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Molecular Subtypes of Oral Squamous Cell Carcinoma Based on Immunosuppression Genes Using a Deep Learning Approach.

ABSTRACT: 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 OSCC-related 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 tumor-infiltrating 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.

SUBMITTER: Li S

PROVIDER: S-EPMC8375681 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundPeriodontitis is a chronic immuno-inflammatory disease characterized by inflammatory destruction of tooth-supporting tissues. Its pathogenesis involves a dysregulated local host immune response that is ineffective in combating microbial challenges. An integrated investigation of genes involved in mediating immune response suppression in periodontitis, based on multiple studies, can reveal genes pivotal to periodontitis pathogenesis. Here, we aimed to apply a deep learning (DL)-based autoencoder (AE) for predicting immunosuppression genes involved in periodontitis by integrating multiples omics datasets.MethodsTwo periodontitis-related GEO transcriptomic datasets (GSE16134 and GSE10334) and immunosuppression genes identified from DisGeNET and HisgAtlas were included. Immunosuppression genes related to periodontitis in GSE16134 were used as input to build an AE, to identify the top disease-representative immunosuppression gene features. Using K-means clustering and ANOVA, immune subtype labels were assigned to disease samples and a support vector machine (SVM) classifier was constructed. This classifier was applied to a validation set (Immunosuppression genes related to periodontitis in GSE10334) for predicting sample labels, evaluating the accuracy of the AE. In addition, differentially expressed genes (DEGs), signaling pathways, and transcription factors (TFs) involved in immunosuppression and periodontitis were determined with an array of bioinformatics analysis. Shared DEGs common to DEGs differentiating periodontitis from controls and those differentiating the immune subtypes were considered as the key immunosuppression genes in periodontitis.ResultsWe produced representative molecular features and identified two immune subtypes in periodontitis using an AE. Two subtypes were also predicted in the validation set with the SVM classifier. Three "master" immunosuppression genes, PECAM1, FCGR3A, and FOS were identified as candidates pivotal to immunosuppressive mechanisms in periodontitis. Six transcription factors, NFKB1, FOS, JUN, HIF1A, STAT5B, and STAT4, were identified as central to the TFs-DEGs interaction network. The two immune subtypes were distinct in terms of their regulating pathways.ConclusionThis study applied a DL-based AE for the first time to identify immune subtypes of periodontitis and pivotal immunosuppression genes that discriminated periodontitis from the healthy. Key signaling pathways and TF-target DEGs that putatively mediate immune suppression in periodontitis were identified. PECAM1, FCGR3A, and FOS emerged as high-value biomarkers and candidate therapeutic targets for periodontitis.

Project description:BackgroundThe overall prognosis of oral cancer remains poor because over half of patients are diagnosed at advanced-stages. Previously reported screening and earlier detection methods for oral cancer still largely rely on health workers' clinical experience and as yet there is no established method. We aimed to develop a rapid, non-invasive, cost-effective, and easy-to-use deep learning approach for identifying oral cavity squamous cell carcinoma (OCSCC) patients using photographic images.MethodsWe developed an automated deep learning algorithm using cascaded convolutional neural networks to detect OCSCC from photographic images. We included all biopsy-proven OCSCC photographs and normal controls of 44,409 clinical images collected from 11 hospitals around China between April 12, 2006, and Nov 25, 2019. We trained the algorithm on a randomly selected part of this dataset (development dataset) and used the rest for testing (internal validation dataset). Additionally, we curated an external validation dataset comprising clinical photographs from six representative journals in the field of dentistry and oral surgery. We also compared the performance of the algorithm with that of seven oral cancer specialists on a clinical validation dataset. We used the pathological reports as gold standard for OCSCC identification. We evaluated the algorithm performance on the internal, external, and clinical validation datasets by calculating the area under the receiver operating characteristic curves (AUCs), accuracy, sensitivity, and specificity with two-sided 95% CIs.Findings1469 intraoral photographic images were used to validate our approach. The deep learning algorithm achieved an AUC of 0·983 (95% CI 0·973-0·991), sensitivity of 94·9% (0·915-0·978), and specificity of 88·7% (0·845-0·926) on the internal validation dataset (n = 401), and an AUC of 0·935 (0·910-0·957), sensitivity of 89·6% (0·847-0·942) and specificity of 80·6% (0·757-0·853) on the external validation dataset (n = 402). For a secondary analysis on the internal validation dataset, the algorithm presented an AUC of 0·995 (0·988-0·999), sensitivity of 97·4% (0·932-1·000) and specificity of 93·5% (0·882-0·979) in detecting early-stage OCSCC. On the clinical validation dataset (n = 666), our algorithm achieved comparable performance to that of the average oral cancer expert in terms of accuracy (92·3% [0·902-0·943] vs 92.4% [0·912-0·936]), sensitivity (91·0% [0·879-0·941] vs 91·7% [0·898-0·934]), and specificity (93·5% [0·909-0·960] vs 93·1% [0·914-0·948]). The algorithm also achieved significantly better performance than that of the average medical student (accuracy of 87·0% [0·855-0·885], sensitivity of 83·1% [0·807-0·854], and specificity of 90·7% [0·889-0·924]) and the average non-medical student (accuracy of 77·2% [0·757-0·787], sensitivity of 76·6% [0·743-0·788], and specificity of 77·9% [0·759-0·797]).InterpretationAutomated detection of OCSCC by deep-learning-powered algorithm is a rapid, non-invasive, low-cost, and convenient method, which yielded comparable performance to that of human specialists and has the potential to be used as a clinical tool for fast screening, earlier detection, and therapeutic efficacy assessment of the cancer.

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Molecular Subtypes of Oral Squamous Cell Carcinoma Based on Immunosuppression Genes Using a Deep Learning Approach.

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