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Li H, Wu H, Li W, Zhou J, Yang J, Peng W. Constructing a Multiple Sclerosis Diagnosis Model Based on Microarray. Front Neurol 2022; 12:721788. [PMID: 35126277 PMCID: PMC8812326 DOI: 10.3389/fneur.2021.721788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 12/27/2021] [Indexed: 11/25/2022] Open
Abstract
Introduction Multiple sclerosis is an immune-mediated demyelinating disorder of the central nervous system. Because of the complexity of etiology, pathology, clinical manifestations, and the diversity of classification, the diagnosis of MS is very difficult. We found that McDonald Criteria is very strict and relies heavily on the evidence for DIS and DIT. Therefore, we hope to find a new method to supplement the evidence and improve the accuracy of MS diagnosis. Results We finally selected GSE61240, GSE18781, and GSE185047 based on the GPL570 platform to build a diagnosis model. We initially selected 54 MS susceptibility locus genes identified by IMSGC and WTCCC2 as predictors for the model. After Random Forests and other series of screening, the logistic regression model was established with 4 genes as the final predictors. In external validation, the model showed high accuracy with an AUC of 0.96 and an accuracy of 86.30%. Finally, we established a nomogram and an online prediction tool to better display the diagnosis model. Conclusion The diagnosis model based on microarray data in this study has a high degree of discrimination and calibration in the validation set, which is helpful for diagnosis in the absence of evidence for DIS and DIT. Only one SLE case was misdiagnosed as MS, indicating that the model has a high specificity (93.93%), which is useful for differential diagnosis. The significance of the study lies in proving that it is feasible to identify MS by peripheral blood RNA, and the further application of the model and be used as a supplement to McDonald Criteria still need to be trained with larger sample size.
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Affiliation(s)
- Haoran Li
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Hongyun Wu
- Department of Neurology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Weiying Li
- Department of Comprehensive Surgery, Weifang Maternal and Child Health Hospital, Weifang, China
| | - Jiapei Zhou
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jie Yang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Wei Peng
- Department of Neurology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
- *Correspondence: Wei Peng ; orcid.org/0000-0003-1384-9014
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2
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Rosenfeld CS, Hekman JP, Johnson JL, Lyu Z, Ortega MT, Joshi T, Mao J, Vladimirova AV, Gulevich RG, Kharlamova AV, Acland GM, Hecht EE, Wang X, Clark AG, Trut LN, Behura SK, Kukekova AV. Hypothalamic transcriptome of tame and aggressive silver foxes (Vulpes vulpes) identifies gene expression differences shared across brain regions. GENES BRAIN AND BEHAVIOR 2019; 19:e12614. [PMID: 31605445 DOI: 10.1111/gbb.12614] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 12/15/2022]
Abstract
The underlying neurological events accompanying dog domestication remain elusive. To reconstruct the domestication process in an experimental setting, silver foxes (Vulpes vulpes) have been deliberately bred for tame vs aggressive behaviors for more than 50 generations at the Institute for Cytology and Genetics in Novosibirsk, Russia. The hypothalamus is an essential part of the hypothalamic-pituitary-adrenal axis and regulates the fight-or-flight response, and thus, we hypothesized that selective breeding for tameness/aggressiveness has shaped the hypothalamic transcriptomic profile. RNA-seq analysis identified 70 differentially expressed genes (DEGs). Seven of these genes, DKKL1, FBLN7, NPL, PRIMPOL, PTGRN, SHCBP1L and SKIV2L, showed the same direction expression differences in the hypothalamus, basal forebrain and prefrontal cortex. The genes differentially expressed across the three tissues are involved in cell division, differentiation, adhesion and carbohydrate processing, suggesting an association of these processes with selective breeding. Additionally, 159 transcripts from the hypothalamus demonstrated differences in the abundance of alternative spliced forms between the tame and aggressive foxes. Weighted gene coexpression network analyses also suggested that gene modules in hypothalamus were significantly associated with tame vs aggressive behavior. Pathways associated with these modules include signal transduction, interleukin signaling, cytokine-cytokine receptor interaction and peptide ligand-binding receptors (eg, G-protein coupled receptor [GPCR] ligand binding). Current studies show the selection for tameness vs aggressiveness in foxes is associated with unique hypothalamic gene profiles partly shared with other brain regions and highlight DEGs involved in biological processes such as development, differentiation and immunological responses. The role of these processes in fox and dog domestication remains to be determined.
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Affiliation(s)
- Cheryl S Rosenfeld
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri.,Biomedical Sciences, University of Missouri, Columbia, Missouri.,Thompson Center for Autism and Neurobehavioral Disorders, University of Missouri, Columbia, Missouri.,MU Informatics Institute, University of Missouri, Columbia, Missouri
| | - Jessica P Hekman
- Department of Animal Sciences, College of Agricultural, Consumer, and Environmental Sciences, University of Illinois, Urbana, Illinois.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jennifer L Johnson
- Department of Animal Sciences, College of Agricultural, Consumer, and Environmental Sciences, University of Illinois, Urbana, Illinois
| | - Zhen Lyu
- Department of Computer Science, University of Missouri, Columbia, Missouri
| | - Madison T Ortega
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri.,Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Trupti Joshi
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri.,MU Informatics Institute, University of Missouri, Columbia, Missouri.,Department of Computer Science, University of Missouri, Columbia, Missouri.,Department of Health Management and Informatics, University of Missouri, Columbia, Missouri
| | - Jiude Mao
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri.,Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Anastasiya V Vladimirova
- The Laboratory of Evolutionary Genetics, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Rimma G Gulevich
- The Laboratory of Evolutionary Genetics, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasiya V Kharlamova
- The Laboratory of Evolutionary Genetics, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Gregory M Acland
- Baker Institute for Animal Health, Cornell University, College of Veterinary Medicine, Ithaca, New York
| | - Erin E Hecht
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Xu Wang
- Department of Pathobiology, Auburn University, College of Veterinary Medicine, Auburn, Alabama
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Lyudmila N Trut
- The Laboratory of Evolutionary Genetics, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Susanta K Behura
- MU Informatics Institute, University of Missouri, Columbia, Missouri.,Division of Animal Sciences, University of Missouri, Columbia, Missouri
| | - Anna V Kukekova
- Department of Animal Sciences, College of Agricultural, Consumer, and Environmental Sciences, University of Illinois, Urbana, Illinois
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3
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Genomic responses to selection for tame/aggressive behaviors in the silver fox ( Vulpes vulpes). Proc Natl Acad Sci U S A 2018; 115:10398-10403. [PMID: 30228118 DOI: 10.1073/pnas.1800889115] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Animal domestication efforts have led to a shared spectrum of striking behavioral and morphological changes. To recapitulate this process, silver foxes have been selectively bred for tame and aggressive behaviors for more than 50 generations at the Institute for Cytology and Genetics in Novosibirsk, Russia. To understand the genetic basis and molecular mechanisms underlying the phenotypic changes, we profiled gene expression levels and coding SNP allele frequencies in two brain tissue specimens from 12 aggressive foxes and 12 tame foxes. Expression analysis revealed 146 genes in the prefrontal cortex and 33 genes in the basal forebrain that were differentially expressed, with a 5% false discovery rate (FDR). These candidates include genes in key pathways known to be critical to neurologic processing, including the serotonin and glutamate receptor pathways. In addition, 295 of the 31,000 exonic SNPs show significant allele frequency differences between the tame and aggressive populations (1% FDR), including genes with a role in neural crest cell fate determination.
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Bagot RC, Cates HM, Purushothaman I, Lorsch ZS, Walker DM, Wang J, Huang X, Schlüter OM, Maze I, Peña CJ, Heller EA, Issler O, Wang M, Song WM, Stein JL, Liu X, Doyle MA, Scobie KN, Sun HS, Neve RL, Geschwind D, Dong Y, Shen L, Zhang B, Nestler EJ. Circuit-wide Transcriptional Profiling Reveals Brain Region-Specific Gene Networks Regulating Depression Susceptibility. Neuron 2016; 90:969-83. [PMID: 27181059 DOI: 10.1016/j.neuron.2016.04.015] [Citation(s) in RCA: 243] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 03/16/2016] [Accepted: 04/11/2016] [Indexed: 12/30/2022]
Abstract
Depression is a complex, heterogeneous disorder and a leading contributor to the global burden of disease. Most previous research has focused on individual brain regions and genes contributing to depression. However, emerging evidence in humans and animal models suggests that dysregulated circuit function and gene expression across multiple brain regions drive depressive phenotypes. Here, we performed RNA sequencing on four brain regions from control animals and those susceptible or resilient to chronic social defeat stress at multiple time points. We employed an integrative network biology approach to identify transcriptional networks and key driver genes that regulate susceptibility to depressive-like symptoms. Further, we validated in vivo several key drivers and their associated transcriptional networks that regulate depression susceptibility and confirmed their functional significance at the levels of gene transcription, synaptic regulation, and behavior. Our study reveals novel transcriptional networks that control stress susceptibility and offers fundamentally new leads for antidepressant drug discovery.
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Affiliation(s)
- Rosemary C Bagot
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hannah M Cates
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Immanuel Purushothaman
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zachary S Lorsch
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Deena M Walker
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Junshi Wang
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Xiaojie Huang
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Oliver M Schlüter
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ian Maze
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Catherine J Peña
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elizabeth A Heller
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Orna Issler
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jason L Stein
- Department of Genetics and Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xiaochuan Liu
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marie A Doyle
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kimberly N Scobie
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hao Sheng Sun
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rachael L Neve
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yan Dong
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Li Shen
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Eric J Nestler
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Alfonso RJ, Gorroño-Etxebarria I, Rabano M, Vivanco MDM, Kypta R. Dickkopf-3 alters the morphological response to retinoic acid during neuronal differentiation of human embryonal carcinoma cells. Dev Neurobiol 2014; 74:1243-54. [DOI: 10.1002/dneu.22201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 06/03/2014] [Indexed: 11/05/2022]
Affiliation(s)
| | | | - Miriam Rabano
- Cell Biology and Stem Cells Unit; CIC bioGUNE; Spain
| | | | - Robert Kypta
- Cell Biology and Stem Cells Unit; CIC bioGUNE; Spain
- Department of Surgery and Cancer; Imperial College London; United Kingdom
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