biostudies-arrayexpressJustin Ooi Seng OoiMus musculusCellrangerhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15296Single-cell RNAseq of PBMC from mice infected with either WT DENV2 or a T209 mutant DENV2biostudies-arrayexpressLibrary Construction - Single cell RNA sequencing libraries were then generated using Chromium Fixed RNA Profiling Kit (10x Genomics).Sequencing - Libraries were sequenced on the Illumina NovaSeq 6000 instrument using 150 paired-end reads.Sample Collection - Blood was centrifuged at 6,000 g for 10 minutes. Red blood cells were subjected to lysis using BD Pharm Lyse™ Lysing Buffer (BD). Dead cells were removed with dead Cell Removal kit (Miltenyi Biotec).Nucleic Acid Extraction - Samples were fixed overnight at 4°C and stored at -80°C, according to the 10x Genomics Demonstrated Protocol CG000478. Fixed cells were hybridised overnight with both mouse whole transcriptome amplification (WTA) probes and spike-in custom probe pool using Chromium Fixed RNA Profiling Kit (10x Genomics).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Mapping and counting were performed using Cell Ranger (version 7.1.0) with the reference genome refdata-gex-mm10-2020-AMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000Non-structural protein 1 (NS1) of dengue virus (DENV) harbours two conserved N-glycosylation sites at positions 130 and 207, whose biological roles have remained elusive. Using a clinically relevant mouse model of severe dengue, we showed that DENV that lacked N207 glycans on NS1 was significantly attenuated, and this phenotype was dominant over wild-type virulent DENV. Mice infected with this mutant exhibited accelerated viral clearance, milder lymphopenia and more functional DENV-specific CD8⁺ T cells. Bulk and single-cell RNA sequencing, cytokine measurements and immune-phenotyping revealed blunted innate inflammatory responses early post-infection, which correlated with reduced PD-L1 expression on innate immune cells and reduced PD-1⁺ T-cells in mice infected with de-glycosylated DENV. PD-1 blockade demonstrated the involvement of premature T-cell apoptosis through the PD-L1/PD-1 axis in DENV pathogenesis. Collectively, our findings support that N207-de-glycosylated NS1 inhibits early inflammatory responses, which restricts PD-L1 upregulation on innate immune cells, which in turn limits PD-L1/PD-1 mediated T-cell apoptosis. Our study uncovers a novel immune evasion strategy and identifies PD-L1/PD-1 as a novel mechanism of dengue immunopathogenesis.RNA-seq of coding RNAMus musculusGlycans on non-structural protein 1 prevent premature T-cell mediated dengue virus clearanceSylvie AlonsoKuan Rong ChanJustin Ooi Seng OoiFakhriedzwan Idris, Justin Seng Geap Ooi, Donald Heng Rong Ting, Eunice Tze Xin Tan, Corrine Wan, Peter I Benke, Jan K Marzinek, Jack M Copping, Qin Hui Li, Lu Yi Ng, Sheau Yng Lim, Ian Walsh, Jane R Allison, Peter J Bond, Federico Torta, Terry Nguyen-Khuong, Kuan Rong Chan, Sylvie AlonsoFakhriedzwan IdrisfalseSingle-cell RNAseq of PBMC from mice infected with Dengue virusSingle-cell RNAseq of PBMC from mice infected with either WT DENV2 or a T209 mutant DENV22026-04-21T00:00:00Z2026-04-21T14:47:03.163Z2025-07-02T09:37:20.416ZE-MTAB-1529640962941ERP174484EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_000418410.1038/s44321-025-00311-6