Detection of multiple sclerosis using blood and brain cells transcript profiles: Insights from comprehensive bioinformatics approach

Multiple sclerosis (MS) is a severely disabling disease affecting the brain and spinal cord. The detection of MS at an early stage is difficult. However, detection of MS from blood cell gene expression may ameliorate the early identification of MS. The present study addressed overlapped genes betwee...

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Published inInformatics in medicine unlocked Vol. 16; p. 100201
Main Authors Islam, Tania, Rahman, Md. Rezanur, Karim, Md. Rezaul, Huq, Fazlul, Quinn, Julian M.W., Moni, Mohammad Ali
Format Journal Article
LanguageEnglish
Published Elsevier Ltd 2019
Elsevier
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Online AccessGet full text
ISSN2352-9148
2352-9148
DOI10.1016/j.imu.2019.100201

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Abstract Multiple sclerosis (MS) is a severely disabling disease affecting the brain and spinal cord. The detection of MS at an early stage is difficult. However, detection of MS from blood cell gene expression may ameliorate the early identification of MS. The present study addressed overlapped genes between blood cell and brain tissues of MS patients. We analyzed microarray gene expression brain tissue datasets and eQTL data to identify overlapped genes in the blood and brain of MS patients. We identified 23 overlapped differentially expressed genes (DEGs) (PWP2, UPK3BL, NFATC3, NPIPA5, KNOP1, PIK3C2B, LDLRAP1, HN1L, FAM226B, STAG3L2, ZNF814, BMS1P5, SDCCAG8, CLN8, ARHGEF7, NEAT1, ANKRD42, C5orf34, DOK6, PKN2, SP1, DBF4B, VAMP3) in the blood cells and brain tissues of MS patients. The axon guidance mediated and postsynaptic differentiation associated pathways were enriched by the DEGs. The significant regulatory transcription factors (TFs) including SP1, ARNT, MEF2A, YY1, EGR1, MIF, FOS, NFYA, TFAP2A, MYC, USF, MXI1, JUN, MAX, E2F1, POU3F2, GABPA, TFAP2C, CUX1, 2623, SPI1 and microRNAs (miRNAs) including miR-650, miR-223, miR-9, miR-181b, miR-190, miR-561, miR-520c-3p, miR-658, miR-199b-5p, miR-660, miR-20 were identified in MS. The candidate drugs were determined from drug target overrepresentation analysis. This study provides biomarkers at protein levels (hub proteins and TFs) and RNA levels (mRNAs, miRNAs) in MS subjects that were similarly dysregulated in both blood and brain tissues.
AbstractList Multiple sclerosis (MS) is a severely disabling disease affecting the brain and spinal cord. The detection of MS at an early stage is difficult. However, detection of MS from blood cell gene expression may ameliorate the early identification of MS. The present study addressed overlapped genes between blood cell and brain tissues of MS patients. We analyzed microarray gene expression brain tissue datasets and eQTL data to identify overlapped genes in the blood and brain of MS patients. We identified 23 overlapped differentially expressed genes (DEGs) (PWP2, UPK3BL, NFATC3, NPIPA5, KNOP1, PIK3C2B, LDLRAP1, HN1L, FAM226B, STAG3L2, ZNF814, BMS1P5, SDCCAG8, CLN8, ARHGEF7, NEAT1, ANKRD42, C5orf34, DOK6, PKN2, SP1, DBF4B, VAMP3) in the blood cells and brain tissues of MS patients. The axon guidance mediated and postsynaptic differentiation associated pathways were enriched by the DEGs. The significant regulatory transcription factors (TFs) including SP1, ARNT, MEF2A, YY1, EGR1, MIF, FOS, NFYA, TFAP2A, MYC, USF, MXI1, JUN, MAX, E2F1, POU3F2, GABPA, TFAP2C, CUX1, 2623, SPI1 and microRNAs (miRNAs) including miR-650, miR-223, miR-9, miR-181b, miR-190, miR-561, miR-520c-3p, miR-658, miR-199b-5p, miR-660, miR-20 were identified in MS. The candidate drugs were determined from drug target overrepresentation analysis. This study provides biomarkers at protein levels (hub proteins and TFs) and RNA levels (mRNAs, miRNAs) in MS subjects that were similarly dysregulated in both blood and brain tissues. Keywords: Multiple sclerosis, Molecular biomarkers, Blood-brain common gene, Differentially expressed genes, Protein-protein interaction, cis-eQTL, Transcription factors, microRNAs
Multiple sclerosis (MS) is a severely disabling disease affecting the brain and spinal cord. The detection of MS at an early stage is difficult. However, detection of MS from blood cell gene expression may ameliorate the early identification of MS. The present study addressed overlapped genes between blood cell and brain tissues of MS patients. We analyzed microarray gene expression brain tissue datasets and eQTL data to identify overlapped genes in the blood and brain of MS patients. We identified 23 overlapped differentially expressed genes (DEGs) (PWP2, UPK3BL, NFATC3, NPIPA5, KNOP1, PIK3C2B, LDLRAP1, HN1L, FAM226B, STAG3L2, ZNF814, BMS1P5, SDCCAG8, CLN8, ARHGEF7, NEAT1, ANKRD42, C5orf34, DOK6, PKN2, SP1, DBF4B, VAMP3) in the blood cells and brain tissues of MS patients. The axon guidance mediated and postsynaptic differentiation associated pathways were enriched by the DEGs. The significant regulatory transcription factors (TFs) including SP1, ARNT, MEF2A, YY1, EGR1, MIF, FOS, NFYA, TFAP2A, MYC, USF, MXI1, JUN, MAX, E2F1, POU3F2, GABPA, TFAP2C, CUX1, 2623, SPI1 and microRNAs (miRNAs) including miR-650, miR-223, miR-9, miR-181b, miR-190, miR-561, miR-520c-3p, miR-658, miR-199b-5p, miR-660, miR-20 were identified in MS. The candidate drugs were determined from drug target overrepresentation analysis. This study provides biomarkers at protein levels (hub proteins and TFs) and RNA levels (mRNAs, miRNAs) in MS subjects that were similarly dysregulated in both blood and brain tissues.
ArticleNumber 100201
Author Quinn, Julian M.W.
Rahman, Md. Rezanur
Karim, Md. Rezaul
Huq, Fazlul
Moni, Mohammad Ali
Islam, Tania
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Keywords microRNAs
Multiple sclerosis
Differentially expressed genes
Transcription factors
Protein-protein interaction
Blood-brain common gene
Molecular biomarkers
cis-eQTL
Language English
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Snippet Multiple sclerosis (MS) is a severely disabling disease affecting the brain and spinal cord. The detection of MS at an early stage is difficult. However,...
SourceID doaj
crossref
elsevier
SourceType Open Website
Enrichment Source
Index Database
Publisher
StartPage 100201
SubjectTerms Blood-brain common gene
cis-eQTL
Differentially expressed genes
microRNAs
Molecular biomarkers
Multiple sclerosis
Protein-protein interaction
Transcription factors
Title Detection of multiple sclerosis using blood and brain cells transcript profiles: Insights from comprehensive bioinformatics approach
URI https://dx.doi.org/10.1016/j.imu.2019.100201
https://doaj.org/article/f8d841aa1bb046ab98e099c87078cb83
Volume 16
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