Virus Dataset Detail

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Dataset Information
Accession GSE139324
Status 2019/11/13
Title Immune landscape of viral- and carcinogen-drived head and neck cancer
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Head and neck squamous cell carcinoma (HNSCC) arises through exposure to environmental carcinogens or malignant transformation by human papillomavirus (HPV). Here, we assessed the transcriptional profiles of 131,224 single cells from peripheral and intra-tumoral CD45+ immune populations from HPV– and HPV+ HNSCC and healthy donors. A spectrum of transcriptional signatures in immune lineages ranging from similar to highly divergent was present in the tumor microenvironments (TME) in HPV– and HPV+ HNSCC. CD8+ and regulatory CD4+ T cells were similar in HPV– and HPV+ HNSCC, compared to significant differences between helper CD4+ T cells, B cells and myeloid cells. Further dissection of the major immune lineages identified unique cell states and differentiation trajectories. We contextualized our results by performing multispectral immunofluorescence and evaluating putative cell-cell communication based on spatial proximity, and found longer progression free survival in patients with enrichment of a CD4+ T follicular helper cell signature.
Samples
GSM ID Sample info Characteristics Description
GSM4138127 HNSCC_9_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138128 HNSCC_10_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138129 HNSCC_10_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138130 HNSCC_11_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138131 HNSCC_11_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138132 HNSCC_12_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138133 HNSCC_12_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138134 HNSCC_13_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138135 HNSCC_13_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138136 HNSCC_14_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138137 HNSCC_14_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138138 HNSCC_15_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138139 HNSCC_15_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138140 HNSCC_16_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138141 HNSCC_16_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138142 HNSCC_17_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138143 HNSCC_17_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138144 HNSCC_18_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138145 HNSCC_18_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138146 HNSCC_19_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_positive -
GSM4138147 HNSCC_19_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_positive -
GSM4138148 HNSCC_20_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_positive -
GSM4138149 HNSCC_20_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_positive -
GSM4138150 HNSCC_21_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_positive -
GSM4138151 HNSCC_21_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_positive -
GSM4138152 HNSCC_22_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_positive -
GSM4138153 HNSCC_22_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_positive -
GSM4138154 HNSCC_23_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_positive -
GSM4138155 HNSCC_23_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_positive -
GSM4138156 HNSCC_24_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_positive -
GSM4138157 HNSCC_24_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_positive -
GSM4138158 HNSCC_25_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_positive -
GSM4138159 HNSCC_25_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_positive -
GSM4138160 HNSCC_26_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_positive -
GSM4138161 HNSCC_26_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_positive -
GSM4138162 HD_PBMC_1 tissue:peripheral blood; disease state:Healthy donor; hpv_status:NA -
GSM4138163 HD_PBMC_2 tissue:peripheral blood; disease state:Healthy donor; hpv_status:NA -
GSM4138164 HD_PBMC_3 tissue:peripheral blood; disease state:Healthy donor; hpv_status:NA -
GSM4138165 HD_PBMC_4 tissue:peripheral blood; disease state:Healthy donor; hpv_status:NA -
GSM4138166 HD_PBMC_5 tissue:peripheral blood; disease state:Healthy donor; hpv_status:NA -
GSM4138167 HD_PBMC_6 tissue:peripheral blood; disease state:Healthy donor; hpv_status:NA -
GSM4138168 HD_Tonsil_1 tissue:tonsil tissue; disease state:Healthy donor; hpv_status:NA -
GSM4138169 HD_Tonsil_2 tissue:tonsil tissue; disease state:Healthy donor; hpv_status:NA -
GSM4138170 HD_Tonsil_3 tissue:tonsil tissue; disease state:Healthy donor; hpv_status:NA -
GSM4138110 HNSCC_1_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138111 HNSCC_1_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138112 HNSCC_2_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138171 HD_Tonsil_4 tissue:tonsil tissue; disease state:Healthy donor; hpv_status:NA -
GSM4138113 HNSCC_2_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138172 HD_Tonsil_5 tissue:tonsil tissue; disease state:Healthy donor; hpv_status:NA -
GSM4138114 HNSCC_3_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138115 HNSCC_3_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138116 HNSCC_4_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138117 HNSCC_4_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138118 HNSCC_5_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138119 HNSCC_5_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138120 HNSCC_6_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138121 HNSCC_6_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138122 HNSCC_7_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138123 HNSCC_7_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138124 HNSCC_8_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138125 HNSCC_8_TIL tissue:tumor tissue; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
GSM4138126 HNSCC_9_PBMC tissue:peripheral blood; disease state:Head and neck squamous cell carcinoma (HNSCC); hpv_status:HPV_negative -
Platform GPL18573  : Illumina NextSeq 500 (Homo sapiens)
Literature 31924475  34099645  
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