Integrative RNA profiling of TBEV-infected neurons and astrocytes reveals potential pathogenic effectors.
A3SS, alternative 3′ splice site
A5SS, alternative 5′ splice site
ACACA, Acetyl-CoA Carboxylase Alpha
AKR1C2, Aldo-Keto Reductase Family 1 Member C2
ANKS1A, Ankyrin Repeat And Sterile Alpha Motif Domain Containing 1A
ANOS1, Anosmin 1
AOX1, Aldehyde Oxidase 1
APOBEC3G, Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 3G
APOL1/6, Apolipoprotein L1/6
ARID2, AT-Rich Interaction Domain 2
AUTS2, Activator Of Transcription And Developmental Regulator AUTS2
Alternative splicing
Astrocytes
BCL11B, BAF Chromatin Remodeling Complex Subunit BCL11B
BCL9L, BCL9 Transcription Coactivator-like
BDKRB2, Bradykinin Receptor B2
BDNF, Brain Derived Neurotrophic Factor
BEND3, BEN Domain Containing 3
BSA, bovine serum albumin
BST2, Bone Marrow Stromal Cell Antigen 2
CALB1, Calbindin 1
CAMK2A, Calcium/Calmodulin Dependent Protein Kinase II Alpha
CD, complement determinant
CDKN1C, Cyclin Dependent Kinase Inhibitor 1C
CFAP61, Cilia And Flagella Associated Protein 61
CHRNA3, Cholinergic Receptor Nicotinic Alpha 3 Subunit
CHRNB4, Cholinergic Receptor Nicotinic Beta 4 Subunit
CLIC5, Chloride Intracellular Channel 5
CMPK2, Cytidine/Uridine Monophosphate Kinase 2
CNS, central nervous system
CNTN2, Contactin 2
CREG2, Cellular Repressor Of E1A Stimulated Genes 2
CXADR, Coxsackievirus B-Adenovirus Receptor
CYYR1, Cysteine And Tyrosine Rich 1
DACH1, Dachshund Family Transcription Factor 1
DAPI, diamidino-2-phenylindole
DCC, Netrin 1 Receptor
DCX, Doublecortin
DDX60, DExD/H-Box Helicase 60
DDX60L, DExD/H-Box 60 Like
DE, differentially expressed
DENV, Dengue virus
DIRAS2, DIRAS Family GTPase 2
DLX1/5/6, Distal-Less Homeobox 1/5/6
DNMT3B, DNA Methyltransferase 3 Beta
DPYSL2, Dihydropyrimidinase Like 2
EBF1, EBF Transcription Factor 1
EGF, Epidermal Growth Factor
ELAVL2/4, ELAV Like RNA Binding Protein 2/4
EPHB1, EPH Receptor B1
EPSTI1, Epithelial Stromal Interaction 1
ERBB4, Erb-B2 Receptor Tyrosine Kinase 4
ES, exon skipping
ESRRG, Estrogen Related Receptor Gamma
FGFb, Fibroblast Growth Factor 2
FPKM, Fragments Per Kilobase of transcript per Million mapped reads
FUT9, Fucosyltransferase 9
G2E3, G2/M−Phase Specific E3 Ubiquitin Protein Ligase
GABRG2, Gamma-Aminobutyric Acid Type A Receptor Subunit Gamma 2
GAPDH, Glyceraldehyde-3-Phosphate Dehydrogenase
GAS2L3, Growth Arrest Specific 2 Like 3
GAS7, Growth Arrest Specific 7
GATAD2B, GATA Zinc Finger Domain Containing 2B
GFAP, Glial Fibrillary Acidic Protein
GIPC2, GIPC PDZ Domain Containing Family Member 2
GLRA2, Glycine Receptor Alpha 2
GNG2, G Protein Subunit Gamma 2
GO, gene ontology
GOLGA4, Golgin A4
GRIN2A, Glutamate Ionotropic Receptor NMDA Type Subunit 2A
GSEA, gene set enrichment analysis
HERC5/6, HECT And RLD Domain Containing E3 Ubiquitin Protein Ligase 5/6
HEYL, Hes Related Family BHLH Transcription Factor With YRPW Motif Like
HPRT1, Hypoxanthine Phosphoribosyltransferase 1
HS, hot-spot
HSPA6, Heat Shock Protein Family A (Hsp70) Member 6
HUDD (ELAV4), Hu-Antigen D/ELAV Like Neuron-Specific RNA Binding Protein 4
IFI6, Interferon Alpha Inducible Protein 6
IFIH1 (MDA5), Interferon Induced With Helicase C Domain 1/Melanoma Differentiation-Associated Protein 5
IFIT1-3, Interferon Induced Protein With Tetratricopeptide Repeats 1–3
IFITM1/2, Interferon Induced Transmembrane Protein 1/2
IFN, interferon
IGB, Integrated Genome Browser
IL6, Interleukin 6
IR, intron retention
ISG20, Interferon Stimulated Exonuclease Gene 20
ISGF3, Interferon-Stimulated Gene Factor 3 Gamma
ISGs, interferon-stimulated genes
JEV, Japanese encephalitis virus
KCND2, Potassium Voltage-Gated Channel Subfamily D Member 2
KCNK10, Potassium Two Pore Domain Channel Subfamily K Member 10
KCNS2, Potassium Voltage-Gated Channel Modifier Subfamily S Member 2
KIT, KIT Proto-Oncogene, Receptor Tyrosine Kinase
KLHDC8A, Kelch Domain Containing 8A
KLHL13, Kelch Like Family Member 13
KRR1, KRR1 Small Subunit Processome Component Homolog
LCOR, Ligand Dependent Nuclear Receptor Corepressor
LEKR1, Leucine, Glutamate And Lysine Rich 1
LGI1, Leucine Rich Glioma Inactivated 1
LRRTM3, Leucine Rich Repeat Transmembrane Neuronal 3
LSV, local splicing variation
LUZP2, Leucine Zipper Protein 2
MAN1A1, Mannosidase Alpha Class 1A Member 1
MAP2, Microtubule Associated Protein 2
MBNL2, Muscleblind Like Splicing Regulator 2
MCTP1, Multiple C2 And Transmembrane Domain Containing 1
MMP13, Matrix Metallopeptidase 13
MN1, MN1 Proto-Oncogene, Transcriptional Regulator
MOI, multiplicity of infection
MTUS2, Microtubule Associated Scaffold Protein 2
MX2, MX Dynamin Like GTPase 2
MYCN, MYCN Proto-Oncogene, BHLH Transcription Factor
NAV1, Neuron Navigator 1
NCAM1, Neural Cell Adhesion Molecule 1
NDRG4, N-Myc Downstream-Regulated Gene 4 Protein
NEK7, NIMA Related Kinase 7
NFASC, Neurofascin
NKAIN1, Sodium/Potassium Transporting ATPase Interacting 1
NMI, N-Myc And STAT Interactor 2
NRAP, Nebulin Related Anchoring Protein
NRARP, NOTCH Regulated Ankyrin Repeat Protein
NREP, Neuronal Regeneration Related Protein
NRN1, Neuritin 1
NS3, flaviviral non-structural protein 3
NXPH2, Neurexophilin 2
NYNRIN, NYN Domain And Retroviral Integrase Containing
Neurons
Neuropathogenesis
OAS, 2′-5′-Oligoadenylate Synthetase
OASL, 2′-5′-Oligoadenylate Synthetase Like
ONECUT2, ONECUT-2 Homeodomain Transcription Factor
OPCML, Opioid Binding Protein/Cell Adhesion Molecule Like
OTX2, Orthodenticle Homeobox 2
PBS, phosphate buffer saline
PBX1, Pre-B-Cell Leukemia Transcription Factor 1
PCDH18/20, Protocadherin 18/20
PFKFB3, 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 3
PIK3C2B, Phosphatidylinositol-4-Phosphate 3-Kinase Catalytic Subunit Type 2 Beta
PIP4P2, Phosphatidylinositol-4,5-Bisphosphate 4-Phosphatase 2
PLCH1, Phospholipase C Eta 1
POU3F4, Brain-Specific Homeobox/POU Domain Protein 4
PPM1L, Protein Phosphatase, Mg2+/Mn2+ Dependent 1L
PPP1R17, Protein Phosphatase 1 Regulatory Subunit 17
PRDM12, PR Domain Zinc Finger Protein 12
PSI, percent selective index
PSRC1, Proline And Serine Rich Coiled-Coil 1
PTPN5, Protein Tyrosine Phosphatase Non-Receptor Type 5
PTPRH, Protein Tyrosine Phosphatase Receptor Type H
RAPGEF5, Rap Guanine Nucleotide Exchange Factor 5
RBFOX1, RNA Binding Fox-1 Homolog 1
RIG-I (DDX58), Retinoic Acid-Inducible Gene 1 Protein
RNF212, Ring Finger Protein 212
RNVU1, RNA, Variant U1 Small Nuclear
RSAD2, Radical S-Adenosyl Methionine Domain Containing 2
RTL8B, Retrotransposon Gag Like 8B
Response to infection
SAMD9, Sterile Alpha Motif Domain Containing 9
SEMA3E, Semaphorin 3E
SH3TC2, SH3 Domain And Tetratricopeptide Repeats 2
SHF, Src Homology 2 Domain Containing F
SHISAL1, Shisa Like 1
SIAH3, Siah E3 Ubiquitin Protein Ligase Family Member 3
SIRPA, Signal Regulatory Protein Alpha
SLITRK5, SLIT And NTRK Like Family Member 5
SNP, single-nucleotide polymorphism
SOGA1, Suppressor Of Glucose, Autophagy Associated 1
SPSB4, SplA/Ryanodine Receptor Domain And SOCS Box Containing 4
ST6GAL1, ST6 Beta-Galactoside Alpha-2,6-Sialyltransferase 1
TBC1D30, TBC1 Domain Family Member 30
TBEV, Tick-borne encephalitis virus
TFAP2A, Transcription Factor AP-2 Alpha
TFAP2B, Transcription Factor AP-2 Beta
THSD7A, Thrombospondin Type 1 Domain Containing 7A
THUMPD2, THUMP Domain-Containing Protein 2/SAM-Dependent Methyltransferase
TIPARP, TCDD Inducible Poly(ADP-Ribose) Polymerase
TM4SF18, Transmembrane 4 L Six Family Member 18
TMC8, Transmembrane Channel Like 6
TMEM229B, Transmembrane Protein 229B
TMTC1, Transmembrane O-Mannosyltransferase Targeting Cadherins 1
TNFSF10, TNF Superfamily Member 10
TRHDE, Thyrotropin Releasing Hormone Degrading Enzyme
TRIM38, Tripartite Motif Containing 38
TSHZ1, Teashirt Zinc Finger Homeobox 1
Tick-borne encephalitis virus
Transcriptomics
USP18, Ubiquitin Specific Peptidase 18/ISG15-Specific-Processing Protease
UTR, untranslated region
UTS2R, Urotensin 2 Receptor
WNV, West Nile virus
XAF1, XIAP Associated Factor 1
XRN1, 5′-3′ Exoribonuclease 1
ZIKV, Zika virus
ZMAT3, Zinc Finger Matrin-Type 3
ZMYM5, Zinc Finger MYM-Type Containing 5
ZNF124, Zinc Finger Protein 124
ZNF730, Zinc Finger Protein 730
gRNA, genomic TBEV RNA
hNSC, human neural stem cells
lncRNA, long non-coding RNA
mRNA, messenger RNA
miRNA
miRNA, micro RNA
ncRNA, non-coding RNA
pc-mRNA, protein-coding mRNA
qRT-PCR, quantitative reverse transcription real-time PCR
snRNP, small nuclear ribonucleoproteins
vd-sRNA, virus-derived small RNA
Journal
Computational and structural biotechnology journal
ISSN: 2001-0370
Titre abrégé: Comput Struct Biotechnol J
Pays: Netherlands
ID NLM: 101585369
Informations de publication
Date de publication:
2022
2022
Historique:
received:
13
02
2022
revised:
27
05
2022
accepted:
27
05
2022
entrez:
10
6
2022
pubmed:
11
6
2022
medline:
11
6
2022
Statut:
epublish
Résumé
Tick-borne encephalitis virus (TBEV), the most medically relevant tick-transmitted flavivirus in Eurasia, targets the host central nervous system and frequently causes severe encephalitis. The severity of TBEV-induced neuropathogenesis is highly cell-type specific and the exact mechanism responsible for such differences has not been fully described yet. Thus, we performed a comprehensive analysis of alterations in host poly-(A)/miRNA/lncRNA expression upon TBEV infection
Identifiants
pubmed: 35685361
doi: 10.1016/j.csbj.2022.05.052
pii: S2001-0370(22)00207-0
pmc: PMC9167876
doi:
Types de publication
Journal Article
Langues
eng
Pagination
2759-2777Informations de copyright
© 2022 The Authors.
Déclaration de conflit d'intérêts
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
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