There is some evidence to suggest that human papilloma virus (HPV) may play a causal role in head and neck carcinoma (HNSCC). The aim of this study was to investigate the prevalence of HPV DNA in HNSCC and to determine whether any correlation exists with p16 or survival. An initial pilot study of sixty formalin-fixed HNSCC was carried out in order to optimise the methodology for the PCR and immunohistochemistry. A further 84 benign lesions, 12 dysplasias and additional 80 HNSCC were also included. In the pilot study the prevalence of all HPV types was 67% of which 18% were high risk-HPV (HR-HPV) and for the combined carcinoma sample it was 59% of which 25% were HR-HPV. The overall HPV prevalence was 51% and 42% for benign lesions and dysplasias with HR-HPV accounting for 14% and 8% respectively. A total of four alpha HPV types were identified and eleven beta HPV types. Multiple HPV types co-existed in the same tissue and in some cases both alpha and beta HPV. The results may suggest that HR-HPV may play a role in a small subset of HNSCC. An association was found between HPV status and gender, age group, survival, nodal metastasis and T3 tumour size and smoking. HPV16 was predominantly present in female patients and was associated with an improved overall survival and recurrence free survival. p16 positivity varied from 76-78% in carcinomas, 51% in benign lesions and 66% in dysplasias. p16 status was not associated with disease recurrence or nodal metastasis. Positive p16 staining and high staining intensity was associated with a poorer overall survival and the male gender, an older age group, anatomic site, and T2 tumour size. Overall HPV status was not correlated with p16 expression but a correlation found between p16 and HPV16 may suggest that p16 could potentially act as a surrogate marker of HPV16. However, the lack of concordance would suggest that in isolation p16 may not be a reliable marker for HR-HPV and should not be relied upon in isolation. Our findings could suggest that HPV16 and p16 status may be independent predictors for prognosis and disease recurrence.

Les télomères sont des structures complexes associant des répétitions de séquences nucléotidiques TTAGGG à diverses protéines dont le complexe shelterin. Le TRF2 (Telomeric repeat-binding Factor 2) est un composant majeur de ce complexe, indispensable à la formation de la boucle télomérique T-loop qui permet la protection des extrémités vis-à-vis des exonucléases et systèmes de réparation de l'ADN. Ce facteur est aussi impliqué dans la tumorigenèse de nombreux cancers. Le carcinome épidermoïde oral représente 90% des cancers des Voies Aéro-Digestives Supérieures (VADS) sixième cause de cancer dans le monde avec une incidence de plus de 14000 nouveaux cas en France en 2012. Souvent diagnostiqué par des chirurgiens-dentistes, c'est un cancer de mauvais pronostic traité par chirurgie, radiothérapie, chimiothérapie et thérapies ciblant le R-EGF. Peu d'études se sont intéressées à l'expression de TRF2 dans le carcinome épidermoïde oral et leurs résultats contradictoires ne permettent pas de comprendre son rôle dans leur agressivité.L'expression de TRF2 a été analysée dans les biopsies de 62 patients atteints d'un carcinome épidermoïde oral, à l'aide d'un score de lecture en immunohistochimie. Une forte expression de TRF2 est associé une survie globale significativement plus faible ce qui en fait un facteur pronostique pertinent. In vitro, une faible expression de TRF2 induit une modification du profil sécrétoire des cellules tumorales qui se traduit in vivo par des modifications de l'architecture tissulaire de tumeurs chez la souris nude. Enfin, TRF2 est un marqueur prédictif de réponse aux thérapies ciblées, leur efficacité étant optimale lorsque TRF2 est faiblement exprimé. / Telomeres are composed of tandmely repeated TTAGGG nucleotidic sequences associated with various proteins including shelterin complex. TRF2 (Telomeric repeat-binding Factor 2) is the major component of this complex, necessary for T-loop formation which protects telomeres from DNA damage response and exonucleases. Oral Squamous Cell Carcinoma (OSCC) is the most incident subtype of head and neck cancer (90%), sixth most common cancer in the world with an incidence of 14000 cases in France in 2012. Often diagnosed by dental surgeons,this bad prognosis malignancy is treated by surgery, radiotherapy, chemotherapy and targeted therapies against EGFR. Few studies evaluated TRF2 expression in OSCC and their results are discrepant. TRF2 expression has been assessed in immunohistochemistry in 62 tumoral samples of patients with an history of OSCC. TRF2 overexpression is associated with bad prognosis. TRF2 knockdown changes cells' secretome thus modifying tumoral tissue architecture. Our results showed that TRF2 is predictive for treatment response in targeted therapies in OSCC.

Leucoplasia bucal (LB) é uma desordem potencialmente maligna, com risco de transformação maligna que varia de 0,13% a 17,5%. Muitos estudos vêm buscando estabelecer biomarcadores capazes de predizer o potencial de transformação maligna dessa lesão. O Ki-67 é uma proteína não-histônica nuclear que tem sido amplamente utilizada para avaliar proliferação celular. O BMI-1 é uma proteína considerada um marcador essencial para a manutenção das propriedades de autorrenovação e da tumorigenicidade do carcinoma espinocelular. O objetivo principal desse estudo observacional transversal foi avaliar proliferação e imortalização celulares em LB a partir da marcação imunoistoquímica do Ki-67 e do BMI-1, comparando lesões displásicas com não displásicas. Casos de LB não displásica - LBND (n=28), LB displásica - LBD (n=33) foram selecionados a partir de prontuários de pacientes e comparados com mucosa clinicamente normal - MN (n=9), hiperplasia inflamatória - HI (n=17) e carcinoma espinocelular - CEC (n=19). Os diagnósticos histopatológicos foram confirmados a partir da revisão de cortes histológicos corados por hematoxilina e eosina. Adicionalmente, cortes histológicos foram submetidos à técnica imunoistoquímica para avaliação de Ki-67 e BMI-1. Para a quantificação foi considerado o percentual de células positivas por 1000 células para o CEC e 1500 células para os demais grupos. O percentual de imunomarcação de Ki-67 e de BMI-1, quando avaliadas todas as camadas epiteliais em conjunto, foi mais alto no CEC quando comparado aos demais grupos (Kruskal-Wallis, p<0.05). A expressão de Ki-67 foi maior em LBND, LBD e HI quando comparada com MN (Kruskal-Wallis, p<0.05). Além disso, a imunomarcação de BMI-1 foi maior em LBD quando comparada com MN, quando analisadas todas as camadas em conjunto (Kruskal-Wallis, p<0.05). A partir da avaliação das camadas epiteliais separadamente, observou-se aumento da expressão de BMI-1 na camada parabasal e suprabasal em LBND quando comparada com MN. Houve correlação positiva entre Ki-67 e BMI-1 (Correlação de Spearman, R=0.37, p<0.05). Conclui-se que a proliferação e as alterações na transição epitélio-mesênquima são eventos relacionados e que estão presentes desde estágios precoces e se acentuam nos estágios mais tardios da carcinogênese. / Oral leukoplakia (OL) is potentially malignant disorder, with a risk of malignant transformation that ranges from 0.13% to 17.5%. Many biological markers have been used as an attempt to predict malignant transformation, but no reliable markers have been established so far. The Ki-67 is a nuclear non-histone regarded as reliable marker of proliferating cells .BMI-1 is a protein considered as an essential marker for maintenance of properties self-renewability and tumorigenicity of squamous cell carcinoma. The main aim this cross-sectional observational study was to evaluate cell proliferation and immortalization in oral leukoplakia, comparing non-dysplastic and dysplastic lesions. Cases of non-dysplastic – Non-dys OL (n=28), dysplastic – Dys OL (n=33) records were selected and compared with normal oral mucosa – NOM (n=9), inflammatory hyperplasia –IH (n=17), and oral squamous cell carcinoma - OSCC (n=19). The histopathological diagnosis was confirmed by the revision of Hematoxilin and Eosin stained slides. Additionally, histological sections were submitted to immunohistochemical technique for evaluation of Ki-67 and BMI-1. The labeling index was determined by counting the labeled nuclei of 1000 cells for OSCC cases and 1500 for the others comparison groups. Ki-67 and BMI-1 immunolabeling percentage were higher in OSCC in comparison of others groups when all epithelial layers were evaluated together (Kruskal-Wallis, p<0.05). Ki-67 immunolabeling increased in Non-dys OL, Dys OL and IH when compared to NOM (Kruskal-Wallis, p<0.05). Furthermore, BMI-1 immunolabeling was higher in Dys OL relation to NOM in the analysis of all epithelial layers together (Kruskal-Wallis, p<0.05). When the evaluation considered the epithelial layer separately, an increased BMI1 expression was observed in the parabasal and suprabasal layers of Non-dys OL when compared to NOM. A significant positive correlation was found between Ki-67 and BMI-1 (Spearman correlation coefficient, R=0.37, p<0.01). In conclusion, the present findings support that proliferation and changes toward epithelial-to-mesenchymal transition increase gradually since early stages of oral carcinogenesis.

Leucoplasia bucal (LB) é uma desordem potencialmente maligna, com risco de transformação maligna que varia de 0,13% a 17,5%. Muitos estudos vêm buscando estabelecer biomarcadores capazes de predizer o potencial de transformação maligna dessa lesão. O Ki-67 é uma proteína não-histônica nuclear que tem sido amplamente utilizada para avaliar proliferação celular. O BMI-1 é uma proteína considerada um marcador essencial para a manutenção das propriedades de autorrenovação e da tumorigenicidade do carcinoma espinocelular. O objetivo principal desse estudo observacional transversal foi avaliar proliferação e imortalização celulares em LB a partir da marcação imunoistoquímica do Ki-67 e do BMI-1, comparando lesões displásicas com não displásicas. Casos de LB não displásica - LBND (n=28), LB displásica - LBD (n=33) foram selecionados a partir de prontuários de pacientes e comparados com mucosa clinicamente normal - MN (n=9), hiperplasia inflamatória - HI (n=17) e carcinoma espinocelular - CEC (n=19). Os diagnósticos histopatológicos foram confirmados a partir da revisão de cortes histológicos corados por hematoxilina e eosina. Adicionalmente, cortes histológicos foram submetidos à técnica imunoistoquímica para avaliação de Ki-67 e BMI-1. Para a quantificação foi considerado o percentual de células positivas por 1000 células para o CEC e 1500 células para os demais grupos. O percentual de imunomarcação de Ki-67 e de BMI-1, quando avaliadas todas as camadas epiteliais em conjunto, foi mais alto no CEC quando comparado aos demais grupos (Kruskal-Wallis, p<0.05). A expressão de Ki-67 foi maior em LBND, LBD e HI quando comparada com MN (Kruskal-Wallis, p<0.05). Além disso, a imunomarcação de BMI-1 foi maior em LBD quando comparada com MN, quando analisadas todas as camadas em conjunto (Kruskal-Wallis, p<0.05). A partir da avaliação das camadas epiteliais separadamente, observou-se aumento da expressão de BMI-1 na camada parabasal e suprabasal em LBND quando comparada com MN. Houve correlação positiva entre Ki-67 e BMI-1 (Correlação de Spearman, R=0.37, p<0.05). Conclui-se que a proliferação e as alterações na transição epitélio-mesênquima são eventos relacionados e que estão presentes desde estágios precoces e se acentuam nos estágios mais tardios da carcinogênese. / Oral leukoplakia (OL) is potentially malignant disorder, with a risk of malignant transformation that ranges from 0.13% to 17.5%. Many biological markers have been used as an attempt to predict malignant transformation, but no reliable markers have been established so far. The Ki-67 is a nuclear non-histone regarded as reliable marker of proliferating cells .BMI-1 is a protein considered as an essential marker for maintenance of properties self-renewability and tumorigenicity of squamous cell carcinoma. The main aim this cross-sectional observational study was to evaluate cell proliferation and immortalization in oral leukoplakia, comparing non-dysplastic and dysplastic lesions. Cases of non-dysplastic – Non-dys OL (n=28), dysplastic – Dys OL (n=33) records were selected and compared with normal oral mucosa – NOM (n=9), inflammatory hyperplasia –IH (n=17), and oral squamous cell carcinoma - OSCC (n=19). The histopathological diagnosis was confirmed by the revision of Hematoxilin and Eosin stained slides. Additionally, histological sections were submitted to immunohistochemical technique for evaluation of Ki-67 and BMI-1. The labeling index was determined by counting the labeled nuclei of 1000 cells for OSCC cases and 1500 for the others comparison groups. Ki-67 and BMI-1 immunolabeling percentage were higher in OSCC in comparison of others groups when all epithelial layers were evaluated together (Kruskal-Wallis, p<0.05). Ki-67 immunolabeling increased in Non-dys OL, Dys OL and IH when compared to NOM (Kruskal-Wallis, p<0.05). Furthermore, BMI-1 immunolabeling was higher in Dys OL relation to NOM in the analysis of all epithelial layers together (Kruskal-Wallis, p<0.05). When the evaluation considered the epithelial layer separately, an increased BMI1 expression was observed in the parabasal and suprabasal layers of Non-dys OL when compared to NOM. A significant positive correlation was found between Ki-67 and BMI-1 (Spearman correlation coefficient, R=0.37, p<0.01). In conclusion, the present findings support that proliferation and changes toward epithelial-to-mesenchymal transition increase gradually since early stages of oral carcinogenesis.

Leucoplasia bucal (LB) é uma desordem potencialmente maligna, com risco de transformação maligna que varia de 0,13% a 17,5%. Muitos estudos vêm buscando estabelecer biomarcadores capazes de predizer o potencial de transformação maligna dessa lesão. O Ki-67 é uma proteína não-histônica nuclear que tem sido amplamente utilizada para avaliar proliferação celular. O BMI-1 é uma proteína considerada um marcador essencial para a manutenção das propriedades de autorrenovação e da tumorigenicidade do carcinoma espinocelular. O objetivo principal desse estudo observacional transversal foi avaliar proliferação e imortalização celulares em LB a partir da marcação imunoistoquímica do Ki-67 e do BMI-1, comparando lesões displásicas com não displásicas. Casos de LB não displásica - LBND (n=28), LB displásica - LBD (n=33) foram selecionados a partir de prontuários de pacientes e comparados com mucosa clinicamente normal - MN (n=9), hiperplasia inflamatória - HI (n=17) e carcinoma espinocelular - CEC (n=19). Os diagnósticos histopatológicos foram confirmados a partir da revisão de cortes histológicos corados por hematoxilina e eosina. Adicionalmente, cortes histológicos foram submetidos à técnica imunoistoquímica para avaliação de Ki-67 e BMI-1. Para a quantificação foi considerado o percentual de células positivas por 1000 células para o CEC e 1500 células para os demais grupos. O percentual de imunomarcação de Ki-67 e de BMI-1, quando avaliadas todas as camadas epiteliais em conjunto, foi mais alto no CEC quando comparado aos demais grupos (Kruskal-Wallis, p<0.05). A expressão de Ki-67 foi maior em LBND, LBD e HI quando comparada com MN (Kruskal-Wallis, p<0.05). Além disso, a imunomarcação de BMI-1 foi maior em LBD quando comparada com MN, quando analisadas todas as camadas em conjunto (Kruskal-Wallis, p<0.05). A partir da avaliação das camadas epiteliais separadamente, observou-se aumento da expressão de BMI-1 na camada parabasal e suprabasal em LBND quando comparada com MN. Houve correlação positiva entre Ki-67 e BMI-1 (Correlação de Spearman, R=0.37, p<0.05). Conclui-se que a proliferação e as alterações na transição epitélio-mesênquima são eventos relacionados e que estão presentes desde estágios precoces e se acentuam nos estágios mais tardios da carcinogênese. / Oral leukoplakia (OL) is potentially malignant disorder, with a risk of malignant transformation that ranges from 0.13% to 17.5%. Many biological markers have been used as an attempt to predict malignant transformation, but no reliable markers have been established so far. The Ki-67 is a nuclear non-histone regarded as reliable marker of proliferating cells .BMI-1 is a protein considered as an essential marker for maintenance of properties self-renewability and tumorigenicity of squamous cell carcinoma. The main aim this cross-sectional observational study was to evaluate cell proliferation and immortalization in oral leukoplakia, comparing non-dysplastic and dysplastic lesions. Cases of non-dysplastic – Non-dys OL (n=28), dysplastic – Dys OL (n=33) records were selected and compared with normal oral mucosa – NOM (n=9), inflammatory hyperplasia –IH (n=17), and oral squamous cell carcinoma - OSCC (n=19). The histopathological diagnosis was confirmed by the revision of Hematoxilin and Eosin stained slides. Additionally, histological sections were submitted to immunohistochemical technique for evaluation of Ki-67 and BMI-1. The labeling index was determined by counting the labeled nuclei of 1000 cells for OSCC cases and 1500 for the others comparison groups. Ki-67 and BMI-1 immunolabeling percentage were higher in OSCC in comparison of others groups when all epithelial layers were evaluated together (Kruskal-Wallis, p<0.05). Ki-67 immunolabeling increased in Non-dys OL, Dys OL and IH when compared to NOM (Kruskal-Wallis, p<0.05). Furthermore, BMI-1 immunolabeling was higher in Dys OL relation to NOM in the analysis of all epithelial layers together (Kruskal-Wallis, p<0.05). When the evaluation considered the epithelial layer separately, an increased BMI1 expression was observed in the parabasal and suprabasal layers of Non-dys OL when compared to NOM. A significant positive correlation was found between Ki-67 and BMI-1 (Spearman correlation coefficient, R=0.37, p<0.01). In conclusion, the present findings support that proliferation and changes toward epithelial-to-mesenchymal transition increase gradually since early stages of oral carcinogenesis.

O carcinoma epidermóide da mucosa oral (CEMO) é uma neoplasia maligna comum; no Brasil, são estimados, para 2016, 15.490 novos casos. A invasão óssea ocorre em casos avançados.; esta é classificada em erosiva e infiltrativa. Aparentemente, o processo de transição epitélio-mesenquimal, com o envolvimento da E-caderina, é implicado. Foi investigada a expressão de E-caderina, por meio da imunoistoquímica em 15 casos avançados de CEMO e avaliada sua correlação com as características clínicas e histológicas da invasão óssea. A imunoexpressão da E-caderina foi estudada nos 15 casos de CEMO com evidência histológica de invasão óssea. A maioria dos pacientes eram homens (10 pacientes) e apresentavam invasão em mandíbula (9 casos). A expressão de E-caderina foi negativa em CEMOs com invasão erosiva e positiva nos casos que apresentavam infiltração óssea. A expressão de E-caderina na invasão óssea sugere que a participação do fenômeno de transição epitélio-mesenquimal é um fator diretamente envolvido com o tipo de invasão óssea. / Oral squamous cell carcinoma (OSCC) is a common malignancy; in Brazil it is estimated, in 2016,15.490 new cases. Bone invasion occurs in advanced cases; it is classified in erosive and infiltrative patterns. Apparently, the epithelial-mesenchymal phenomenon, with important participation of E-cadherin is implicated. We investigated the expression of E-cadherin in advanced OSSC and correlated its expression with the clinical characteristics and histologic patterns of bone invasion. Immunoexpression of E-cadherin was studied in 15 cases of OSCC with histological evidence of bone invasion. Most patients were men (10 patients) and presented mandible invasion (9 cases). The expression of E-cadherin was negative in OSCC in erosive bone invasion and positive in the infiltrative bone invasion. E-cadherin expression in bone invasion suggests that participation of epithelial-mesenchymal phenomenon is dependent on the patterns of tumour bone invasion.

The overall aim of this project was first to investigate the genetic and epigenetic mechanisms underlying periodontal diseases and oral squamous cell carcinomas respectively, particularly in terms of competing endogenous RNA networks. Second, the aim was to explore the possible shared mechanisms between chronic periodontitis and oral squamous cell carcinoma regarding mRNAs, miRNAs, and signaling pathways. The results obtained from the first two publications may point to putative diagnostic or prognostic biomarkers and therapeutic targets for periodontal diseases and oral cancer respectively. The third and final publication aimed to reveal overlapping molecular mechanisms underlying both diseases that may bear translational value toward screening of the periodontitis patients with a high risk of oral cancer. In theory, if successful, such biomarkers based on screening may lead to the clinical application of tailored periodontal maintenance programs for high-risk individuals, including environmental factor mitigation. Such interceptive therapy could potentially reduce the risk of oral carcinogenesis.:1 Introduction ............................................................................................................................ 1 1.1 General aspects of periodontitis and oral squamous cell carcinoma.......................... 1 1.1.1 General aspects of periodontitis.......................................................................... 1 1.1.2 General aspects of oral squamous cell carcinoma .............................................. 2 1.1.3 The association of chronic periodontitis and oral squamous cell carcinoma...... 3 1.2 Genetic and epigenetic mechanisms of oral diseases ...................................................... 4 1.2.1 General aspects of various genetic and epigenetic factors........................................ 4 1.2.2 Genetic and epigenetic mechanisms of chronic periodontitis................................... 5 1.2.2.1 Alteration of mRNA gene expression in chronic periodontitis.......................... 5 1.2.2.2 Alteration of miRNA expression in chronic periodontitis ................................. 7 1.2.2.3 Alteration of lncRNA expression in chronic periodontitis................................. 7 1.2.2.4 Alteration of signaling pathway in chronic periodontitis................................... 8 1.2.3 Genetic and epigenetic mechanisms of oral squamous cell carcinoma .................... 9 1.2.3.1 Alteration of mRNA gene expression of oral squamous cell carcinoma ........... 9 1.2.3.2 Alteration of miRNA expression in oral squamous cell carcinoma................... 9 1.2.3.3 Alteration of lncRNA expression in oral squamous cell carcinoma ................ 10 1.2.3.4 Alteration of signaling pathway involved in oral squamous cell carcinoma ... 11 1.2.4 The shared genetic and epigenetic mechanisms between chronic periodontitis and oral squamous cell carcinoma.......................................................................................... 12 1.2.4.1 Genes as links between chronic periodontitis and oral squamous cell carcinoma ..................................................................................................................................... 12 1.2.4.2 miRNAs as links between chronic periodontitis and oral squamous cell carcinoma..................................................................................................................... 12 1.2.4.3 lncRNAs as links between chronic periodontitis and oral squamous cell carcinoma..................................................................................................................... 15 1.2.4.4 Signaling pathways as links between chronic periodontitis and oral squamous cell carcinoma .............................................................................................................. 15 1.3 Rationale of the current project ..................................................................................... 16 2 Objectives of the current project .......................................................................................... 18 2.1 General objective........................................................................................................... 18 2.2 Specific objectives......................................................................................................... 18 3 Publications .......................................................................................................................... 19 4 Summary of dissertation....................................................................................................... 49 5 References ............................................................................................................................ 53 6 Presentation of my own contribution ................................................................................... 63 6.1 Publication I................................................................................................................... 636.2 Publication II ................................................................................................................. 65 6.3 Publication III................................................................................................................ 67 7 Declaration of Authorship .................................................................................................... 69 8 Curriculum Vitae.................................................................................................................. 70 9 Acknowledgement................................................................................................................ 72

No description available.

Head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy associated with molecular heterogeneity, locoregional spread, resistance to therapy and relapse after initial treatment. Increasing evidence suggests that master developmental pathways with key roles in adult tissue homeostasis, including Hippo and Wnt/β-catenin signaling, are dysregulated in the initiation and progression of HNSCC. However, a comprehensive investigation into the crosstalk between these pathways is currently lacking, and may prove crucial to the discovery of novel targets for HNSCC therapy. More recent evidence points to the tumor microenvironment, mainly comprising cancer-associated fibroblasts (CAFs), as capable of influencing tumor cell behavior and promoting invasive HNSCC phenotypes. Nonetheless, current methods to screen for CAF markers in tumors are restricted to targeted immunostaining experiments with limited success and robustness across tissue types. The Cancer Genome Atlas network has generated multi-tiered molecular profiles for over 10,000 tumors spanning more than two dozen different cancer types, providing an unprecedented opportunity for the application and development of integrative methods aimed at the in silico interrogation of experimentally-derived signatures. These multi-omic profiles further enable one to link genomic anomalies, including somatic mutations and DNA copy number alterations, with phenotypic effects driven by pathogenic pathway activity. Effectively querying this vast amount of information to help elucidate subsets of functionally and clinically-relevant oncogenic drivers, however, remains an ongoing challenge. To address these issues, I first investigate the effects of oncogenic pathway perturbation in HNSCC using experimental models coupled with in vitro genome-wide transcriptional profiling. Next, I describe a new computational approach for the unbiased identification of CAF markers in HNSCC solely using bulk tumor RNA-sequencing information. Lastly, I have developed Candidate Driver Analysis or CaDrA - a statistical framework that allows one to query genetic and epigenetic alterations for candidate drivers of signature activity within a given disease context. Collectively, this work offers new perspectives on the molecular cues underlying HNSCC development, while simultaneously highlighting the power of integrative genomics methods capable of accelerating the discovery of novel targets for cancer diagnosis and therapy.

Background: The mechanisms through which immunosuppressed patients bear increased risk and worse survival in oral squamous cell carcinoma (OSCC) are unclear. Here, we used deep learning to investigate the genetic mechanisms underlying immunosuppression in the survival of OSCC patients, especially from the aspect of various survival-related subtypes. Materials and methods: OSCC samples data were obtained from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and OSCCrelated genetic datasets with survival data in the National Center for Biotechnology Information (NCBI). Immunosuppression genes (ISGs) were obtained from the HisgAtlas and DisGeNET databases. Survival analyses were performed to identify the ISGs with significant prognostic values in OSCC. A deep learning (DL)-based model was established for robustly differentiating the survival subpopulations of OSCC samples. In order to understand the characteristics of the different survival-risk subtypes of OSCC samples, differential expression analysis and functional enrichment analysis were performed. Results: A total of 317 OSCC samples were divided into one inferring cohort (TCGA) and four confirmation cohorts (ICGC set, GSE41613, GSE42743, and GSE75538). Eleven ISGs (i.e., BGLAP, CALCA, CTLA4, CXCL8, FGFR3, HPRT1, IL22, ORMDL3, TLR3, SPHK1, and INHBB) showed prognostic value in OSCC. The DL-based model provided two optimal subgroups of TCGA-OSCC samples with significant differences (p = 4.91E-22) and good model fitness [concordance index (C-index) = 0.77]. The DL model was validated by using four external confirmation cohorts: ICGC cohort (n = 40, C-index = 0.39), GSE41613 dataset (n = 97, C-index = 0.86), GSE42743 dataset (n = 71, C-index = 0.87), and GSE75538 dataset (n = 14, C-index = 0.48). Importantly, subtype Sub1 demonstrated a lower probability of survival and thus a more aggressive nature compared with subtype Sub2. ISGs in subtype Sub1 were enriched in the tumorinfiltrating immune cells-related pathways and cancer progression-related pathways, while those in subtype Sub2 were enriched in the metabolism-related pathways. Conclusion: The two survival subtypes of OSCC identified by deep learning can benefit clinical practitioners to divide immunocompromised patients with oral cancer into two subpopulations and give them target drugs and thus might be helpful for improving the survival of these patients and providing novel therapeutic strategies in the precision medicine area.