{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T09:46:00Z","timestamp":1753868760627,"version":"3.41.2"},"reference-count":18,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2021,5,25]],"date-time":"2021-05-25T00:00:00Z","timestamp":1621900800000},"content-version":"vor","delay-in-days":24,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Current Protocols"],"published-print":{"date-parts":[[2021,5]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Human papillomaviruses (HPVs), specifically high\u2010risk HPVs, are responsible for up to 3% of all cancers in women and up to 2% of all cancers in men. They have been identified as the etiological agent of cervical cancer and have been increasingly found to be the driver behind head and neck cancers of the oropharynx. A system in which we can simultaneously observe transcriptional changes to both a host's tumor microenvironment and its associated oncogenic driver (e.g., HPV) would be highly valuable for understanding HPV's role in tumorigenesis. This article describes a detailed methodology for utilizing high\u2010throughput RNA analysis to study viral transcription in formalin\u2010fixed, paraffin\u2010embedded clinical tumor samples. Although our lab utilizes these methods for the study of head and neck cancer, the principles contained within are widely applicable to all fields of HPV study. \u00a9 2021 Wiley Periodicals LLC.<\/jats:p><jats:p><jats:bold>Basic Protocol<\/jats:bold>: HPV16 transcript analysis using NanoString<\/jats:p><jats:p><jats:bold>Support Protocol 1<\/jats:bold>: Preparation of RNA from formalin\u2010fixed, paraffin\u2010embedded slides<\/jats:p><jats:p><jats:bold>Support Protocol 2<\/jats:bold>: Preparation of RNA from cell lysates<\/jats:p><jats:p><jats:bold>Support Protocol 3<\/jats:bold>: Fluorometric RNA concentration and RNA integrity analysis<\/jats:p><jats:p><jats:bold>Support Protocol 4<\/jats:bold>: Determination of input RNA based on DV<jats:sub>300<\/jats:sub> calculation<\/jats:p>","DOI":"10.1002\/cpz1.146","type":"journal-article","created":{"date-parts":[[2021,5,25]],"date-time":"2021-05-25T19:57:26Z","timestamp":1621972646000},"source":"Crossref","is-referenced-by-count":1,"title":["High\u2010Throughput NanoString Analysis of Oncogenic Human Papillomavirus and Tumor Microenvironment Transcription in Head and Neck Squamous Cell Carcinoma"],"prefix":"10.1002","volume":"1","author":[{"given":"Wesley H.","family":"Stepp","sequence":"first","affiliation":[{"name":"Department of Otolaryngology\/Head and Neck Surgery The University of North Carolina at Chapel Hill School of Medicine  Chapel Hill North Carolina"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2021,5,25]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt1385"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1053\/j.seminoncol.2004.09.011"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/jnci\/djn025"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/jnci\/92.9.709"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140\u20106736(04)16194\u20101"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/bjc.2014.42"},{"issue":"2","key":"e_1_2_10_8_1","first-page":"132","article-title":"Prognostic significance of p16 cellular localization in oropharyngeal squamous cell carcinoma","volume":"46","author":"Lai S.","year":"2016","journal-title":"Annals of Clinical and Laboratory Science"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1002\/j.1460\u20102075.1989.tb08594.x"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep25533"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cyto.2018.10.023"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/onc.2010.614"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12105\u2010014\u20100566\u20100"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1001\/jamaoto.2018.0602"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1093\/jnci\/djx135"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1158\/0008\u20105472.CAN\u201015\u20100262"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2018.00248"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12920\u2010015\u20100129\u20106"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/bjc.2012.264"}],"container-title":["Current Protocols"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cpz1.146","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/cpz1.146","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/currentprotocols.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cpz1.146","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,21]],"date-time":"2023-08-21T15:16:16Z","timestamp":1692630976000},"score":1,"resource":{"primary":{"URL":"https:\/\/currentprotocols.onlinelibrary.wiley.com\/doi\/10.1002\/cpz1.146"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5]]},"references-count":18,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2021,5]]}},"alternative-id":["10.1002\/cpz1.146"],"URL":"https:\/\/doi.org\/10.1002\/cpz1.146","archive":["Portico"],"relation":{},"ISSN":["2691-1299","2691-1299"],"issn-type":[{"type":"print","value":"2691-1299"},{"type":"electronic","value":"2691-1299"}],"subject":[],"published":{"date-parts":[[2021,5]]},"article-number":"e146"}}