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Smith NJ, Reddin I, Policelli P, Oh S, Zainal N, Howes E, Jenkins B, Tracy I, Edmond M, Sharpe B, Amendra D, Zheng K, Egawa N, Doorbar J, Rao A, Mahadevan S, Carpenter MA, Harris RS, Ali S, Hanley C, Buisson R, King E, Thomas GJ, Fenton TR. Differentiation signals induce APOBEC3A expression via GRHL3 in squamous epithelia and squamous cell carcinoma. RESEARCH SQUARE 2024:rs.3.rs-3997426. [PMID: 38496447 PMCID: PMC10942551 DOI: 10.21203/rs.3.rs-3997426/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Two APOBEC (apolipoprotein-B mRNA editing enzyme catalytic polypeptide-like) DNA cytosine deaminase enzymes (APOBEC3A and APOBEC3B) generate somatic mutations in cancer, driving tumour development and drug resistance. Here we used single cell RNA sequencing to study APOBEC3A and APOBEC3B expression in healthy and malignant mucosal epithelia, validating key observations with immunohistochemistry, spatial transcriptomics and functional experiments. Whereas APOBEC3B is expressed in keratinocytes entering mitosis, we show that APOBEC3A expression is confined largely to terminally differentiating cells and requires Grainyhead-like transcription factor 3 (GRHL3). Thus, in normal tissue, neither deaminase appears to be expressed at high levels during DNA replication, the cell cycle stage associated with APOBEC-mediated mutagenesis. In contrast, we show that in squamous cell carcinoma tissues, there is expansion of GRHL3 expression and activity to a subset of cells undergoing DNA replication and concomitant extension of APOBEC3A expression to proliferating cells. These findings indicate a mechanism for acquisition of APOBEC3A mutagenic activity in tumours.
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Affiliation(s)
- Nicola J. Smith
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- School of Biosciences, University of Kent, UK
| | - Ian Reddin
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Bio-R Bioinformatics Research Facility, Faculty of Medicine, University of Southampton, UK
| | - Paige Policelli
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Sunwoo Oh
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Nur Zainal
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Emma Howes
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Benjamin Jenkins
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Ian Tracy
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Mark Edmond
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Benjamin Sharpe
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Damian Amendra
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Ke Zheng
- Department of Pathology, University of Cambridge, UK
| | | | - John Doorbar
- Department of Pathology, University of Cambridge, UK
| | - Anjali Rao
- Gilead Sciences, Research Department, 324 Lakeside Dr. Foster City, CA 94404, USA
| | - Sangeetha Mahadevan
- Gilead Sciences, Research Department, 324 Lakeside Dr. Foster City, CA 94404, USA
| | - Michael A. Carpenter
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Christopher Hanley
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Rémi Buisson
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Emma King
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Gareth J. Thomas
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Institute for Life Sciences, University of Southampton, UK
| | - Tim R. Fenton
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Institute for Life Sciences, University of Southampton, UK
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2
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Kim HK, Kim H, Lee MK, Choi WH, Jang Y, Shin JS, Park JY, Bae DH, Hyun SI, Kim KH, Han HW, Lim B, Choi G, Kim M, Chang Lim Y, Yoo J. Generation of human tonsil epithelial organoids as an ex vivo model for SARS-CoV-2 infection. Biomaterials 2022; 283:121460. [PMID: 35286852 PMCID: PMC8901203 DOI: 10.1016/j.biomaterials.2022.121460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 12/14/2022]
Abstract
The palatine tonsils (hereinafter referred to as "tonsils") serve as a reservoir for viral infections and play roles in the immune system's first line of defense. The aims of this study were to establish tonsil epithelial cell-derived organoids and examine their feasibility as an ex vivo model for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The tonsil organoids successfully recapitulated the key characteristics of the tonsil epithelium, including cellular composition, histologic properties, and biomarker distribution. Notably, the basal layer cells of the organoids express molecules essential for SARS-CoV-2 entry, such as angiotensin-converting enzyme 2 (ACE2), transmembrane serine protease 2 (TMPRSS2) and furin, being susceptible to the viral infection. Changes in the gene expression profile in tonsil organoids revealed that 395 genes associated with oncostatin M signaling and lipid metabolism were highly upregulated within 72 h after SARS-CoV-2 infection. Notably, remdesivir suppressed the viral RNA copy number in organoid culture supernatants and intracellular viral protein levels in a dose-dependent manner. Here, we suggest that tonsil epithelial organoids could provide a preclinical and translational research platform for investigating SARS-CoV-2 infectivity and transmissibility or for evaluating antiviral candidates.
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Affiliation(s)
- Han Kyung Kim
- Department of Microbiology, CHA University School of Medicine, Seongnam, Republic of Korea; CHA Organoid Research Center, CHA University, Seongnam, Republic of Korea; R&D Institute, Organoidsciences Ltd., Seongnam, Republic of Korea
| | - Hyeryeon Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, The Research Institute, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Myoung Kyu Lee
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea
| | - Woo Hee Choi
- Department of Microbiology, CHA University School of Medicine, Seongnam, Republic of Korea; CHA Organoid Research Center, CHA University, Seongnam, Republic of Korea
| | - Yejin Jang
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea
| | - Jin Soo Shin
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea
| | - Jun-Yeol Park
- Department of Microbiology, CHA University School of Medicine, Seongnam, Republic of Korea; CHA Organoid Research Center, CHA University, Seongnam, Republic of Korea
| | - Dong Hyuck Bae
- Department of Microbiology, CHA University School of Medicine, Seongnam, Republic of Korea; CHA Organoid Research Center, CHA University, Seongnam, Republic of Korea
| | - Seong-In Hyun
- Department of Microbiology, CHA University School of Medicine, Seongnam, Republic of Korea
| | - Kang Hyun Kim
- Department of Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam, Republic of Korea
| | - Hyun Wook Han
- Department of Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam, Republic of Korea
| | - Byungho Lim
- Data Convergence Drug Research Center, KRICT, Daejeon, Republic of Korea
| | - Gildon Choi
- Data Convergence Drug Research Center, KRICT, Daejeon, Republic of Korea; Department of Medicinal Chemistry and Pharmacology, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Meehyein Kim
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea; Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, Republic of Korea.
| | - Young Chang Lim
- Department of Otorhinolaryngology-Head and Neck Surgery, The Research Institute, Konkuk University School of Medicine, Seoul, Republic of Korea.
| | - Jongman Yoo
- Department of Microbiology, CHA University School of Medicine, Seongnam, Republic of Korea; CHA Organoid Research Center, CHA University, Seongnam, Republic of Korea; R&D Institute, Organoidsciences Ltd., Seongnam, Republic of Korea.
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3
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Sato K, Nishiyama K, Taguchi K, Jiromaru R, Yamamoto H, Matsunaga A, Nagata R, Rikimaru F, Toh S, Higaki Y, Oda S, Nakagawa T, Masuda M. Genetic and transcriptomic analyses in a rare case of human papillomavirus-related oropharyngeal squamous-cell carcinoma combined with small-cell carcinoma. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006102. [PMID: 34462366 PMCID: PMC8559619 DOI: 10.1101/mcs.a006102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/19/2021] [Indexed: 11/24/2022] Open
Abstract
Human papillomavirus (HPV)-related oropharyngeal small-cell carcinoma (OPSmCC) is a rare malignancy with aggressive behavior, whereas HPV-related oropharyngeal squamous-cell carcinoma (OPSqCC) displays a favorable prognosis. Notably, these two malignancies occasionally arise in an identical tumor. In this case study, we explored the molecular characteristics that distinguishes these two carcinomas using a rare case of HPV-related oropharyngeal carcinoma (OPC) with the combined histology of SmCC and SqCC. Immunohistochemical analysis and HPV-RNA in situ hybridization (ISH) suggested that both SmCC and SqCC were HPV-related malignancies. Targeted exome sequencing revealed that SmCC and SqCC had no significant difference in mutations of known driver genes. In contrast, RNA sequencing followed by bioinformatic analyses suggested that aberrant transcriptional programs may be responsible for the neuroendocrine differentiation of HPV-related OPC. Compared to SqCC, genes up-regulated in SmCC were functionally enriched in inflammatory and immune responses (e.g., arachidonic acid metabolism). We then developed a SmCC-like gene module (top 10 up-regulated genes) and found that OPC patients with high module activity showed poor prognosis in The Cancer Genome Atlas (TCGA) and GSE65858 cohort. Gene set enrichment analysis of the SmCC-like gene module suggested its link to MYC proto-oncogene in the TCGA data set. Taken together, these findings suggest that the SmCC-like gene module may contribute to acquisition of aggressive phenotypes and tumor heterogeneity of HPV-related OPC. The present case study is the first report of genetic and transcriptomic aberrations in HPV-related OPSmCC combined with SqCC.
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Affiliation(s)
- Kuniaki Sato
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center 3-1-1 Minami-ku, Notame, Fukuoka, 874-0838, Japan
| | - Kazuo Nishiyama
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center 3-1-1 Minami-ku, Notame, Fukuoka, 874-0838, Japan
| | - Kenichi Taguchi
- Department of Pathology, National Hospital Organization Kyushu Cancer Center 3-1-1 Minami-ku, Notame, Fukuoka, 874-0838, Japan
| | - Rina Jiromaru
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Higashi-ku, Fukuoka, Fukuoka, 860-8556, Japan.,Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Higashi-ku, Fukuoka, Fukuoka, 860-8556, Japan
| | - Hidetaka Yamamoto
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Higashi-ku, Fukuoka, Fukuoka, 860-8556, Japan
| | - Akihide Matsunaga
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center 3-1-1 Minami-ku, Notame, Fukuoka, 874-0838, Japan
| | - Ryozaburo Nagata
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center 3-1-1 Minami-ku, Notame, Fukuoka, 874-0838, Japan
| | - Fumihide Rikimaru
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center 3-1-1 Minami-ku, Notame, Fukuoka, 874-0838, Japan
| | - Satoshi Toh
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center 3-1-1 Minami-ku, Notame, Fukuoka, 874-0838, Japan
| | - Yuichiro Higaki
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center 3-1-1 Minami-ku, Notame, Fukuoka, 874-0838, Japan
| | - Shinya Oda
- Clinical Research Institute, National Hospital Organization Kyushu Cancer Center 3-1-1 Minami-ku, Notame, Fukuoka, 874-0838, Japan
| | - Takashi Nakagawa
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Higashi-ku, Fukuoka, Fukuoka, 860-8556, Japan
| | - Muneyuki Masuda
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center 3-1-1 Minami-ku, Notame, Fukuoka, 874-0838, Japan
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4
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Allam M, Hu T, Cai S, Laxminarayanan K, Hughley RB, Coskun AF. Spatially visualized single-cell pathology of highly multiplexed protein profiles in health and disease. Commun Biol 2021; 4:632. [PMID: 34045665 PMCID: PMC8160218 DOI: 10.1038/s42003-021-02166-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/29/2021] [Indexed: 11/08/2022] Open
Abstract
Deep molecular profiling of biological tissues is an indicator of health and disease. We used imaging mass cytometry (IMC) to acquire spatially resolved 20-plex protein data in tissue sections from normal and chronic tonsillitis cases. We present SpatialViz, a suite of algorithms to explore spatial relationships in multiplexed tissue images by visualizing and quantifying single-cell granularity and anatomical complexity in diverse multiplexed tissue imaging data. Single-cell and spatial maps confirmed that CD68+ cells were correlated with the enhanced Granzyme B expression and CD3+ cells exhibited enrichment of CD4+ phenotype in chronic tonsillitis. SpatialViz revealed morphological distributions of cellular organizations in distinct anatomical areas, spatially resolved single-cell associations across anatomical categories, and distance maps between the markers. Spatial topographic maps showed the unique organization of different tissue layers. The spatial reference framework generated network-based comparisons of multiplex data from healthy and diseased tonsils. SpatialViz is broadly applicable to multiplexed tissue biology.
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Affiliation(s)
- Mayar Allam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Thomas Hu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shuangyi Cai
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Krishnan Laxminarayanan
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Robert B Hughley
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ahmet F Coskun
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA, USA.
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5
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Human Papillomavirus Prevalence in Oral and Oropharyngeal Rinse and Gargle Specimens of Dental Patients and of an HIV-Positive Cohort from Pretoria, South Africa. Adv Virol 2020; 2020:2395219. [PMID: 32908509 PMCID: PMC7471795 DOI: 10.1155/2020/2395219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/27/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022] Open
Abstract
Introduction Studies on HPV prevalence in the head and neck region of South Africans are sparse. Of the available reports in the literature, there were no studies on the association between HPV-DNA presence in the mouth and oropharynx in relation to high-risk behaviours such as oral sex practice or tobacco and alcohol use. Materials and Methods Following ethical clearance and informed consent, patients attending a regional HIV-management clinic and patients attending a dental hospital were recruited to this study. The participants completed an interview-based questionnaire obtaining demographic information, data on HIV serostatus, and behavioural data including sexual practices and tobacco and alcohol use, and a rinse-and-gargle specimen was taken. Specimens were analysed for HPV DNA on 3 separate PCR/qPCR platforms. Statistical analyses were performed for associations between the study group and categorical variables, HPV status, and data from the questionnaires. Results Of 221 participants, 149 were from a general population and 72 from the HIV-management clinic. Smokers comprised 29.4% of the sample, and 45.2% of participants reported to have ever used alcohol. Open mouth kissing during teenage years was confirmed by 64.7% of participants, 40.3% have given oral sex with their mouth, and 44.8% confirmed to have received oral sex from their partner's mouth. Seven participants (3.2%) had detectable α-HPV DNA, and 1 (0.4%) had detectable β-HPV DNA in their rinse-and-gargle specimens. Two participants were from the HIV-management clinic and 6 from the general dental population (overall 3.6%). Conclusion Five high-risk HPV, 2 low-risk HPV, and one β-HPV types were detected. The low prevalence of 3.6% compares well to similar studies in different cohorts studied in South Africa and falls within the global oral/oropharyngeal prevalence spectrum. Only 4 participants, all from the HIV-management clinic, had palatine tonsils. No significant relationships were found between HPV presence and demographic data or sexual, oral sexual, tobacco use, or alcohol use, and no associations were seen with numbers of sexual and oral-sex partners.
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6
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Roberts S, Evans D, Mehanna H, Parish JL. Modelling human papillomavirus biology in oropharyngeal keratinocytes. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180289. [PMID: 30955493 PMCID: PMC6501899 DOI: 10.1098/rstb.2018.0289] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Most human papillomavirus (HPV) positive head and neck cancers arise in the tonsil crypts; deep invaginations at the tonsil surface that are lined with reticulated epithelium infiltrated by immune cells. As in cervical HPV infections, HPV16 is the most prevalent high-risk type in the oropharyngeal cancers, and a genital-oral route of infection is most likely. However, the natural history of HPV-driven oropharyngeal pathogenesis is an enigma, although there is evidence that it is different to that of cervical disease. It is not known if the virus establishes a productive or abortive infection in keratinocytes of the tonsil crypt, or if viral infections progress to cancer via a neoplastic phase, as in cervical HPV infection. The HPV DNA is more frequently found unintegrated in the cancers of the oropharynx compared to those that arise in the cervix, and may include novel HPV-human DNA hybrids episomes. Here, we review current understanding of HPV biology in the oropharynx and discuss the cell-based systems being used to model the HPV life cycle in tonsil keratinocytes and how they can be used to inform on HPV-driven neoplastic progression in the oropharynx. This article is part of the theme issue ‘Silent cancer agents: multi-disciplinary modelling of human DNA oncoviruses’.
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Affiliation(s)
- Sally Roberts
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham , Vincent Drive, Birmingham B15 2TT , UK
| | - Dhananjay Evans
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham , Vincent Drive, Birmingham B15 2TT , UK
| | - Hisham Mehanna
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham , Vincent Drive, Birmingham B15 2TT , UK
| | - Joanna L Parish
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham , Vincent Drive, Birmingham B15 2TT , UK
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7
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Tissue-Specific Gene Expression during Productive Human Papillomavirus 16 Infection of Cervical, Foreskin, and Tonsil Epithelium. J Virol 2019; 93:JVI.00915-19. [PMID: 31189705 DOI: 10.1128/jvi.00915-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 06/03/2019] [Indexed: 02/06/2023] Open
Abstract
Epidemiological data confirm a much higher incidence of high-risk human papillomavirus 16 (HPV16)-mediated carcinogenesis of the cervical epithelium than for other target sites. In order to elucidate tissue-specific responses to virus infection, we compared gene expression changes induced by productive HPV16 infection of cervical, foreskin, and tonsil organotypic rafts. These rafts closely mimic persistent HPV16 infection, long before carcinogenesis sets in. The total number of gene expression changes varied considerably across the tissue types, with only 32 genes being regulated in common. Among them, we confirmed the Kelch-like family protein KLHL35 and the laminin-5 complex to be upregulated and downregulated, respectively, in all the three tissues. HPV16 infection induces upregulation of genes involved in cell cycle control, cell division, mitosis, DNA replication, and DNA damage repair in all the three tissues, indicative of a hyperproliferative environment. In the cervical and tonsil epithelium, we observe significant downregulation of genes involved in epidermis development, keratinocyte differentiation, and extracellular matrix organization. On the other hand, in HPV16-positive foreskin (HPV16 foreskin) tissue, several genes involved in interferon-mediated innate immunity, cytokine signaling, and cellular defenses were downregulated. Furthermore, pathway analysis and experimental validations identified important cellular pathways like STAT1 and transforming growth factor β (TGF-β) to be differentially regulated among the three tissue types. The differential modulation of important cellular pathways like TGF-β1 and STAT1 can explain the sensitivity of tissues to HPV cancer progression.IMPORTANCE Although the high-risk human papillomavirus 16 infects anogenital and oropharyngeal sites, the cervical epithelium has a unique vulnerability to progression of cancer. Host responses during persistent infection and preneoplastic stages can shape the outcome of cancer progression in a tissue-dependent manner. Our study for the first time reports differential regulation of critical cellular functions and signaling pathways during productive HPV16 infection of cervical, foreskin, and tonsil tissues. While the virus induces hyperproliferation in infected cells, it downregulates epithelial differentiation, epidermal development, and innate immune responses, according to the tissue type. Modulation of these biological functions can determine virus fitness and pathogenesis and illuminate key cellular mechanisms that the virus employs to establish persistence and finally initiate disease progression.
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8
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Dogan S, Xu B, Middha S, Vanderbilt CM, Bowman AS, Migliacci J, Morris LGT, Seshan VE, Ganly I. Identification of prognostic molecular biomarkers in 157 HPV-positive and HPV-negative squamous cell carcinomas of the oropharynx. Int J Cancer 2019; 145:3152-3162. [PMID: 31093971 DOI: 10.1002/ijc.32412] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/23/2019] [Accepted: 04/30/2019] [Indexed: 12/12/2022]
Abstract
The incidence of oropharyngeal squamous cell carcinoma (OPSCC) has been increasing due to high-risk HPV infection. We explored the significance of genetic alterations in HPV-positive (HPV-P) and HPV-negative (HPV-N) OPSCC patients on long-term outcome. A total of 157 cases of primary resected OPSCC diagnosed from 1978 to 2005 were subjected to a targeted exome sequencing by MSK-IMPACT™ interrogating somatic mutations in 410 cancer-related genes. Mutational profiles were correlated to recurrence and survival outcomes. OPSCC included 47% HPV-positive (HPV-P) and 53% HPV-negative (HPV-N) tumors arising in the base of tongue (BOT, 43%), palatine tonsil (30%) and soft palate (SP, 27%). HPV negative status, SP location and smoking were associated with poorer outcome. Poorer overall survival was found in NOTCH1-mutated HPV-P (p = 0.039), and in SOX2-amplified HPV-N cases (p = 0.036). Chromosomal arm gains in 8p and 8q, and 16q loss were more common in HPV-P (p = 0.005, 0.04 and 0.01, respectively), while 9p, 18q and 21q losses were more frequent in HPV-N OPSCC (p = 0.006, 0.002 and 0.01, respectively). Novel, potentially functional JAK3, MYC and EP300 intragenic deletions were found in HPV-P, and FOXP1, CDKN2A, CCND1 and RUNX1 intragenic deletions and one FGFR3 inversion were detected in HPV-N tumors. HPV-N/TP53-wild-type OPSCC harbored recurrent mutations in NOTCH1/3/4 (39%), PIK3CA, FAT1 and TERT. In comparison to their oral and laryngeal counterparts, HPV-N OPSCC were genetically distinct. In OPSCC, HPV status, tumor subsite and smoking determine outcome. Risk-stratification can be further refined based on the mutational signature, namely, NOTCH1 and SOX2 mutation status.
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Affiliation(s)
- Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Bin Xu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chad M Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anita S Bowman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jocelyn Migliacci
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Luc G T Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ian Ganly
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
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9
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Wu V, Auchman M, Mollica PA, Sachs PC, Bruno RD. ALDH1A1 positive cells are a unique component of the tonsillar crypt niche and are lost along with NGFR positive stem cells during tumourigenesis. Pathology 2018; 50:524-529. [PMID: 29891189 DOI: 10.1016/j.pathol.2018.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/05/2018] [Accepted: 03/09/2018] [Indexed: 01/11/2023]
Abstract
Interest into the cellular biology of human tonsillar crypts has grown in recent years because it is now known to be the site of origin of most human papilloma virus (HPV) induced oropharyngeal squamous cell carcinomas (OPSCC). Despite the interest, still relatively little is known regarding the cellular hierarchy and dynamics of this anatomical subsite. Here we evaluate normal tonsillar crypts for expression of putative stem cell markers. We found that ALDH1A1 was uniquely expressed in a subset of suprabasal tonsillar crypt epithelium. This cell population was unique from NGFR expressing cells, which were previously identified to have stem/progenitor activity in vitro. In vivo mitochondrial lineage tracing was consistent with a basal to luminal progression of cellular development. This provides support for NGFR cells as the resident stem/progenitor cells in tonsillar crypts, and suggests that the ALDH1A1 cells are not stem/progenitor cells, but merely a unique component of the crypt cellular microenvironment. Analysis of tumours found that both NGFR and ALDH1A1 are lost in HPV+ and HPV- tumours, while LGR5 expression is induced in the same tumours. These results identify a unique component of the tonsillar crypt epithelium-ALDH1A1 cells-and support a cellular model where NGFR+ cells are the long-lived progenitor cells within tonsillar crypts. They also provide evidence that NGFR and ALDH1A1+ cells are lost during tumourigenesis.
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Affiliation(s)
- Vivian Wu
- Department of Otolaryngology, Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Megan Auchman
- School of Medical Diagnostic and Translational Sciences, College of Health Sciences, Old Dominion University, Norfolk, VA, United States
| | - Peter A Mollica
- School of Medical Diagnostic and Translational Sciences, College of Health Sciences, Old Dominion University, Norfolk, VA, United States
| | - Patrick C Sachs
- School of Medical Diagnostic and Translational Sciences, College of Health Sciences, Old Dominion University, Norfolk, VA, United States
| | - Robert D Bruno
- School of Medical Diagnostic and Translational Sciences, College of Health Sciences, Old Dominion University, Norfolk, VA, United States.
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Stem Cell Properties of Normal Human Keratinocytes Determine Transformation Responses to Human Papillomavirus 16 DNA. J Virol 2018; 92:JVI.00331-18. [PMID: 29593030 DOI: 10.1128/jvi.00331-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 03/17/2018] [Indexed: 01/22/2023] Open
Abstract
Human papillomavirus (HPV) infection of the genital tract is common; however, only about 10 to 15% of infections persist, and approximately 10 to 15% of these persistent infections result in cancer. Basal epidermal stem cells are the presumed target cells for HPV infection, providing a reservoir of latently infected cells that persist over time and initiate lesions. However, it is not known whether stem cell density has any influence on transformation of human keratinocytes by HPV. We explored the relationship between stem cell properties of normal human keratinocytes and their susceptibility to transformation by HPV16 DNA. Normal human keratinocyte isolates (NHKc) derived from different donors were cultured in three-dimensional anchorage-free suspension to assess their spheroid-forming ability. NHKc spheroids were then plated back into plastic monolayer culture and transfected with full-length HPV16 DNA, which we have previously shown to integrate into the host cell genome upon transfection. Spheroid-derived NHKc (SD-NHKc) and fluorescence-activated cell sorting-purified populations of basal stem-like keratinocytes, expressing low levels of epidermal growth factor receptor and high levels of integrin alpha 6 (EGFRlo/ITGα6hi), responded to transfection with HPV16 DNA with more vigorous proliferation, greater immortalization efficiency, and faster progression to differentiation resistance than autologous mass-cultured cells. Conversely, cells committed to terminal differentiation (EGFRhi/ITGα6lo) grew slowly after transfection with HPV16 and failed to generate immortalized or DR clones. HPV16 DNA induced stem cell properties in mass-cultured NHKc. We conclude that HPV16 preferentially immortalizes basal keratinocytes with stem cell properties and that these cells readily achieve a differentiation-resistant phenotype upon immortalization by HPV16.IMPORTANCE This paper explores the relationship between the stem cell properties of normal human epidermal cells in culture and these cells' susceptibility to transformation by HPV16 DNA, the HPV type present in about 50% of cervical cancers. We report variable susceptibilities to HPV16-mediated transformation among different keratinocyte isolates derived from neonatal foreskin. Our findings provide strong experimental evidence that HPV16 preferentially transforms basal keratinocytes with stem cell properties. Insights gained from these studies increase our understanding of the host cell-specific factors influencing individual susceptibility to HPV-driven transformation and the contributing factors leading to preneoplastic and neoplastic progression of HPV-positive lesions.
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11
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Abstract
Head and neck squamous cell carcinomas (HNSCCs) arise in the mucosal linings of the upper aerodigestive tract and are unexpectedly heterogeneous in nature. Classical risk factors are smoking and excessive alcohol consumption, and in recent years, the role of human papillomavirus (HPV) has emerged, particularly in oropharyngeal tumours. HPV-induced oropharyngeal tumours are considered a separate disease entity, which recently has manifested in an adapted prognostic staging system while the results of de-intensified treatment trials are awaited. Carcinogenesis caused by HPV in the mucosal linings of the upper aerodigestive tract remains an enigma, but with some recent observations, a model can be proposed. In 2015, The Cancer Genome Atlas (TCGA) consortium published a comprehensive molecular catalogue on HNSCC. Frequent mutations of novel druggable oncogenes were not demonstrated, but the existence of a subgroup of genetically distinct HPV-negative head and neck tumours with favourable prognoses was confirmed. Tumours can be further subclassified based on genomic profiling. However, the amount of molecular data is currently overwhelming and requires detailed biological interpretation. It also became apparent that HNSCC is a disease characterized by frequent mutations that create neoantigens, indicating that immunotherapies might be effective. In 2016, the first results of immunotherapy trials with immune checkpoint inhibitors were published, and these may be considered as a paradigm shift in head and neck oncology.
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Affiliation(s)
- C René Leemans
- Department of Otolaryngology/Head and Neck Surgery, VU University Medical Center
| | - Peter J F Snijders
- Department of Pathology, VU University Medical Center, Amsterdam, Netherlands
| | - Ruud H Brakenhoff
- Department of Otolaryngology/Head and Neck Surgery, VU University Medical Center
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12
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Xiao L, Wu J, Wang JY, Chung HK, Kalakonda S, Rao JN, Gorospe M, Wang JY. Long Noncoding RNA uc.173 Promotes Renewal of the Intestinal Mucosa by Inducing Degradation of MicroRNA 195. Gastroenterology 2018; 154:599-611. [PMID: 29042220 PMCID: PMC5811324 DOI: 10.1053/j.gastro.2017.10.009] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 09/25/2017] [Accepted: 10/07/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS The mammalian intestinal epithelium self-renews rapidly and homeostasis is preserved via tightly controlled mechanisms. Long noncoding RNAs transcribed from ultraconserved regions (T-UCRs) control different cell functions, but little is known about their role in maintaining the integrity of the intestinal epithelium. We searched for T-UCRs that regulate growth of the intestinal mucosa and investigated the mechanism by which T-UCR uc.173 regulates epithelial renewal. METHODS C57BL/6J mice were deprived of food for 48 hours in fasting experiments. Some mice were given intraperitoneal injections of a plasmid encoding LNA-anti-uc.173, to knock down endogenous uc.173. For studies using organoids, primary enterocytes were isolated from the intestine and transfected with the uc.173 transgene to increase uc.173 levels. Intestinal epithelial cells (Caco-2 and IEC-6 lines) were transfected with LNA-anti-uc.173 or uc.173 transgene. We quantified intestinal epithelial renewal based on BrdU incorporation, villus height and crypt depth, and cell number. The association of uc.173 with microRNA 195 (miRNA195) was determined by RNA pull-down assays. RESULTS Genome-wide profile analyses identified 21 T-UCRs, including uc.173, that were differentially expressed between intestinal mucosa of fasted vs non-fasted mice. Increasing levels of uc.173 by expression of a transgene increased growth of intestinal epithelial cells and organoids. Decreasing uc.173 levels by LNA-anti-uc.173 in mice reduced renewal of the intestinal epithelium. We found that uc.173 interacted directly with the primary transcript of miRNA195, leading to miRNA195 degradation. CONCLUSIONS In analyses of intestinal epithelial cells and mice, we identified uc.173 noncoding RNA that regulates growth of the intestinal mucosa and stimulates intestinal epithelial renewal by reducing levels of miRNA195.
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Affiliation(s)
- Lan Xiao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Maryland 21201,Baltimore Veterans Affairs Medical Center, Maryland 21201
| | - Jing Wu
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Maryland 21201,Baltimore Veterans Affairs Medical Center, Maryland 21201
| | - Jun-Yao Wang
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Maryland 21201,Baltimore Veterans Affairs Medical Center, Maryland 21201
| | - Hee Kyoung Chung
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Maryland 21201,Baltimore Veterans Affairs Medical Center, Maryland 21201
| | - Sudhakar Kalakonda
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Maryland 21201,Baltimore Veterans Affairs Medical Center, Maryland 21201
| | - Jaladanki N. Rao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Maryland 21201,Baltimore Veterans Affairs Medical Center, Maryland 21201
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging-IRP, NIH, Baltimore, Maryland 21224
| | - Jian-Ying Wang
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland; Baltimore Veterans Affairs Medical Center, Baltimore, Maryland; Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland.
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13
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Grayson AK, Hearnden V, Bolt R, Jebreel A, Colley HE, Murdoch C. Use of a Rho kinase inhibitor to increase human tonsil keratinocyte longevity for three-dimensional, tissue engineered tonsil epithelium equivalents. J Tissue Eng Regen Med 2017; 12:e1636-e1646. [PMID: 29048773 DOI: 10.1002/term.2590] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/18/2017] [Accepted: 10/09/2017] [Indexed: 12/25/2022]
Abstract
The generation of tissue-engineered epithelial models is often hampered by the limited proliferative capacity of primary epithelial cells. This study aimed to isolate normal tonsillar keratinocytes (NTK) from human tonsils, increase the lifespan of these cells using the Rho kinase inhibitor Y-27632 and to develop tissue-engineered equivalents of healthy and infected tonsil epithelium. The proliferation rate of isolated NTK and expression of c-MYC and p16INK4A were measured in the absence or presence of the inhibitor. Y-27632-treated NTK were used to generate tissue-engineered tonsil epithelium equivalents using de-epidermised dermis that were then incubated with Streptococcus pyogenes to model bacterial tonsillitis, and the expression of pro-inflammatory cytokines was measured by cytokine array and ELISA. NTK cultured in the absence of Y-27632 rapidly senesced whereas cells cultured in the presence of this inhibitor proliferated for over 30 population doublings without changing their phenotype. Y-27632-treated NTK produced a multi-layered differentiated epithelium that histologically resembled normal tonsillar surface epithelium and responded to S. pyogenes infection by increased expression of pro-inflammatory cytokines including CXCL5 and IL-6. NTK can be isolated and successfully cultured in vitro with Y-27632 leading to a markedly prolonged lifespan without any deleterious consequences to cell morphology. This functional tissue-engineered equivalent of tonsil epithelium will provide a valuable tool for studying tonsil biology and host-pathogen interactions in a more physiologically relevant manner.
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Affiliation(s)
- Amy K Grayson
- School of Clinical Dentistry, Claremont Crescent, University of Sheffield, UK
| | - Vanessa Hearnden
- Department of Materials Science and Engineering, University of Sheffield, UK
| | - Robert Bolt
- School of Clinical Dentistry, Claremont Crescent, University of Sheffield, UK
| | - Ala Jebreel
- Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Sheffield, UK
| | - Helen E Colley
- School of Clinical Dentistry, Claremont Crescent, University of Sheffield, UK
| | - Craig Murdoch
- School of Clinical Dentistry, Claremont Crescent, University of Sheffield, UK
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Inhibitor of DNA binding 2 is a novel therapeutic target for stemness of head and neck squamous cell carcinoma. Br J Cancer 2017; 117:1810-1818. [PMID: 29096401 PMCID: PMC5729481 DOI: 10.1038/bjc.2017.373] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/17/2017] [Accepted: 09/22/2017] [Indexed: 12/21/2022] Open
Abstract
Background: Head and neck squamous cell carcinomas (HNSCCs) are highly lethal epithelial tumours containing self-renewal cancer stem cells (CSCs). CSCs in HNSCCs are strongly associated with tumour initiation, invasion, and chemoradiation resistance. However, the important factors regulating stemness in HNSCCs remain unclear. Here, we investigated the molecular roles and clinical significance of inhibitor of DNA binding 2 (Id2) protein to determine if it constitutes a novel therapeutic target for ablating HNSCC cells with stemness. Methods: We performed in vitro and in vivo studies of Id2 function and its effects on stemness using HNSCC cells. We also examined whether Id2 expression could be used as a prognostic indicator through immunohistochemical staining of 119 human HNSCC tumours. Results: Expression of Id2 was higher in HNSCC cells with stemness compared with differentiated HNSCC cells. Overexpression of Id2 increased proliferation, self-renewal, and expression of the putative stemness marker CD44 in HNSCC cells in vitro and in vivo. In contrast, silencing of Id2 using short hairpin RNA attenuated the stemness phenotype of HNSCC cells by reducing self-renewal, CD44 expression, cisplatin chemoresistance, and xenograft tumourigenicity. Most importantly, increased expression of Id2 was closely associated with poorer post-treatment survival rates in HNSCC patients. Conclusions: Inhibitor of DNA binding2 represents a novel and promising therapeutic target for treating and improving the clinical outcomes for patients with HNSCC.
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