Transcriptome sequencing in a 6-hydroxydopamine rat model of Parkinson’s disease

The neurotoxin 6-hydroxydopamine (6-OHDA) has been widely exploited as a tool for modeling Parkinson’s disease (PD) in the rat. This study aimed to provide a comprehensive profile of the mRNAs and long noncoding RNAs (lncRNAs) in rats treated with 6-OHDA as a model of PD. Female SPF Wistar rats were...

Full description

Saved in:

Bibliographic Details
Published in:	Genes & Genetic Systems Vol. 94; no. 2; pp. 61 - 69
Main Authors:	Chen, Jiajun, Li, Jia, Sun, Yajuan
Format:	Journal Article
Language:	English
Published:	Japan The Genetics Society of Japan 01.04.2019 Japan Science and Technology Agency
Subjects:	6-Hydroxydopamine functional enrichment Gene expression Guanosine triphosphatases Guanosine triphosphate Immune response Innate immunity Interferon regulatory factor 7 lncRNA miRNA Movement disorders Neurodegenerative diseases Parkinson's disease Rodents Signal transduction 6-hydroxydopamine lncRNA functional enrichment Parkinson’s disease
ISSN:	1341-7568, 1880-5779, 1880-5779
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Abstract	The neurotoxin 6-hydroxydopamine (6-OHDA) has been widely exploited as a tool for modeling Parkinson’s disease (PD) in the rat. This study aimed to provide a comprehensive profile of the mRNAs and long noncoding RNAs (lncRNAs) in rats treated with 6-OHDA as a model of PD. Female SPF Wistar rats were randomly divided into two groups: a PD model group and a control group. The PD model was induced by 6-OHDA injection. RNA-seq analysis was performed on 6-OHDA-treated rats and corresponding controls. Novel lncRNAs were identified. Differentially expressed genes (DEGs) and differentially expressed lncRNAs were identified in the PD group compared with controls. Gene Ontology function and pathway enrichment analyses were conducted on the DEGs, followed by construction of a protein–protein interaction (PPI) network. In addition, prediction of lncRNA target genes and function prediction of lncRNAs were performed. Moreover, microRNAs (miRNAs) that interacted with the DEGs and differentially expressed lncRNAs were predicted to construct a miRNA–lncRNA–mRNA regulatory network. A total of 536 DEGs and 512 differentially expressed lncRNAs (44 up-regulated and 10 down-regulated known lncRNAs; 407 up-regulated and 51 down-regulated novel lncRNAs) were identified in the PD rat model compared with controls. The DEGs and target genes of lncRNAs were mainly associated with the innate immune response, 2′-5′-oligoadenylate synthetase activity, GTPase activity, GTP binding and the RIG-I-like receptor signaling pathway. IRF7 and ISG15 were hub proteins in the PPI network. Many mRNAs and lncRNAs interacted with other molecules in a competing endogenous RNA network, such as MAS1, TMPRSS2, NPTX1, XLOC_016191, XLOC_026924 and XLOC_005439. We conclude that IRF7, ISG15, MAS1, TMPRSS2, NPTX1, XLOC_016191, XLOC_026924 and XLOC_005439 may contribute critical roles in the pathogenesis of PD.
AbstractList	The neurotoxin 6-hydroxydopamine (6-OHDA) has been widely exploited as a tool for modeling Parkinson's disease (PD) in the rat. This study aimed to provide a comprehensive profile of the mRNAs and long noncoding RNAs (lncRNAs) in rats treated with 6-OHDA as a model of PD. Female SPF Wistar rats were randomly divided into two groups: a PD model group and a control group. The PD model was induced by 6-OHDA injection. RNA-seq analysis was performed on 6-OHDA-treated rats and corresponding controls. Novel lncRNAs were identified. Differentially expressed genes (DEGs) and differentially expressed lncRNAs were identified in the PD group compared with controls. Gene Ontology function and pathway enrichment analyses were conducted on the DEGs, followed by construction of a protein-protein interaction (PPI) network. In addition, prediction of lncRNA target genes and function prediction of lncRNAs were performed. Moreover, microRNAs (miRNAs) that interacted with the DEGs and differentially expressed lncRNAs were predicted to construct a miRNA-lncRNA-mRNA regulatory network. A total of 536 DEGs and 512 differentially expressed lncRNAs (44 up-regulated and 10 down-regulated known lncRNAs; 407 up-regulated and 51 down-regulated novel lncRNAs) were identified in the PD rat model compared with controls. The DEGs and target genes of lncRNAs were mainly associated with the innate immune response, 2'-5'-oligoadenylate synthetase activity, GTPase activity, GTP binding and the RIG-I-like receptor signaling pathway. IRF7 and ISG15 were hub proteins in the PPI network. Many mRNAs and lncRNAs interacted with other molecules in a competing endogenous RNA network, such as MAS1, TMPRSS2, NPTX1, XLOC_016191, XLOC_026924 and XLOC_005439. We conclude that IRF7, ISG15, MAS1, TMPRSS2, NPTX1, XLOC_016191, XLOC_026924 and XLOC_005439 may contribute critical roles in the pathogenesis of PD. The neurotoxin 6-hydroxydopamine (6-OHDA) has been widely exploited as a tool for modeling Parkinson's disease (PD) in the rat. This study aimed to provide a comprehensive profile of the mRNAs and long noncoding RNAs (lncRNAs) in rats treated with 6-OHDA as a model of PD. Female SPF Wistar rats were randomly divided into two groups: a PD model group and a control group. The PD model was induced by 6-OHDA injection. RNA-seq analysis was performed on 6-OHDA-treated rats and corresponding controls. Novel lncRNAs were identified. Differentially expressed genes (DEGs) and differentially expressed lncRNAs were identified in the PD group compared with controls. Gene Ontology function and pathway enrichment analyses were conducted on the DEGs, followed by construction of a protein-protein interaction (PPI) network. In addition, prediction of lncRNA target genes and function prediction of lncRNAs were performed. Moreover, microRNAs (miRNAs) that interacted with the DEGs and differentially expressed lncRNAs were predicted to construct a miRNA-lncRNA-mRNA regulatory network. A total of 536 DEGs and 512 differentially expressed lncRNAs (44 up-regulated and 10 down-regulated known lncRNAs; 407 up-regulated and 51 down-regulated novel lncRNAs) were identified in the PD rat model compared with controls. The DEGs and target genes of lncRNAs were mainly associated with the innate immune response, 2'-5'-oligoadenylate synthetase activity, GTPase activity, GTP binding and the RIG-I-like receptor signaling pathway. IRF7 and ISG15 were hub proteins in the PPI network. Many mRNAs and lncRNAs interacted with other molecules in a competing endogenous RNA network, such as MAS1, TMPRSS2, NPTX1, XLOC_016191, XLOC_026924 and XLOC_005439. We conclude that IRF7, ISG15, MAS1, TMPRSS2, NPTX1, XLOC_016191, XLOC_026924 and XLOC_005439 may contribute critical roles in the pathogenesis of PD.The neurotoxin 6-hydroxydopamine (6-OHDA) has been widely exploited as a tool for modeling Parkinson's disease (PD) in the rat. This study aimed to provide a comprehensive profile of the mRNAs and long noncoding RNAs (lncRNAs) in rats treated with 6-OHDA as a model of PD. Female SPF Wistar rats were randomly divided into two groups: a PD model group and a control group. The PD model was induced by 6-OHDA injection. RNA-seq analysis was performed on 6-OHDA-treated rats and corresponding controls. Novel lncRNAs were identified. Differentially expressed genes (DEGs) and differentially expressed lncRNAs were identified in the PD group compared with controls. Gene Ontology function and pathway enrichment analyses were conducted on the DEGs, followed by construction of a protein-protein interaction (PPI) network. In addition, prediction of lncRNA target genes and function prediction of lncRNAs were performed. Moreover, microRNAs (miRNAs) that interacted with the DEGs and differentially expressed lncRNAs were predicted to construct a miRNA-lncRNA-mRNA regulatory network. A total of 536 DEGs and 512 differentially expressed lncRNAs (44 up-regulated and 10 down-regulated known lncRNAs; 407 up-regulated and 51 down-regulated novel lncRNAs) were identified in the PD rat model compared with controls. The DEGs and target genes of lncRNAs were mainly associated with the innate immune response, 2'-5'-oligoadenylate synthetase activity, GTPase activity, GTP binding and the RIG-I-like receptor signaling pathway. IRF7 and ISG15 were hub proteins in the PPI network. Many mRNAs and lncRNAs interacted with other molecules in a competing endogenous RNA network, such as MAS1, TMPRSS2, NPTX1, XLOC_016191, XLOC_026924 and XLOC_005439. We conclude that IRF7, ISG15, MAS1, TMPRSS2, NPTX1, XLOC_016191, XLOC_026924 and XLOC_005439 may contribute critical roles in the pathogenesis of PD.
Author	Chen, Jiajun Sun, Yajuan Li, Jia
Author_xml	– sequence: 1 fullname: Chen, Jiajun organization: Department of Neurology, China–Japan Union Hospital of Jilin University – sequence: 1 fullname: Li, Jia organization: Department of Neurology, China–Japan Union Hospital of Jilin University – sequence: 1 fullname: Sun, Yajuan organization: Department of Neurology, China–Japan Union Hospital of Jilin University
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/30713215$$D View this record in MEDLINE/PubMed
BookMark	eNp1kU2LFDEQhoOsuB968ywNXjzYaz6608lRF12FBUXWc6iuTs9k7E7GJAPOzb_h3_OXmJnZHWFBSKoCed6qN6lzcuKDt4Q8Z_SScSnfLBbpkqmaUirkI3LGlKJ123X6pJxFw-quleqUnKe0opRTrcQTcipoxwRn7Rn5ehvBJ4xuncNsq2R_bKxH5xeV8xVUsl5uhxh-boewhtl5W0XI1RwGO1VhrL5A_O58Cv7Pr9-pGlyykOxT8niEKdlnd_mCfPvw_vbqY33z-frT1dubGmXb5BokSgp26Jph7JEPqsMeew1C9s3QSo2yV1qrsdcdpS1r0SLqTmiEfvckIS7Iq0PddQzFdcpmdgntNIG3YZMMZ50uukbogr58gK7CJvriznDelNVQoQr14o7a9LMdzDq6GeLW3P9WAV4fAIwhpWjHI8Ko2Q3DlGEYpsx-GAXnD3B0GbILPkdw0_9E1wdRceAQpuCn8u3__OJSFH5bjFOmi0Y3lJfEypb7oAVXVCpeKr07VFqlDAt79AoxO5zsvq1uDN-F-_bHS1xCNNaLvy2Pu8E
CitedBy_id	crossref_primary_10_1111_cns_13702 crossref_primary_10_3389_fcell_2020_584513 crossref_primary_10_1155_2022_3012778 crossref_primary_10_3389_fimmu_2020_01757 crossref_primary_10_1007_s11064_021_03230_3 crossref_primary_10_1186_s13024_021_00439_2 crossref_primary_10_1002_ame2_12093 crossref_primary_10_1007_s13205_020_02483_z crossref_primary_10_1007_s10753_023_01918_y crossref_primary_10_4103_aian_AIAN_292_20 crossref_primary_10_3389_fneur_2020_01044 crossref_primary_10_3390_molecules27217414 crossref_primary_10_1080_17590914_2025_2513881 crossref_primary_10_3390_neuroglia6030036 crossref_primary_10_1016_j_expneurol_2023_114651 crossref_primary_10_3389_fcimb_2022_1041682 crossref_primary_10_1111_psyg_12900 crossref_primary_10_1007_s11011_022_01034_0 crossref_primary_10_1007_s12035_021_02450_6 crossref_primary_10_1515_revneuro_2021_0047 crossref_primary_10_1155_2020_5374307 crossref_primary_10_1016_j_neuint_2024_105906 crossref_primary_10_3389_fncel_2020_581191
Cites_doi	10.1002/glia.23028 10.1016/j.cell.2018.01.011 10.1016/j.gene.2018.03.086 10.1093/nar/gkt646 10.1021/bi061960m 10.1371/journal.pone.0135458 10.1007/978-3-642-00296-0_5 10.1371/journal.pone.0016422 10.1093/bioinformatics/btr026 10.1016/j.yexcr.2007.07.007 10.1007/s11481-009-9176-0 10.1038/nature03464 10.1016/j.nbd.2009.11.004 10.1186/1471-2105-8-298 10.1073/pnas.1423573112 10.1007/s00401-007-0309-3 10.1371/journal.pcbi.1003517 10.1111/j.2517-6161.1995.tb02031.x 10.3791/1376 10.1093/nar/gkm391 10.1177/1535370218761149 10.1186/gb-2010-11-8-r90 10.1101/gr.1239303 10.1007/978-1-4939-3578-9_19 10.1038/nprot.2008.211 10.3389/fncel.2015.00114 10.2147/OTT.S149308 10.1007/s00109-017-1533-5 10.1089/omi.2011.0118 10.1073/pnas.0504754102
ContentType	Journal Article
Copyright	2019 by The Genetics Society of Japan Copyright Japan Science and Technology Agency 2019
Copyright_xml	– notice: 2019 by The Genetics Society of Japan – notice: Copyright Japan Science and Technology Agency 2019
CorporateAuthor	Department of Neurology China-Japan Union Hospital of Jilin University
CorporateAuthor_xml	– name: China-Japan Union Hospital of Jilin University – name: Department of Neurology
DBID	AAYXX CITATION NPM 7SS 7TK 8FD FR3 K9. NAPCQ P64 RC3 7X8
DOI	10.1266/ggs.18-00036
DatabaseName	CrossRef PubMed Entomology Abstracts (Full archive) Neurosciences Abstracts Technology Research Database Engineering Research Database ProQuest Health & Medical Complete (Alumni) ProQuest Nursing and Allied Health Premium Biotechnology and BioEngineering Abstracts Genetics Abstracts MEDLINE - Academic
DatabaseTitle	CrossRef PubMed Entomology Abstracts Nursing & Allied Health Premium Genetics Abstracts Technology Research Database ProQuest Health & Medical Complete (Alumni) Engineering Research Database Neurosciences Abstracts Biotechnology and BioEngineering Abstracts MEDLINE - Academic
DatabaseTitleList	PubMed MEDLINE - Academic Entomology Abstracts
Database_xml	– sequence: 1 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: 7X8 name: MEDLINE - Academic url: https://search.proquest.com/medline sourceTypes: Aggregation Database
DeliveryMethod	fulltext_linktorsrc
Discipline	Biology
EISSN	1880-5779
EndPage	69
ExternalDocumentID	30713215 10_1266_ggs_18_00036 ch3ggsys_2019_009402_001_0061_00693280682 article_ggs_94_2_94_18_00036_article_char_en
Genre	Journal Article
GroupedDBID	--- -~X .55 29H 2WC 36B 53G 5GY ACGFO ACPRK ADBBV AENEX AHMBA ALMA_UNASSIGNED_HOLDINGS BAWUL BKOMP CS3 DIK DU5 E3Z EBD EBS EJD EMB EMOBN F5P GROUPED_DOAJ GX1 JMI JSF JSH KQ8 L7B MOJWN OK1 OVT PQQKQ RJT RNS RZJ SV3 TR2 W2D X7M XSB AAYXX CITATION NPM 7SS 7TK 8FD FR3 K9. NAPCQ P64 RC3 7X8
ID	FETCH-LOGICAL-c654t-a6c60aed74dfbc2d87cbcb9a36b4d569c6b8998fb9700515cecc9739cab756833
ISICitedReferencesCount	27
ISICitedReferencesURI	http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000474329800001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
ISSN	1341-7568 1880-5779
IngestDate	Thu Oct 02 04:03:31 EDT 2025 Tue Oct 07 06:19:51 EDT 2025 Thu Apr 03 07:00:51 EDT 2025 Tue Nov 18 21:02:09 EST 2025 Sat Nov 29 06:43:45 EST 2025 Thu Jul 10 16:10:18 EDT 2025 Wed Sep 03 05:59:39 EDT 2025
IsDoiOpenAccess	true
IsOpenAccess	true
IsPeerReviewed	true
IsScholarly	true
Issue	2
Keywords	6-hydroxydopamine lncRNA functional enrichment Parkinson’s disease
Language	English
LinkModel	OpenURL
MergedId	FETCHMERGED-LOGICAL-c654t-a6c60aed74dfbc2d87cbcb9a36b4d569c6b8998fb9700515cecc9739cab756833
Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
OpenAccessLink	http://dx.doi.org/10.1266/ggs.18-00036
PMID	30713215
PQID	2242244038
PQPubID	1996350
PageCount	9
ParticipantIDs	proquest_miscellaneous_2179515439 proquest_journals_2242244038 pubmed_primary_30713215 crossref_primary_10_1266_ggs_18_00036 crossref_citationtrail_10_1266_ggs_18_00036 medicalonline_journals_ch3ggsys_2019_009402_001_0061_00693280682 jstage_primary_article_ggs_94_2_94_18_00036_article_char_en
PublicationCentury	2000
PublicationDate	2019-04-01
PublicationDateYYYYMMDD	2019-04-01
PublicationDate_xml	– month: 04 year: 2019 text: 2019-04-01 day: 01
PublicationDecade	2010
PublicationPlace	Japan
PublicationPlace_xml	– name: Japan – name: Mishima
PublicationTitle	Genes & Genetic Systems
PublicationTitleAlternate	Genes Genet. Syst.
PublicationYear	2019
Publisher	The Genetics Society of Japan Japan Science and Technology Agency
Publisher_xml	– name: The Genetics Society of Japan – name: Japan Science and Technology Agency
References	Lahiry, P., Racacho, L., Wang, J., Robinson, J. F., Gloor, G. B., Rupar, C. A., Siu, V. M., Bulman, D. E., and Hegele, R. A. (2013) A mutation in the serine protease TMPRSS4 in a novel pediatric neurodegenerative disorder. Orphanet J. Rare Dis. 8, 126. Betel, D., Koppal, A., Agius, P., Sander, C., and Leslie, C. (2010) Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol. 11, R90. Zhao, C., Denison, C., Huibregtse, J. M., Gygi, S., and Krug, R. M. (2005) Human ISG15 conjugation targets both IFN-induced and constitutively expressed proteins functioning in diverse cellular pathways. Proc. Natl. Acad. Sci. USA 102, 10200–10205. Guo, L., Gandhi, P. N., Wang, W., Petersen, R. B., Wilson-Delfosse, A. L., and Chen, S. G. (2007) The Parkinson’s disease-associated protein, leucine-rich repeat kinase 2 (LRRK2), is an authentic GTPase that stimulates kinase activity. Exp. Cell Res. 313, 3658–3670. Tansey, M. G., and Goldberg, M. S. (2010) Neuroinflammation in Parkinson’s disease: its role in neuronal death and implications for therapeutic intervention. Neurobiol. Dis. 37, 510–518. Santiago, J. A., and Potashkin, J. A. (2015) Network-based metaanalysis identifies HNF4A and PTBP1 as longitudinally dynamic biomarkers for Parkinson’s disease. Proc. Natl. Acad. Sci. USA 112, 2257–2262. Kopp, F., and Mendell, J. T. (2018) Functional classification and experimental dissection of long noncoding RNAs. Cell 172, 393–407. Paxinos, G., and Watson, C. (1997) The Rat Brain in Stereotaxic Coordinates, 3rd Ed. Academic Press, San Diego, USA. Goldknopf, I. L., Sheta, E. A., Appel, S. H., Simpson, E. P., and Yen, A. A. (2006) 2’-5’-oligoadenylate synthetase like protein as a biomarker for neurodegenerative disease. U.S. Patent US20060115856A1. 2006-06-01. Wood, L. M., Sankar, S., Reed, R. E., Haas, A. L., Liu, L. F., McKinnon, P., and Desai, S. D. (2011) A novel role for ATM in regulating proteasome-mediated protein degradation through suppression of the ISG15 conjugation pathway. PLoS One 6, e16422. Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. B (Methodological), 57, 289–300. Liu, F. C., Huang, W. Y., Lin, T. Y., Shen, C. H., Chou, Y. C., Lin, C. L., Lin, K. T., and Kao, C. H. (2015) Inverse sssociation of Parkinson disease with systemic lupus erythematosus: a nationwide population-based study. Medicine (Baltimore) 94, e2097. Mistry, J., Bateman, A., and Finn, R. D. (2007) Predicting active site residue annotations in the Pfam database. BMC Bioinformatics 8, 298. Jungverdorben, J., Till, A., and Brüstle, O. (2017) Induced pluripotent stem cell-based modeling of neurodegenerative diseases: a focus on autophagy. J. Mol. Med. (Berl) 95, 705–718. West, A. B., Moore, D. J., Choi, C., Andrabi, S. A., Li, X., Dikeman, D., Biskup, S., Zhang, Z., Lim, K. L., Dawson, V. L., et al. (2007) Parkinson’s disease-associated mutations in LRRK2 link enhanced GTP-binding and kinase activities to neuronal toxicity. Hum. Mol. Genet. 16, 223–232. Kong, L., Zhang, Y., Ye, Z.-Q., Liu, X.-Q., Zhao, S.-Q., Wei, L., and Gao, G. (2007) CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 35, W345–W349. Lun, A. T. L., Chen, Y., and Smyth, G. K. (2016) It’s DE-licious: a recipe for differential expression analyses of RNA-seq experiments using quasi-likelihood methods in edgeR. Methods Mol. Biol. 1418, 391–416. Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504. Wennström, M., Surova, Y., Hall, S., Nilsson, C., Minthon, L., Hansson, O., and Nielsen, H. M. (2015) The inflammatory marker YKL-40 is elevated in cerebrospinal fluid from patients with Alzheimer’s but Not Parkinson’s disease or dementia with Lewy bodies. PLoS One 10, e0135458. Yu, G., Wang, L.-G., Han, Y., and He, Q.-Y. (2012) clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284–287. Yuan, N., Zhang, G., Bie, F., Ma, M., Ma, Y., Jiang, X., Wang, Y., and Hao, X. (2017) Integrative analysis of lncRNAs and miRNAs with coding RNAs associated with ceRNA crosstalk network in triple negative breast cancer. OncoTargets Ther. 10, 5883–5897. Sun, L., Luo, H., Bu, D., Zhao, G., Yu, K., Zhang, C., Liu, Y., Chen, R., and Zhao, Y. (2013) Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res. 41, e166. Benesty, J., Chen, J., Huang, Y., and Cohen, I. (2009) Pearson correlation coefficient. In: Noise Reduction in Speech Processing, vol. 2. pp. 37–40. Springer, Heidelberg. Honda, K., Yanai, H., Negishi, H., Asagiri, M., Sato, M., Mizutani, T., Shimada, N., Ohba, Y., Takaoka, A., Yoshida, N., et al. (2005) IRF-7 is the master regulator of type-I interferon-dependent immune responses. Nature 434, 772–777. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628. Carrieri, C., Forrest, A. R. R., Santoro, C., Persichetti, F., Carninci, P., Zucchelli, S., and Gustincich, S. (2015) Expression analysis of the long non-coding RNA antisense to Uchl1 (AS Uchl1) during dopaminergic cells’ differentiation in vitro and in neurochemical models of Parkinson’s disease. Front. Cell. Neurosci. 9, 114. Qu, Z., and D’Mello, S. R. (2018) Proteomic analysis identifies NPTX1 and HIP1R as potential targets of histone deacetylase-3-mediated neurodegeneration. Exp. Biol. Med. (Maywood) 243, 627–638. Vo, A., Sako, W., Fujita, K., Peng, S., Mattis, P. J., Skidmore, F. M., Ma, Y., Uluğ, A. M., and Eidelberg, D. (2017) Parkinson’s disease-related network topographies characterized with resting state functional MRI. Hum. Brain Mapp. 38, 617–630. Ito, G., Okai, T., Fujino, G., Takeda, K., Ichijo, H., Katada, T., and Iwatsubo, T. (2007) GTP binding is essential to the protein kinase activity of LRRK2, a causative gene product for familial Parkinson’s disease. Biochemistry 46, 1380–1388. Schmieder, R., and Edwards, R. (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863–864. da Conceição, F. S. L., Ngo-Abdalla, S., Houzel, J.-C., and Rehen, S. K. (2010) Murine model for Parkinson’s disease: from 6-OH dopamine lesion to behavioral test. J. Vis. Exp. 15, 1376. Main, B. S., Zhang, M., Brody, K. M., Ayton, S., Frugier, T., Steer, D., Finkelstein, D., Crack, P. J., and Taylor, J. M. (2016) Type-1 interferons contribute to the neuroinflammatory response and disease progression of the MPTP mouse model of Parkinson’s disease. Glia 64, 1590–1604. Huang, D. W., Sherman, B. T., and Lempicki, R. A. (2008) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57. Soreq, L., Guffanti, A., Salomonis, N., Simchovitz, A., Israel, Z., Bergman, H., and Soreq, H. (2014) Long non-coding RNA and alternative splicing modulations in Parkinson’s leukocytes identified by RNA sequencing. PLoS Comput. Biol. 10, e1003517. Moran, L. B., Hickey, L., Michael, G. J., Derkacs, M., Christian, L. M., Kalaitzakis, M. E., Pearce, R. K. B., and Graeber, M. B. (2008) Neuronal pentraxin II is highly upregulated in Parkinson’s disease and a novel component of Lewy bodies. Acta Neuropathol. 115, 471–478. Yeo, S., Sung, B., Hong, Y. M., van den Noort, M., Bosch, P., Lee, S. H., Song, J., Park, S. K., and Lim, S. (2018) Decreased expression of serum- and glucocorticoid-inducible kinase 1 (SGK1) promotes alpha-synuclein increase related with down-regulation of dopaminergic cell in the Substantia Nigra of chronic MPTP-induced Parkinsonism mice and in SH-SY5Y cells. Gene 661, 189–195. Lee, J. K., Tran, T., and Tansey, M. G. (2009) Neuroinflammation in Parkinson’s disease. J. Neuroimmune Pharmacol. 4, 419–429. Dann, A., Poeck, H., Croxford, A. L., Gaupp, S., Kierdorf, K., Knust, M., Pfeifer, D., Maihoefer, C., Endres, S., Kalinke, U., et al. (2011) Cytosolic RIG-I-like helicases act as negative regulators of sterile inflammation in the CNS. Nat. Neurosci. 15, 98–106. 22 23 24 25 26 27 28 29 30 31 10 32 11 33 12 34 13 35 36 15 37 (14) 2018; 172 16 17 18 19 1 2 3 4 5 6 7 8 9 (20) 2007; 8 21
References_xml	– reference: Lee, J. K., Tran, T., and Tansey, M. G. (2009) Neuroinflammation in Parkinson’s disease. J. Neuroimmune Pharmacol. 4, 419–429. – reference: Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. B (Methodological), 57, 289–300. – reference: Lahiry, P., Racacho, L., Wang, J., Robinson, J. F., Gloor, G. B., Rupar, C. A., Siu, V. M., Bulman, D. E., and Hegele, R. A. (2013) A mutation in the serine protease TMPRSS4 in a novel pediatric neurodegenerative disorder. Orphanet J. Rare Dis. 8, 126. – reference: Yuan, N., Zhang, G., Bie, F., Ma, M., Ma, Y., Jiang, X., Wang, Y., and Hao, X. (2017) Integrative analysis of lncRNAs and miRNAs with coding RNAs associated with ceRNA crosstalk network in triple negative breast cancer. OncoTargets Ther. 10, 5883–5897. – reference: Honda, K., Yanai, H., Negishi, H., Asagiri, M., Sato, M., Mizutani, T., Shimada, N., Ohba, Y., Takaoka, A., Yoshida, N., et al. (2005) IRF-7 is the master regulator of type-I interferon-dependent immune responses. Nature 434, 772–777. – reference: Tansey, M. G., and Goldberg, M. S. (2010) Neuroinflammation in Parkinson’s disease: its role in neuronal death and implications for therapeutic intervention. Neurobiol. Dis. 37, 510–518. – reference: Soreq, L., Guffanti, A., Salomonis, N., Simchovitz, A., Israel, Z., Bergman, H., and Soreq, H. (2014) Long non-coding RNA and alternative splicing modulations in Parkinson’s leukocytes identified by RNA sequencing. PLoS Comput. Biol. 10, e1003517. – reference: Dann, A., Poeck, H., Croxford, A. L., Gaupp, S., Kierdorf, K., Knust, M., Pfeifer, D., Maihoefer, C., Endres, S., Kalinke, U., et al. (2011) Cytosolic RIG-I-like helicases act as negative regulators of sterile inflammation in the CNS. Nat. Neurosci. 15, 98–106. – reference: Liu, F. C., Huang, W. Y., Lin, T. Y., Shen, C. H., Chou, Y. C., Lin, C. L., Lin, K. T., and Kao, C. H. (2015) Inverse sssociation of Parkinson disease with systemic lupus erythematosus: a nationwide population-based study. Medicine (Baltimore) 94, e2097. – reference: Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504. – reference: Wood, L. M., Sankar, S., Reed, R. E., Haas, A. L., Liu, L. F., McKinnon, P., and Desai, S. D. (2011) A novel role for ATM in regulating proteasome-mediated protein degradation through suppression of the ISG15 conjugation pathway. PLoS One 6, e16422. – reference: Benesty, J., Chen, J., Huang, Y., and Cohen, I. (2009) Pearson correlation coefficient. In: Noise Reduction in Speech Processing, vol. 2. pp. 37–40. Springer, Heidelberg. – reference: Santiago, J. A., and Potashkin, J. A. (2015) Network-based metaanalysis identifies HNF4A and PTBP1 as longitudinally dynamic biomarkers for Parkinson’s disease. Proc. Natl. Acad. Sci. USA 112, 2257–2262. – reference: Carrieri, C., Forrest, A. R. R., Santoro, C., Persichetti, F., Carninci, P., Zucchelli, S., and Gustincich, S. (2015) Expression analysis of the long non-coding RNA antisense to Uchl1 (AS Uchl1) during dopaminergic cells’ differentiation in vitro and in neurochemical models of Parkinson’s disease. Front. Cell. Neurosci. 9, 114. – reference: Ito, G., Okai, T., Fujino, G., Takeda, K., Ichijo, H., Katada, T., and Iwatsubo, T. (2007) GTP binding is essential to the protein kinase activity of LRRK2, a causative gene product for familial Parkinson’s disease. Biochemistry 46, 1380–1388. – reference: Wennström, M., Surova, Y., Hall, S., Nilsson, C., Minthon, L., Hansson, O., and Nielsen, H. M. (2015) The inflammatory marker YKL-40 is elevated in cerebrospinal fluid from patients with Alzheimer’s but Not Parkinson’s disease or dementia with Lewy bodies. PLoS One 10, e0135458. – reference: Lun, A. T. L., Chen, Y., and Smyth, G. K. (2016) It’s DE-licious: a recipe for differential expression analyses of RNA-seq experiments using quasi-likelihood methods in edgeR. Methods Mol. Biol. 1418, 391–416. – reference: Paxinos, G., and Watson, C. (1997) The Rat Brain in Stereotaxic Coordinates, 3rd Ed. Academic Press, San Diego, USA. – reference: Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628. – reference: Sun, L., Luo, H., Bu, D., Zhao, G., Yu, K., Zhang, C., Liu, Y., Chen, R., and Zhao, Y. (2013) Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res. 41, e166. – reference: Kopp, F., and Mendell, J. T. (2018) Functional classification and experimental dissection of long noncoding RNAs. Cell 172, 393–407. – reference: Kong, L., Zhang, Y., Ye, Z.-Q., Liu, X.-Q., Zhao, S.-Q., Wei, L., and Gao, G. (2007) CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 35, W345–W349. – reference: Huang, D. W., Sherman, B. T., and Lempicki, R. A. (2008) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57. – reference: Mistry, J., Bateman, A., and Finn, R. D. (2007) Predicting active site residue annotations in the Pfam database. BMC Bioinformatics 8, 298. – reference: Qu, Z., and D’Mello, S. R. (2018) Proteomic analysis identifies NPTX1 and HIP1R as potential targets of histone deacetylase-3-mediated neurodegeneration. Exp. Biol. Med. (Maywood) 243, 627–638. – reference: Yu, G., Wang, L.-G., Han, Y., and He, Q.-Y. (2012) clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284–287. – reference: Main, B. S., Zhang, M., Brody, K. M., Ayton, S., Frugier, T., Steer, D., Finkelstein, D., Crack, P. J., and Taylor, J. M. (2016) Type-1 interferons contribute to the neuroinflammatory response and disease progression of the MPTP mouse model of Parkinson’s disease. Glia 64, 1590–1604. – reference: Zhao, C., Denison, C., Huibregtse, J. M., Gygi, S., and Krug, R. M. (2005) Human ISG15 conjugation targets both IFN-induced and constitutively expressed proteins functioning in diverse cellular pathways. Proc. Natl. Acad. Sci. USA 102, 10200–10205. – reference: Goldknopf, I. L., Sheta, E. A., Appel, S. H., Simpson, E. P., and Yen, A. A. (2006) 2’-5’-oligoadenylate synthetase like protein as a biomarker for neurodegenerative disease. U.S. Patent US20060115856A1. 2006-06-01. – reference: Guo, L., Gandhi, P. N., Wang, W., Petersen, R. B., Wilson-Delfosse, A. L., and Chen, S. G. (2007) The Parkinson’s disease-associated protein, leucine-rich repeat kinase 2 (LRRK2), is an authentic GTPase that stimulates kinase activity. Exp. Cell Res. 313, 3658–3670. – reference: Yeo, S., Sung, B., Hong, Y. M., van den Noort, M., Bosch, P., Lee, S. H., Song, J., Park, S. K., and Lim, S. (2018) Decreased expression of serum- and glucocorticoid-inducible kinase 1 (SGK1) promotes alpha-synuclein increase related with down-regulation of dopaminergic cell in the Substantia Nigra of chronic MPTP-induced Parkinsonism mice and in SH-SY5Y cells. Gene 661, 189–195. – reference: Vo, A., Sako, W., Fujita, K., Peng, S., Mattis, P. J., Skidmore, F. M., Ma, Y., Uluğ, A. M., and Eidelberg, D. (2017) Parkinson’s disease-related network topographies characterized with resting state functional MRI. Hum. Brain Mapp. 38, 617–630. – reference: da Conceição, F. S. L., Ngo-Abdalla, S., Houzel, J.-C., and Rehen, S. K. (2010) Murine model for Parkinson’s disease: from 6-OH dopamine lesion to behavioral test. J. Vis. Exp. 15, 1376. – reference: Jungverdorben, J., Till, A., and Brüstle, O. (2017) Induced pluripotent stem cell-based modeling of neurodegenerative diseases: a focus on autophagy. J. Mol. Med. (Berl) 95, 705–718. – reference: West, A. B., Moore, D. J., Choi, C., Andrabi, S. A., Li, X., Dikeman, D., Biskup, S., Zhang, Z., Lim, K. L., Dawson, V. L., et al. (2007) Parkinson’s disease-associated mutations in LRRK2 link enhanced GTP-binding and kinase activities to neuronal toxicity. Hum. Mol. Genet. 16, 223–232. – reference: Betel, D., Koppal, A., Agius, P., Sander, C., and Leslie, C. (2010) Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol. 11, R90. – reference: Schmieder, R., and Edwards, R. (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863–864. – reference: Moran, L. B., Hickey, L., Michael, G. J., Derkacs, M., Christian, L. M., Kalaitzakis, M. E., Pearce, R. K. B., and Graeber, M. B. (2008) Neuronal pentraxin II is highly upregulated in Parkinson’s disease and a novel component of Lewy bodies. Acta Neuropathol. 115, 471–478. – ident: 19 doi: 10.1002/glia.23028 – volume: 172 start-page: 393 issn: 0092-8674 year: 2018 ident: 14 publication-title: Cell doi: 10.1016/j.cell.2018.01.011 – ident: 34 doi: 10.1016/j.gene.2018.03.086 – ident: 29 doi: 10.1093/nar/gkt646 – ident: 11 doi: 10.1021/bi061960m – ident: 31 doi: 10.1371/journal.pone.0135458 – ident: 1 doi: 10.1007/978-3-642-00296-0_5 – ident: 33 doi: 10.1371/journal.pone.0016422 – ident: 26 doi: 10.1093/bioinformatics/btr026 – ident: 8 doi: 10.1016/j.yexcr.2007.07.007 – ident: 16 doi: 10.1007/s11481-009-9176-0 – ident: 9 doi: 10.1038/nature03464 – ident: 30 doi: 10.1016/j.nbd.2009.11.004 – volume: 8 start-page: 298 issn: 1471-2105 year: 2007 ident: 20 publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-8-298 – ident: 25 doi: 10.1073/pnas.1423573112 – ident: 7 – ident: 22 – ident: 17 – ident: 21 doi: 10.1007/s00401-007-0309-3 – ident: 28 doi: 10.1371/journal.pcbi.1003517 – ident: 2 doi: 10.1111/j.2517-6161.1995.tb02031.x – ident: 5 doi: 10.3791/1376 – ident: 13 doi: 10.1093/nar/gkm391 – ident: 24 doi: 10.1177/1535370218761149 – ident: 3 doi: 10.1186/gb-2010-11-8-r90 – ident: 15 – ident: 32 – ident: 27 doi: 10.1101/gr.1239303 – ident: 18 doi: 10.1007/978-1-4939-3578-9_19 – ident: 10 doi: 10.1038/nprot.2008.211 – ident: 4 doi: 10.3389/fncel.2015.00114 – ident: 36 doi: 10.2147/OTT.S149308 – ident: 6 – ident: 12 doi: 10.1007/s00109-017-1533-5 – ident: 35 doi: 10.1089/omi.2011.0118 – ident: 37 doi: 10.1073/pnas.0504754102 – ident: 23
SSID	ssj0020983 ssib058492816 ssib044737543
Score	2.3166442
Snippet	The neurotoxin 6-hydroxydopamine (6-OHDA) has been widely exploited as a tool for modeling Parkinson’s disease (PD) in the rat. This study aimed to provide a... The neurotoxin 6-hydroxydopamine (6-OHDA) has been widely exploited as a tool for modeling Parkinson's disease (PD) in the rat. This study aimed to provide a...
SourceID	proquest pubmed crossref medicalonline jstage
SourceType	Aggregation Database Index Database Enrichment Source Publisher
StartPage	61
SubjectTerms	6-Hydroxydopamine functional enrichment Gene expression Guanosine triphosphatases Guanosine triphosphate Immune response Innate immunity Interferon regulatory factor 7 lncRNA miRNA Movement disorders Neurodegenerative diseases Parkinson's disease Rodents Signal transduction
Title	Transcriptome sequencing in a 6-hydroxydopamine rat model of Parkinson’s disease
URI	https://www.jstage.jst.go.jp/article/ggs/94/2/94_18-00036/_article/-char/en http://mol.medicalonline.jp/library/journal/download?GoodsID=ch3ggsys/2019/009402/001&name=0061-0069e https://www.ncbi.nlm.nih.gov/pubmed/30713215 https://www.proquest.com/docview/2242244038 https://www.proquest.com/docview/2179515439
Volume	94
WOSCitedRecordID	wos000474329800001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
hasFullText	1
inHoldings	1
isFullTextHit
isPrint
ispartofPNX	Genes & Genetic Systems, 2019/04/01, Vol.94(2), pp.61-69
journalDatabaseRights	– providerCode: PRVAON databaseName: DOAJ Directory of Open Access Journals customDbUrl: eissn: 1880-5779 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0020983 issn: 1341-7568 databaseCode: DOA dateStart: 20120101 isFulltext: true titleUrlDefault: https://www.doaj.org/ providerName: Directory of Open Access Journals – providerCode: PRVHPJ databaseName: ROAD: Directory of Open Access Scholarly Resources customDbUrl: eissn: 1880-5779 dateEnd: 99991231 omitProxy: false ssIdentifier: ssib044737543 issn: 1341-7568 databaseCode: M~E dateStart: 19960101 isFulltext: true titleUrlDefault: https://road.issn.org providerName: ISSN International Centre
link	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwtV3db9MwELfYGBISQnxTGFOQqHioMtI4iW3xAhqtECplEp1UnqzYSUYnmpalResLfzt3tpO2GpPGA1JlVc7ly_fz-S6-D0JesTAReSEKv5tH1I90rn0FK7nPVZenYZjFSWQChQdsOOTjsTh2sSeVKSfAypJfXIj5f2U19AGzMXT2H9jdXBQ64D8wHVpgO7TXYzyuPkYWzKZ5x7lKu8iVtJP431cZuq5kYC1PUcUECNh6OMYdLsVv58ZBhFVbuzdOgcU01ZXBCzwABkC6XNCNaj4w7gGfJo24_7o0gu1berZcI_GoDgqZQHe5-emhKzY8Vqy0hMnvx8xWgznM_9LnRKytY-ygFG7IS5uI_ZIYB60Bhvn0tDrsct_kzFkvV_UW_fCL7J8MBnLUG4_atD__6WMpMdxyb9MPlq075GbIYiFqS9vZ4YEw2VmbJ3XxEHDTN5u33NJU9s5AWccsDHemdgPNJjK52i4x-snoHrnrDAvvvQXEfXIjLx-QW7bU6OohOd6ChbeGhTcpvdS7BAsPYOEZWHizwmtg8bryHCgekZN-b3T00XfVNHydxNHCTxOdBGmesSgrlA4zzrTSSqQ0URFMSaEThbZ3oQQzhX9g2mrBqNCpYnHCKX1MdstZmT8lXoQR3RoUa66KiGrFWabiohBUhZGG3hbp1CMntUs1jxVPfkg0OWGcJYyz7HJpxrlF2g313KZYuYLurWVCQ-XmmKESkQyxqambgxi9CHKhRd5tcU66KVsBAYULrCqJEJfoahuE6OopUb3HBkwcHiQ8bJH9mtnrs0EFhl8UUHjrl81hkNG48ZaW-WwJNLDqwYiC7t8iTyxImneg-JkI9O5n1zj7Obm9nob7ZHdxvsxfkD39azGpzg_IDhvzAwN1aD__7v0BWDS8eg
linkProvider	Directory of Open Access Journals
openUrl	ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Transcriptome+sequencing+in+a+6-hydroxydopamine+rat+model+of+Parkinson%27s+disease&rft.jtitle=Genes+%26+genetic+systems&rft.au=Li%2C+Jia&rft.au=Sun%2C+Yajuan&rft.au=Chen%2C+Jiajun&rft.date=2019-04-01&rft.issn=1880-5779&rft.eissn=1880-5779&rft.volume=94&rft.issue=2&rft.spage=61&rft_id=info:doi/10.1266%2Fggs.18-00036&rft.externalDBID=NO_FULL_TEXT
thumbnail_l	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1341-7568&client=summon
thumbnail_m	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1341-7568&client=summon
thumbnail_s	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1341-7568&client=summon