{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Justin Ooi"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16202"],"description":["Primary human monocytes were isolated and differentiated into moDCs. These moDCs were infected with WT Dengue virus 2 and its attenuated mutants (generated using infectious clone construction with site-directed mutagenesis) to better understand the gene expression changes induced by these different attenuated viruses."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - RNA was extracted from whole blood using the Tempus Spin RNA Isolation Kit, according to manufacturer's instructions.","Sample Collection - Peripheral blood mononuclear cells (PBMCs) were isolated from venous blood collected from a flavivirus-naïve healthy donor. Cells were incubated at 37°C for 2.5 hr to allow monocytes to adhere to the tissue culture flask surface. Monocytes were incubated overnight at 37°C before use in experiments","Scaning - Hybridized samples were loaded on the nCounter cartridge and post-hybridization steps and scanning was performed on the nCounter Sprint Profiler. RCC files were analyzed using nSolver analysis software (Version 4.0) as per the manufacturer’s protocols.","Hybridization - Total RNA (50ng) was hybridized to reporter and capture probe sets at 65°C for 24h.","Labeling - Not Applicable as this is a Nanostring platform and no labelling performed"],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Data Transformation - Negative and positive controls included in probe sets were used for background thresholding, and normalizing samples for differences in hybridization or sample input respectively."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["To successfully complete an infection lifecycle, viruses have to avoid activating host antiviral and transcriptional responses to avoid disrupting cellular processes and cause premature host cell death. How the host transcriptional response to dengue virus (DENV) infection and its impact on pathogenesis, however, remain unclear. Herein, we examined a pair of DENV-2, where the wild-type strain (16681) elicited few host transcriptional responses following infection, in contrast to its clinically tested attenuated derivative (PDK53 strain). Site-directed mutagenesis studies revealed a single D29V substitution on the pre-membrane (prM) protein, present not in 16681 but in PDK53, that altered transcriptional response to infection. Mechanistically, prM D29V substitution impaired interaction of prM protein with host high mobility group box 1 (HMGB1) protein; wild-type prM-HMGB1 interaction prevented HMGB1 cytoplasmic-nuclear translocation to support transcriptional response to infection. Remarkably, HMGB1 knockdown not only reduced transcriptional response but also slowed virus replication rate, suggesting that HMGB1 also controlled the expression of host factors necessary for DENV replication. Indeed, introducing 29 V to prM increased virus replication rate and transcription of antiviral response genes in both wild-type DENV-3 as well as chimeric DENV-3/-2, the DENV-3 component of TAK-003. Our findings suggest exploiting this interaction to improve immunogenicity and potentially efficacy of current vaccines."],"study_type":["transcription profiling by array"],"species":["Homo sapiens"],"pubmed_title":["Reduced dengue virus pre-membrane protein-HMGB1 interaction activates host cell transcription to attenuate infection","Reduced dengue virus pre-membrane protein-HMGB1 interaction activates host cell transcription to attenuate infection."],"pubmed_authors":["Siriphanitchakorn T, Ooi JSG, Ng WC, Tan HC, Zhang SL, Ng DHL, Yap X, Yee JX, Zheng Q, Tan YT, Ong EZ, Chan KR, Choy MM, Ooi EE.","Kuan Rong Chan","Tanamas Siriphanitchakorn, Justin S. G. Ooi, Wy Ching Ng, Hwee Cheng Tan, Summer L. Zhang, Dorothy H. L. Ng, Xin Yap, Jia Xin Yee, Qiao Zheng, Yi Ting Tan, Eugenia Z. Ong, Kuan Rong Chan, Milly M. Choy, Eng Eong Ooi","Justin Ooi"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptional analysis (nCounter Human Immunology v2 Panel) of primary human monocyte-derived dendritic cells (moDCs) infected with WT and attenuated mutant Dengue virus 2 strains","description":"Primary human monocytes were isolated and differentiated into moDCs. These moDCs were infected with WT Dengue virus 2 and its attenuated mutants (generated using infectious clone construction with site-directed mutagenesis) to better understand the gene expression changes induced by these different attenuated viruses.","dates":{"release":"2026-04-14T00:00:00Z","modification":"2026-05-14T18:46:00.149Z","creation":"2025-11-20T09:43:28.69Z"},"accession":"E-MTAB-16202","cross_references":{"pubmed":["publ-0-79cf-removable","41702930"],"Biostudies":["E-MTAB-16204","E-MTAB-16201"],"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0005518","EFO_0003816","EFO_0003815"],"doi":["10.1038/s41541-026-01401-3"]}}