunobiological mechanisms in Major Depressive Disorder (MDD) might provide some explanation forthe variance in this heterogeneous condition. Peripheral blood measures of cytokines and chemokines constitute the bulk of evidence, with consistent meta-analytic data implicating raised proinflammatory cytokines such as IL6, IL1β and TNF. Among the potential mechanisms linking immunobiological changes to affective neurobiology is the accelerated biological ageing seen in MDD, particularly via the senescence associated secretory phenotype (SASP). However, the cellular source of immunobiological markers remains unclear. Pre-clinical evidence suggests a role for peripheral blood mononuclear cells (PBMC), thus here we aimed to explore the transcriptomic profile using RNA sequencing in PBMCs in a clinical sample of people with various levels of depression and treatment response comparing it with that in healthy controls (HCs). There were three groups with major depressive disorder (MDD): treatment-resistant (n = 94), treatment-responsive (n = 47) and untreated (n = 46). Healthy controls numbered 44. Using PBMCs gene expression analysis was conducted using RNAseq to a depth of 54.5 million reads. Differential gene expression analysis was performed using DESeq2. The data showed no robust signal differentiating MDD and HCs. There was, however, significant evidence of elevated biological ageing in MDD vs HC. Biological ageing was evident in these data as a transcriptional signature of 888 age-associated genes (adjusted p < 0.05, absolute log2fold > 0.6) that also correlated strongly with chronological age (spearman correlation coefficient of 0.72). Future work should expand clinical sample sizes and reduce clinical heterogeneity. Exploration of RNA-seq signatures in other leukocyte populations and single cell RNA sequencing may help uncover more subtle differences. However, currently the subtlety of any PBMC signature mitigates against its convincing use as a diagnostic or predictive biomarker.
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Affiliation(s)
- John J. Cole
- grid.8756.c0000 0001 2193 314XInstitute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UK
| | - Alison McColl
- grid.8756.c0000 0001 2193 314XInstitute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UK
| | - Robin Shaw
- grid.23636.320000 0000 8821 5196Cancer Research UK Beatson Institute, Glasgow, UK
| | - Mary-Ellen Lynall
- grid.5335.00000000121885934Department of Psychiatry, University of Cambridge, UK and Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | - Philip J. Cowen
- grid.416938.10000 0004 0641 5119Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, CB2 0SZ UK
| | - Peter de Boer
- grid.419619.20000 0004 0623 0341Janssen Research and Development, Experimental Medicine-Neuroscience Therapeutic Area, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Wayne C. Drevets
- grid.497530.c0000 0004 0389 4927Neuroscience Therapeutic Area, Janssen Research & Development, LLC, San Diego, CA USA
| | - Neil Harrison
- grid.5600.30000 0001 0807 5670Cardiff University Brain Research Imaging Centre, Maindy Road, Cardiff, UK
| | - Carmine Pariante
- grid.13097.3c0000 0001 2322 6764Stress, Psychiatry and Immunology Laboratory & Section of Perinatal Psychiatry, King’s College, University of London, London, UK
| | - Linda Pointon
- grid.5335.00000000121885934Department of Psychiatry, University of Cambridge, UK and Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | | | - Carl Goodyear
- grid.8756.c0000 0001 2193 314XInstitute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UK
| | - Edward Bullmore
- grid.5335.00000000121885934Department of Psychiatry, University of Cambridge, UK and Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | - Jonathan Cavanagh
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UK.
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16
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Zheng PF, Chen LZ, Guan YZ, Liu P. Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease. Sci Rep 2021; 11:6711. [PMID: 33758323 PMCID: PMC7988178 DOI: 10.1038/s41598-021-86207-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/12/2021] [Indexed: 12/21/2022] Open
Abstract
This investigation seeks to dissect coronary artery disease molecular target candidates along with its underlying molecular mechanisms. Data on patients with CAD across three separate array data sets, GSE66360, GSE19339 and GSE97320 were extracted. The gene expression profiles were obtained by normalizing and removing the differences between the three data sets, and important modules linked to coronary heart disease were identified using weighted gene co-expression network analysis (WGCNA). Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and genomes (KEGG) pathway enrichment analyses were applied in order to identify statistically significant genetic modules with the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool (version 6.8; http://david.abcc.ncifcrf.gov ). The online STRING tool was used to construct a protein-protein interaction (PPI) network, followed by the use of Molecular Complex Detection (MCODE) plug-ins in Cytoscape software to identify hub genes. Two significant modules (green-yellow and magenta) were identified in the CAD samples. Genes in the magenta module were noted to be involved in inflammatory and immune-related pathways, based on GO and KEGG enrichment analyses. After the MCODE analysis, two different MCODE complexes were identified in the magenta module, and four hub genes (ITGAM, degree = 39; CAMP, degree = 37; TYROBP, degree = 28; ICAM1, degree = 18) were uncovered to be critical players in mediating CAD. Independent verification data as well as our RT-qPCR results were highly consistent with the above finding. ITGAM, CAMP, TYROBP and ICAM1 are potential targets in CAD. The underlying mechanism may be related to the transendothelial migration of leukocytes and the immune response.
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Affiliation(s)
- Peng-Fei Zheng
- Department of Cardiology, The Central Hospital of Shao Yang, 36 QianYuan lane, Shaoyang, 422000, Hunan, People's Republic of China.,Graduate School of Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
| | - Lu-Zhu Chen
- Department of Cardiology, The Central Hospital of Shao Yang, 36 QianYuan lane, Shaoyang, 422000, Hunan, People's Republic of China
| | - Yao-Zong Guan
- Graduate School of Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, Guangxi, People's Republic of China
| | - Peng Liu
- Department of Cardiology, The Central Hospital of Shao Yang, 36 QianYuan lane, Shaoyang, 422000, Hunan, People's Republic of China.
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17
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Dmitrzak-Weglarz M, Szczepankiewicz A, Kapelski, Chaberska J, Kwiatkowska K, Duda J, Dziuda S, Skibinska M, Reszka E, Pawlak J. Transcripts of orphan nuclear receptor (NR4A1) & potassium channel (KCNK17) genes as new potential biomarkers for depression. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022] Open
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18
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Gong L, Lv Y, Li S, Feng T, Zhou Y, Sun Y, Mi D. Changes in transcriptome profiling during the acute/subacute phases of contusional spinal cord injury in rats. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1682. [PMID: 33490194 PMCID: PMC7812200 DOI: 10.21037/atm-20-6519] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background Spinal cord injuries (SCIs), along with subsequent secondary injuries, often result in irreversible damage to both sensory and motor functions. However, a thorough view of the underlying pathological mechanisms of SCIs, especially in a temporal-spatial manner, is still lacking. Methods To obtain a comprehensive, real-time view of multiple subsets of the cellular mechanisms involved in SCIs, we applied RNA-sequencing technology to characterize the temporal changes in gene expression around the lesion site of contusion SCI in rats. First, we identified the differentially expressed genes (DEGs) in contrast to sham controls at 1, 4, and 7 days post SCI. Through bioinformatics analysis, including Pathway analysis, Gene-act-net, and Pathway-act-net, we screened and verified potential key pathways and genes associated with either the acute or subacute stages of SCI pathology. Results The top three overrepresented pathways were associated with cytokine-cytokine receptor interaction, TNF signaling pathway, and cell cycle at day 1; lysosome, cytokine-cytokine receptor interaction, phagosome at day 4; and phagosome, lysosome, cytokine-cytokine receptor interaction at day 7 post injury. Further, we identified uniquely enriched genes at each time point, such as Ccr1 and Nos2 at day 1; as well as Mgst2, and Pla2g3 at 4 and 7 days post-injury. Conclusions Our pathway analysis suggested a transition from inflammatory responses to multiple forms of cell death processes from the acute to subacute stages of SCI. Further, our results revealed a continuous transformation from a more inflammatory to an apoptotic/self-repairing transcriptome following the time-course of SCIs. Our research provides novel insights into the molecular mechanisms of SCI pathophysiology and identifies potential targets for therapeutic intervention after SCI.
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Affiliation(s)
- Leilei Gong
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Yehua Lv
- Department of Orthopedic, Nantong Traditional Chinese Medicine Hospital, Nantong, China
| | - Shenglong Li
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Tao Feng
- Department of Orthopedic, Nantong Traditional Chinese Medicine Hospital, Nantong, China
| | - Yi Zhou
- Department of Orthopedic, Nantong Traditional Chinese Medicine Hospital, Nantong, China
| | - Yuyu Sun
- Department of Orthopedic, Nantong Third People's Hospital, Nantong University, Nantong, China
| | - Daguo Mi
- Department of Orthopedic, Nantong Traditional Chinese Medicine Hospital, Nantong, China
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19
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Wittenberg GM, Greene J, Vértes PE, Drevets WC, Bullmore ET. Major Depressive Disorder Is Associated With Differential Expression of Innate Immune and Neutrophil-Related Gene Networks in Peripheral Blood: A Quantitative Review of Whole-Genome Transcriptional Data From Case-Control Studies. Biol Psychiatry 2020; 88:625-637. [PMID: 32653108 DOI: 10.1016/j.biopsych.2020.05.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/11/2020] [Accepted: 05/03/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Whole-genome transcription has been measured in peripheral blood samples as a candidate biomarker of inflammation associated with major depressive disorder. METHODS We searched for all case-control studies on major depressive disorder that reported microarray or RNA sequencing measurements on whole blood or peripheral blood mononuclear cells. Primary datasets were reanalyzed, when openly accessible, to estimate case-control differences and to evaluate the functional roles of differentially expressed gene lists by technically harmonized methods. RESULTS We found 10 eligible studies (N = 1754 depressed cases and N = 1145 healthy controls). Fifty-two genes were called significant by 2 of the primary studies (published overlap list). After harmonization of analysis across 8 accessible datasets (n = 1706 cases, n = 1098 controls), 272 genes were coincidentally listed in the top 3% most differentially expressed genes in 2 or more studies of whole blood or peripheral blood mononuclear cells with concordant direction of effect (harmonized overlap list). By meta-analysis of standardized mean difference across 4 studies of whole-blood samples (n = 1567 cases, n = 954 controls), 343 genes were found with false discovery rate <5% (standardized mean difference meta-analysis list). These 3 lists intersected significantly. Genes abnormally expressed in major depressive disorder were enriched for innate immune-related functions, coded for nonrandom protein-protein interaction networks, and coexpressed in the normative transcriptome module specialized for innate immune and neutrophil functions. CONCLUSIONS Quantitative review of existing case-control data provided robust evidence for abnormal expression of gene networks important for the regulation and implementation of innate immune response. Further development of white blood cell transcriptional biomarkers for inflamed depression seems warranted.
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Affiliation(s)
- Gayle M Wittenberg
- Neuroscience, Janssen Research & Development, LLC, Titusville, New Jersey
| | - Jon Greene
- Bioinformatics, Rancho BioSciences, LLC, San Diego, California
| | - Petra E Vértes
- Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom; Alan Turing Institute, London, United Kingdom
| | - Wayne C Drevets
- Neuroscience, Janssen Research & Development, LLC, San Diego, California
| | - Edward T Bullmore
- Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom; Cambridgeshire and Peterborough National Health Service Foundation Trust, Cambridge, United Kingdom.
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Le TT, Fu W, Moore JH. Scaling tree-based automated machine learning to biomedical big data with a feature set selector. Bioinformatics 2020; 36:250-256. [PMID: 31165141 PMCID: PMC6956793 DOI: 10.1093/bioinformatics/btz470] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 05/17/2019] [Accepted: 06/02/2019] [Indexed: 12/13/2022] Open
Abstract
Motivation Automated machine learning (AutoML) systems are helpful data science assistants designed to scan data for novel features, select appropriate supervised learning models and optimize their parameters. For this purpose, Tree-based Pipeline Optimization Tool (TPOT) was developed using strongly typed genetic programing (GP) to recommend an optimized analysis pipeline for the data scientist’s prediction problem. However, like other AutoML systems, TPOT may reach computational resource limits when working on big data such as whole-genome expression data. Results We introduce two new features implemented in TPOT that helps increase the system’s scalability: Feature Set Selector (FSS) and Template. FSS provides the option to specify subsets of the features as separate datasets, assuming the signals come from one or more of these specific data subsets. FSS increases TPOT’s efficiency in application on big data by slicing the entire dataset into smaller sets of features and allowing GP to select the best subset in the final pipeline. Template enforces type constraints with strongly typed GP and enables the incorporation of FSS at the beginning of each pipeline. Consequently, FSS and Template help reduce TPOT computation time and may provide more interpretable results. Our simulations show TPOT-FSS significantly outperforms a tuned XGBoost model and standard TPOT implementation. We apply TPOT-FSS to real RNA-Seq data from a study of major depressive disorder. Independent of the previous study that identified significant association with depression severity of two modules, TPOT-FSS corroborates that one of the modules is largely predictive of the clinical diagnosis of each individual. Availability and implementation Detailed simulation and analysis code needed to reproduce the results in this study is available at https://github.com/lelaboratoire/tpot-fss. Implementation of the new TPOT operators is available at https://github.com/EpistasisLab/tpot. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Trang T Le
- Department of Biostatistics, Epidemiology and Informatics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Weixuan Fu
- Department of Biostatistics, Epidemiology and Informatics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jason H Moore
- Department of Biostatistics, Epidemiology and Informatics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
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Qin FL, Xu ZY, Yuan LQ, Chen WJ, Wei JB, Sun Y, Li SK. Novel immune subtypes of lung adenocarcinoma identified through bioinformatic analysis. FEBS Open Bio 2020; 10:1921-1933. [PMID: 32686362 PMCID: PMC7459417 DOI: 10.1002/2211-5463.12934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/23/2020] [Accepted: 07/15/2020] [Indexed: 12/29/2022] Open
Abstract
The magnitude of the immune response is closely associated with clinical outcome in patients with cancer. However, finding potential therapeutic targets for lung cancer in the immune system remains challenging. Here, we constructed a vital immune‐prognosis genes (VIPGs) based cluster of lung adenocarcinoma (LUAD) from IMMPORT databases and The Cancer Genome Atlas. A transcription factor regulatory network for the VIPGs was also established. The tumor microenvironment of LUAD was analyzed using the ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data) algorithm and single‐sample Gene Set Enrichment Analysis. The immune checkpoints and genomic alterations were explored in the different immune clusters. We identified 15 VIPGs for patients with LUAD and clustered the patients into low‐immunity and high‐immunity subtypes. The immune score, stromal score and ESTIMATE score were significantly higher in the high‐immunity subtype, whereas tumor purity was higher in the low‐immunity subtype. In addition, the immune checkpoints cytotoxic T lymphocyte associate protein‐4(CTLA4), programmed cell death protein‐1 and programmed death‐ligand were elevated in the low‐immunity subtype. The genomic results also showed that the tumor mutation burden was higher in the high‐immunity subtype. Finally, Gene Set Enrichment Analysis showed that several immune‐related gene sets, including interleukin‐2/STAT5 signaling, inflammatory response, interleukin‐6/Janus kinase(JAK)/signal transducer and activator of transcription 3 (STAT3) signaling, interferon‐gamma response and allograft rejection, were elevated in the high‐immunity subtype. Finally, high‐immunity patients exhibited greater overall and disease‐specific survival outcome compared with low‐immunity patients (log rank P = 0.013 and P = 0.0097). Altogether, here we have identified 15 immune‐prognosis genes and a potential immune subtype for patients with LUAD, which may provide new insights into the prognosis and treatment of LUAD.
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Affiliation(s)
- Fang-Lu Qin
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhan-Yu Xu
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Li-Qiang Yuan
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Wen-Jie Chen
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jiang-Bo Wei
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yu Sun
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shi-Kang Li
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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22
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Cattaneo A, Ferrari C, Turner L, Mariani N, Enache D, Hastings C, Kose M, Lombardo G, McLaughlin AP, Nettis MA, Nikkheslat N, Sforzini L, Worrell C, Zajkowska Z, Cattane N, Lopizzo N, Mazzelli M, Pointon L, Cowen PJ, Cavanagh J, Harrison NA, de Boer P, Jones D, Drevets WC, Mondelli V, Bullmore ET, Pariante CM. Whole-blood expression of inflammasome- and glucocorticoid-related mRNAs correctly separates treatment-resistant depressed patients from drug-free and responsive patients in the BIODEP study. Transl Psychiatry 2020; 10:232. [PMID: 32699209 PMCID: PMC7376244 DOI: 10.1038/s41398-020-00874-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/13/2022] Open
Abstract
The mRNA expression signatures associated with the 'pro-inflammatory' phenotype of depression, and the differential signatures associated with depression subtypes and the effects of antidepressants, are still unknown. We examined 130 depressed patients (58 treatment-resistant, 36 antidepressant-responsive and 36 currently untreated) and 40 healthy controls from the BIODEP study, and used whole-blood mRNA qPCR to measure the expression of 16 candidate mRNAs, some never measured before: interleukin (IL)-1-beta, IL-6, TNF-alpha, macrophage inhibiting factor (MIF), glucocorticoid receptor (GR), SGK1, FKBP5, the purinergic receptor P2RX7, CCL2, CXCL12, c-reactive protein (CRP), alpha-2-macroglobulin (A2M), acquaporin-4 (AQP4), ISG15, STAT1 and USP-18. All genes but AQP4, ISG15 and USP-18 were differentially regulated. Treatment-resistant and drug-free depressed patients had both increased inflammasome activation (higher P2RX7 and proinflammatory cytokines/chemokines mRNAs expression) and glucocorticoid resistance (lower GR and higher FKBP5 mRNAs expression), while responsive patients had an intermediate phenotype with, additionally, lower CXCL12. Most interestingly, using binomial logistics models we found that a signature of six mRNAs (P2RX7, IL-1-beta, IL-6, TNF-alpha, CXCL12 and GR) distinguished treatment-resistant from responsive patients, even after adjusting for other variables that were different between groups, such as a trait- and state-anxiety, history of childhood maltreatment and serum CRP. Future studies should replicate these findings in larger, longitudinal cohorts, and test whether this mRNA signature can identify patients that are more likely to respond to adjuvant strategies for treatment-resistant depression, including combinations with anti-inflammatory medications.
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Affiliation(s)
- Annamaria Cattaneo
- Biological Psychiatric Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125, Brescia, Italy
| | - Clarissa Ferrari
- Statistical Service, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125, Brescia, Italy
| | - Lorinda Turner
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Nicole Mariani
- Stress, Psychiatry and Immunology Laboratory & Perinatal Psychiatry, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, SE5 9RT, London, UK
| | - Daniela Enache
- Stress, Psychiatry and Immunology Laboratory & Perinatal Psychiatry, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, SE5 9RT, London, UK
| | - Caitlin Hastings
- Stress, Psychiatry and Immunology Laboratory & Perinatal Psychiatry, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, SE5 9RT, London, UK
| | - Melisa Kose
- Stress, Psychiatry and Immunology Laboratory & Perinatal Psychiatry, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, SE5 9RT, London, UK
| | - Giulia Lombardo
- Stress, Psychiatry and Immunology Laboratory & Perinatal Psychiatry, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, SE5 9RT, London, UK
| | - Anna P McLaughlin
- Stress, Psychiatry and Immunology Laboratory & Perinatal Psychiatry, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, SE5 9RT, London, UK
| | - Maria A Nettis
- Stress, Psychiatry and Immunology Laboratory & Perinatal Psychiatry, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, SE5 9RT, London, UK
| | - Naghmeh Nikkheslat
- Stress, Psychiatry and Immunology Laboratory & Perinatal Psychiatry, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, SE5 9RT, London, UK
| | - Luca Sforzini
- Stress, Psychiatry and Immunology Laboratory & Perinatal Psychiatry, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, SE5 9RT, London, UK
| | - Courtney Worrell
- Stress, Psychiatry and Immunology Laboratory & Perinatal Psychiatry, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, SE5 9RT, London, UK
| | - Zuzanna Zajkowska
- Stress, Psychiatry and Immunology Laboratory & Perinatal Psychiatry, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, SE5 9RT, London, UK
| | - Nadia Cattane
- Biological Psychiatric Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125, Brescia, Italy
| | - Nicola Lopizzo
- Biological Psychiatric Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125, Brescia, Italy
| | - Monica Mazzelli
- Biological Psychiatric Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125, Brescia, Italy
| | - Linda Pointon
- Department of Psychiatry, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SZ, UK
| | - Philip J Cowen
- University of Oxford Department of Psychiatry, Warneford Hospital, Oxford, OX3 7JX, UK
| | - Jonathan Cavanagh
- Centre for Immunobiology, University of Glasgow and Sackler Institute of Psychobiological Research, Queen Elizabeth University Hospital, Glasgow, G51 4TF, UK
| | - Neil A Harrison
- School of Medicine, School of Psychology, Cardiff University Brain Research Imaging Centre, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Peter de Boer
- Neuroscience, Janssen Research & Development, Janssen Pharmaceutica NV, 2340, Beerse, Belgium
| | - Declan Jones
- Neuroscience External Innovation, Janssen Pharmaceuticals, J&J Innovation Centre, London, W1G 0BG, UK
| | - Wayne C Drevets
- Janssen Research & Development, Neuroscience Therapeutic Area, 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Valeria Mondelli
- Stress, Psychiatry and Immunology Laboratory & Perinatal Psychiatry, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, SE5 9RT, London, UK
| | - Edward T Bullmore
- Department of Psychiatry, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SZ, UK
| | - Carmine M Pariante
- Stress, Psychiatry and Immunology Laboratory & Perinatal Psychiatry, King's College London, Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, SE5 9RT, London, UK.
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Pawar S, Liew TO, Stanam A, Lahiri C. Common cancer biomarkers of breast and ovarian types identified through artificial intelligence. Chem Biol Drug Des 2020; 96:995-1004. [DOI: 10.1111/cbdd.13672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/16/2020] [Accepted: 02/19/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Shrikant Pawar
- Yale Center for Genome Analysis (YCGA) Yale University New Haven CT USA
| | - Tuck Onn Liew
- Department of Biological Sciences Sunway University Petaling Jaya Malaysia
| | - Aditya Stanam
- College of Public Health The University of Iowa Iowa City IA USA
| | - Chandrajit Lahiri
- Department of Biological Sciences Sunway University Petaling Jaya Malaysia
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24
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Choe HK, Cho J. Comprehensive Genome-Wide Approaches to Activity-Dependent Translational Control in Neurons. Int J Mol Sci 2020; 21:ijms21051592. [PMID: 32111062 PMCID: PMC7084349 DOI: 10.3390/ijms21051592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 02/06/2023] Open
Abstract
Activity-dependent regulation of gene expression is critical in experience-mediated changes in the brain. Although less appreciated than transcriptional control, translational control is a crucial regulatory step of activity-mediated gene expression in physiological and pathological conditions. In the first part of this review, we overview evidence demonstrating the importance of translational controls under the context of synaptic plasticity as well as learning and memory. Then, molecular mechanisms underlying the translational control, including post-translational modifications of translation factors, mTOR signaling pathway, and local translation, are explored. We also summarize how activity-dependent translational regulation is associated with neurodevelopmental and psychiatric disorders, such as autism spectrum disorder and depression. In the second part, we highlight how recent application of high-throughput sequencing techniques has added insight into genome-wide studies on translational regulation of neuronal genes. Sequencing-based strategies to identify molecular signatures of the active neuronal population responding to a specific stimulus are discussed. Overall, this review aims to highlight the implication of translational control for neuronal gene regulation and functions of the brain and to suggest prospects provided by the leading-edge techniques to study yet-unappreciated translational regulation in the nervous system.
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Affiliation(s)
- Han Kyoung Choe
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
- Correspondence: (H.K.C.); (J.C.)
| | - Jun Cho
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
- Correspondence: (H.K.C.); (J.C.)
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25
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Le TT, Urbanowicz RJ, Moore JH, McKinney BA. STatistical Inference Relief (STIR) feature selection. Bioinformatics 2020; 35:1358-1365. [PMID: 30239600 PMCID: PMC6477983 DOI: 10.1093/bioinformatics/bty788] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/13/2018] [Accepted: 09/14/2018] [Indexed: 12/02/2022] Open
Abstract
Motivation Relief is a family of machine learning algorithms that uses nearest-neighbors to select features whose association with an outcome may be due to epistasis or statistical interactions with other features in high-dimensional data. Relief-based estimators are non-parametric in the statistical sense that they do not have a parameterized model with an underlying probability distribution for the estimator, making it difficult to determine the statistical significance of Relief-based attribute estimates. Thus, a statistical inferential formalism is needed to avoid imposing arbitrary thresholds to select the most important features. We reconceptualize the Relief-based feature selection algorithm to create a new family of STatistical Inference Relief (STIR) estimators that retains the ability to identify interactions while incorporating sample variance of the nearest neighbor distances into the attribute importance estimation. This variance permits the calculation of statistical significance of features and adjustment for multiple testing of Relief-based scores. Specifically, we develop a pseudo t-test version of Relief-based algorithms for case-control data. Results We demonstrate the statistical power and control of type I error of the STIR family of feature selection methods on a panel of simulated data that exhibits properties reflected in real gene expression data, including main effects and network interaction effects. We compare the performance of STIR when the adaptive radius method is used as the nearest neighbor constructor with STIR when the fixed-k nearest neighbor constructor is used. We apply STIR to real RNA-Seq data from a study of major depressive disorder and discuss STIR’s straightforward extension to genome-wide association studies. Availability and implementation Code and data available at http://insilico.utulsa.edu/software/STIR. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Trang T Le
- Department of Biostatistics, Epidemiology and Informatics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan J Urbanowicz
- Department of Biostatistics, Epidemiology and Informatics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason H Moore
- Department of Biostatistics, Epidemiology and Informatics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Brett A McKinney
- Department of Mathematics, University of Tulsa, Tulsa, OK, USA.,Tandy School of Computer Science, University of Tulsa, Tulsa, OK, USA
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26
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Andrade A, Brennecke A, Mallat S, Brown J, Gomez-Rivadeneira J, Czepiel N, Londrigan L. Genetic Associations between Voltage-Gated Calcium Channels and Psychiatric Disorders. Int J Mol Sci 2019; 20:E3537. [PMID: 31331039 PMCID: PMC6679227 DOI: 10.3390/ijms20143537] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/12/2019] [Accepted: 07/13/2019] [Indexed: 12/23/2022] Open
Abstract
Psychiatric disorders are mental, behavioral or emotional disorders. These conditions are prevalent, one in four adults suffer from any type of psychiatric disorders world-wide. It has always been observed that psychiatric disorders have a genetic component, however, new methods to sequence full genomes of large cohorts have identified with high precision genetic risk loci for these conditions. Psychiatric disorders include, but are not limited to, bipolar disorder, schizophrenia, autism spectrum disorder, anxiety disorders, major depressive disorder, and attention-deficit and hyperactivity disorder. Several risk loci for psychiatric disorders fall within genes that encode for voltage-gated calcium channels (CaVs). Calcium entering through CaVs is crucial for multiple neuronal processes. In this review, we will summarize recent findings that link CaVs and their auxiliary subunits to psychiatric disorders. First, we will provide a general overview of CaVs structure, classification, function, expression and pharmacology. Next, we will summarize tools to study risk loci associated with psychiatric disorders. We will examine functional studies of risk variations in CaV genes when available. Finally, we will review pharmacological evidence of the use of CaV modulators to treat psychiatric disorders. Our review will be of interest for those studying pathophysiological aspects of CaVs.
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Affiliation(s)
- Arturo Andrade
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA.
| | - Ashton Brennecke
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Shayna Mallat
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Julian Brown
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| | | | - Natalie Czepiel
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Laura Londrigan
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
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Parvandeh S, Poland GA, Kennedy RB, McKinney BA. Multi-Level Model to Predict Antibody Response to Influenza Vaccine Using Gene Expression Interaction Network Feature Selection. Microorganisms 2019; 7:microorganisms7030079. [PMID: 30875727 PMCID: PMC6462975 DOI: 10.3390/microorganisms7030079] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/24/2019] [Accepted: 03/08/2019] [Indexed: 11/18/2022] Open
Abstract
Vaccination is an effective prevention of influenza infection. However, certain individuals develop a lower antibody response after vaccination, which may lead to susceptibility to subsequent infection. An important challenge in human health is to find baseline gene signatures to help identify individuals who are at higher risk for infection despite influenza vaccination. We developed a multi-level machine learning strategy to build a predictive model of vaccine response using pre−vaccination antibody titers and network interactions between pre−vaccination gene expression levels. The first-level baseline−antibody model explains a significant amount of variation in post-vaccination response, especially for subjects with large pre−existing antibody titers. In the second level, we clustered individuals based on pre−vaccination antibody titers to focus gene−based modeling on individuals with lower baseline HAI where additional response variation may be predicted by baseline gene expression levels. In the third level, we used a gene−association interaction network (GAIN) feature selection algorithm to find the best pairs of genes that interact to influence antibody response within each baseline titer cluster. We used ratios of the top interacting genes as predictors to stabilize machine learning model generalizability. We trained and tested the multi-level approach on data with young and older individuals immunized against influenza vaccine in multiple cohorts. Our results indicate that the GAIN feature selection approach improves model generalizability and identifies genes enriched for immunologically relevant pathways, including B Cell Receptor signaling and antigen processing. Using a multi-level approach, starting with a baseline HAI model and stratifying on baseline HAI, allows for more targeted gene−based modeling. We provide an interactive tool that may be extended to other vaccine studies.
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Affiliation(s)
- Saeid Parvandeh
- Tandy School of Computer Science, University of Tulsa, Tulsa, OK 74104, USA.
| | - Greg A Poland
- Mayo Vaccine Group, Mayo Clinic, Rochester, MN 55905, USA.
| | | | - Brett A McKinney
- Tandy School of Computer Science, University of Tulsa, Tulsa, OK 74104, USA.
- Department of Mathematics, University of Tulsa, Tulsa, OK 74104, USA.
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Pezeshki A, Ovsyannikova IG, McKinney BA, Poland GA, Kennedy RB. The role of systems biology approaches in determining molecular signatures for the development of more effective vaccines. Expert Rev Vaccines 2019; 18:253-267. [PMID: 30700167 DOI: 10.1080/14760584.2019.1575208] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Emerging infectious diseases are a major threat to public health, and while vaccines have proven to be one of the most effective preventive measures for infectious diseases, we still do not have safe and effective vaccines against many human pathogens, and emerging diseases continually pose new threats. The purpose of this review is to discuss how the creation of vaccines for these new threats has been hindered by limitations in the current approach to vaccine development. Recent advances in high-throughput technologies have enabled scientists to apply systems biology approaches to collect and integrate increasingly large datasets that capture comprehensive biological changes induced by vaccines, and then decipher the complex immune response to those vaccines. AREAS COVERED This review covers advances in these technologies and recent publications that describe systems biology approaches to understanding vaccine immune responses and to understanding the rational design of new vaccine candidates. EXPERT OPINION Systems biology approaches to vaccine development provide novel information regarding both the immune response and the underlying mechanisms and can inform vaccine development.
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Affiliation(s)
| | | | - Brett A McKinney
- b Department of Mathematics , University of Tulsa , Tulsa , OK , USA.,c Tandy School of Computer Science , University of Tulsa , Tulsa , OK , USA
| | - Gregory A Poland
- a Mayo Vaccine Research Group , Mayo Clinic , Rochester , MN , USA
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REM sleep's unique associations with corticosterone regulation, apoptotic pathways, and behavior in chronic stress in mice. Proc Natl Acad Sci U S A 2019; 116:2733-2742. [PMID: 30683720 PMCID: PMC6377491 DOI: 10.1073/pnas.1816456116] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Sleep disturbances are common in stress-related disorders but the nature of these sleep disturbances and how they relate to changes in the stress hormone corticosterone and changes in gene expression remained unknown. Here we demonstrate that in response to chronic mild stress, rapid–eye-movement sleep (REMS), a sleep state involved in emotion regulation and fear conditioning, changed first and more so than any other measured sleep characteristic. Transcriptomic profiles related to REMS continuity and theta oscillations overlapped with those for corticosterone, as well as with predictors for anhedonia, and were enriched for apoptotic pathways. These data highlight the central role of REMS in response to stress and warrant further investigation into REMS’s involvement in stress-related mental health disorders. One of sleep’s putative functions is mediation of adaptation to waking experiences. Chronic stress is a common waking experience; however, which specific aspect of sleep is most responsive, and how sleep changes relate to behavioral disturbances and molecular correlates remain unknown. We quantified sleep, physical, endocrine, and behavioral variables, as well as the brain and blood transcriptome in mice exposed to 9 weeks of unpredictable chronic mild stress (UCMS). Comparing 46 phenotypic variables revealed that rapid–eye-movement sleep (REMS), corticosterone regulation, and coat state were most responsive to UCMS. REMS theta oscillations were enhanced, whereas delta oscillations in non-REMS were unaffected. Transcripts affected by UCMS in the prefrontal cortex, hippocampus, hypothalamus, and blood were associated with inflammatory and immune responses. A machine-learning approach controlling for unspecific UCMS effects identified transcriptomic predictor sets for REMS parameters that were enriched in 193 pathways, including some involved in stem cells, immune response, and apoptosis and survival. Only three pathways were enriched in predictor sets for non-REMS. Transcriptomic predictor sets for variation in REMS continuity and theta activity shared many pathways with corticosterone regulation, in particular pathways implicated in apoptosis and survival, including mitochondrial apoptotic machinery. Predictor sets for REMS and anhedonia shared pathways involved in oxidative stress, cell proliferation, and apoptosis. These data identify REMS as a core and early element of the response to chronic stress, and identify apoptosis and survival pathways as a putative mechanism by which REMS may mediate the response to stressful waking experiences.
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Li Y, Chen Y, Li X, Wu J, Pan JY, Cai RX, Yang RY, Wang XD. RNA sequencing screening of differentially expressed genes after spinal cord injury. Neural Regen Res 2019; 14:1583-1593. [PMID: 31089057 PMCID: PMC6557110 DOI: 10.4103/1673-5374.255994] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In the search for a therapeutic schedule for spinal cord injury, it is necessary to understand key genes and their corresponding regulatory networks involved in the spinal cord injury process. However, ad hoc selection and analysis of one or two genes cannot fully reveal the complex molecular biological mechanisms of spinal cord injury. The emergence of second-generation sequencing technology (RNA sequencing) has provided a better method. In this study, RNA sequencing technology was used to analyze differentially expressed genes at different time points after spinal cord injury in rat models established by contusion of the eighth thoracic segment. The numbers of genes that changed significantly were 944, 1362 and 1421 at 1, 4 and 7 days after spinal cord injury respectively. After gene ontology analysis and temporal expression analysis of the differentially expressed genes, C5ar1, Socs3 and CCL6 genes were then selected and identified by real-time polymerase chain reaction and western blot assay. The mRNA expression trends of C5ar1, Socs3 and CCL6 genes were consistent with the RNA sequencing results. Further verification and analysis of C5ar1 indicate that the level of protein expression of C5ar1 was consistent with its nucleic acid level after spinal cord injury. C5ar1 was mainly expressed in neurons and astrocytes. Finally, the gene Itgb2, which may be related to C5ar1, was found by Chilibot database and literature search. Immunofluorescence histochemical results showed that the expression of Itgb2 was highly consistent with that of C5ar1. Itgb2 was expressed in astrocytes. RNA sequencing technology can screen differentially expressed genes at different time points after spinal cord injury. Through analysis and verification, genes strongly associated with spinal cord injury can be screened. This can provide experimental data for further determining the molecular mechanism of spinal cord injury, and also provide possible targets for the treatment of spinal cord injury. This study was approved ethically by the Laboratory Animal Ethics Committee of Jiangsu Province, China (approval No. 2018-0306-001) on March 6, 2018.
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Affiliation(s)
- Yi Li
- School of Biology & Basic Medical Sciences, Soochow University, Suzhou; Department of Histology and Embryology, Medical College, Nantong University, Nantong, Jiangsu Province, China
| | - Ying Chen
- Department of Histology and Embryology, Medical College, Nantong University, Nantong, Jiangsu Province, China
| | - Xiang Li
- Department of Histology and Embryology, Medical College, Nantong University, Nantong, Jiangsu Province, China
| | - Jian Wu
- Department of Histology and Embryology, Medical College, Nantong University, Nantong, Jiangsu Province, China
| | - Jing-Ying Pan
- Department of Histology and Embryology, Medical College, Nantong University, Nantong, Jiangsu Province, China
| | - Ri-Xin Cai
- Department of Histology and Embryology, Medical College, Nantong University, Nantong, Jiangsu Province, China
| | - Ri-Yun Yang
- Department of Histology and Embryology, Medical College, Nantong University, Nantong, Jiangsu Province, China
| | - Xiao-Dong Wang
- Department of Histology and Embryology, Medical College, Nantong University; Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
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