title: Gene expression analysis of TIL rich HPV-driven head and neck tumors reveals a distinct B-cell signature when compared to HPV independent tumors.
abstract: Human papilloma virus (HPV)-associated head and neck squamous cell carcinoma (HNSCC) has a better prognosis than it's HPV negative (HPV(-)) counterpart. This may be due to the higher numbers of tumor-infiltrating lymphocytes (TILs) in HPV positive (HPV(+)) tumors. RNA-Sequencing (RNA-Seq) was used to evaluate whether the differences in clinical behaviour simply reflect a numerical difference in TILs or whether there is a fundamental behavioural difference between TILs in these two settings. Thirty-nine HNSCC tumors were scored for TIL density by immunohistochemistry. After the removal of 16 TILlow tumors, RNA-Seq analysis was performed on 23 TILhigh/med tumors (HPV(+) n=10 and HPV(-) n=13). Using EdgeR, differentially expressed genes (DEG) were identified. Immune subset analysis was performed using Functional Analysis of Individual RNA-Seq/ Microarray Expression (FAIME) and immune gene RNA transcript count analysis. In total, 1,634 DEGs were identified, with a dominant immune signature observed in HPV(+) tumors. After normalizing the expression profiles to account for differences in B- and T-cell number, 437 significantly DEGs remained. A B-cell associated signature distinguished HPV(+) from HPV(-) tumors, and included the DEGs CD200, GGA2, ADAM28, STAG3, SPIB, VCAM1, BCL2 and ICOSLG; the immune signal relative to T-cells was qualitatively similar between TILs of both tumor cohorts. Our findings were validated and confirmed in two independent cohorts using TCGA data and tumor-infiltrating B-cells from additional HPV(+) HNSCC patients. A B-cell associated signal segregated tumors relative to HPV status. Our data suggests that the role of B-cells in the adaptive immune response to HPV(+) HNSCC requires re-assessment.
authors.affiliation: Faculty of Medicine, University of Southampton & University Hospital Southampton, Southampton, UK.
authors.forename: Oliver
authors.initials: O
authors.lastname: Wood
authors.affiliation: Faculty of Medicine, University of Southampton & University Hospital Southampton, Southampton, UK.
authors.forename: Jeongmin
authors.initials: J
authors.lastname: Woo
authors.affiliation: La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA.
authors.forename: Gregory
authors.initials: G
authors.lastname: Seumois
authors.affiliation: Faculty of Medicine, University of Southampton & University Hospital Southampton, Southampton, UK.
authors.forename: Natalia
authors.initials: N
authors.lastname: Savelyeva
authors.affiliation: Faculty of Medicine, University of Southampton & University Hospital Southampton, Southampton, UK.
authors.forename: Katy J
authors.initials: KJ
authors.lastname: McCann
authors.affiliation: La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA.
authors.forename: Divya
authors.initials: D
authors.lastname: Singh
authors.affiliation: Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK.
authors.forename: Terry
authors.initials: T
authors.lastname: Jones
authors.affiliation: Faculty of Medicine, University of Southampton & University Hospital Southampton, Southampton, UK.
authors.forename: Lailah
authors.initials: L
authors.lastname: Peel
authors.affiliation: Faculty of Medicine, University of Southampton & University Hospital Southampton, Southampton, UK.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Breen
authors.affiliation: Faculty of Medicine, University of Southampton & University Hospital Southampton, Southampton, UK.
authors.forename: Matthew
authors.initials: M
authors.lastname: Ward
authors.affiliation: Faculty of Medicine, University of Southampton & University Hospital Southampton, Southampton, UK.
authors.forename: Eva
authors.initials: E
authors.lastname: Garrido Martin
authors.affiliation: Faculty of Medicine, University of Southampton & University Hospital Southampton, Southampton, UK.
authors.forename: Tilman
authors.initials: T
authors.lastname: Sanchez-Elsner
authors.affiliation: Faculty of Medicine, University of Southampton & University Hospital Southampton, Southampton, UK.
authors.forename: Gareth
authors.initials: G
authors.lastname: Thomas
authors.affiliation: Faculty of Medicine, University of Southampton & University Hospital Southampton, Southampton, UK.|La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA.
authors.forename: Pandurangan
authors.initials: P
authors.lastname: Vijayanand
authors.affiliation: Faculty of Medicine, University of Southampton & University Hospital Southampton, Southampton, UK.
authors.forename: Christopher H
authors.initials: CH
authors.lastname: Woelk
authors.affiliation: Faculty of Medicine, University of Southampton & University Hospital Southampton, Southampton, UK.
authors.forename: Emma
authors.initials: E
authors.lastname: King
authors.affiliation: Faculty of Medicine, University of Southampton & University Hospital Southampton, Southampton, UK.
authors.forename: Christian
authors.initials: C
authors.lastname: Ottensmeier
mesh_terms: D000368:Aged; D001402:B-Lymphocytes / Q000166:cytology* / Q000821:virology; D002294:Carcinoma, Squamous Cell / Q000276:immunology / Q000378:metabolism* / Q000821:virology; D016000:Cluster Analysis; D005260:Female; D020869:Gene Expression Profiling; D006258:Head and Neck Neoplasms / Q000276:immunology / Q000378:metabolism* / Q000821:virology; D052162:Human papillomavirus 16; D006801:Humans; D007150:Immunohistochemistry; D053208:Kaplan-Meier Estimate; D016246:Lymphocytes, Tumor-Infiltrating / Q000378:metabolism / Q000821:virology*; D008297:Male; D008875:Middle Aged; D030361:Papillomavirus Infections / Q000150:complications*; D011379:Prognosis; D017423:Sequence Analysis, RNA; D000077195:Squamous Cell Carcinoma of Head and Neck; D059467:Transcriptome
keywords: RNA-sequencing; head and neck squamous cell carcinoma; human papilloma virus; transcriptome; tumor-infiltrating lymphocyte