Models for predicting stage in head and neck squamous cell carcinoma using proteomic data

Head and neck squamous cell carcinoma (HNSCC) that is detected at an advanced stage is associated with much worse patient outcomes than if detected at early stages. This study uses reverse phase protein array (RPPA) data to build predictive models that discriminate between early and advanced stage HNSCC. Individual and ensemble binary classifiers, using filter-based and wrapper-based feature selection, are used to build several models which achieve moderate MCC and AUC values. This study identifies informative protein feature sets which may contribute to an increased understanding of the molecular basis of HNSCC.

Models for Predicting Stage in Head and Neck Squamous Cell Carcinoma Using Proteomic and Transcriptomic Data

Late diagnosis is one of the reasons that head and neck squamous cell carcinoma (HNSCC) patients experience relative five-year survival rates ranging from 40%-66%. The molecular-level differences between early and advanced stage HNSCC may provide insight into therapeutic targets and strategies. Previous bioinformatics studies have shown mixed or limited results in identifying gene and protein markers and in developing models for discriminating between early and advanced stage HNSCC. Thus, we have investigated models for HNSCC stage prediction using RNAseq and reverse phase protein array data from The Cancer Genome Atlas and The Cancer Proteome Atlas. We systematically assessed individual and ensemble binary classifiers, using filter and wrapper feature selection methods, to develop several well-performing models. In particular, integrated models harnessing both data types consistently resulted in better performance. This study identifies informative protein and gene feature sets which may increase understanding of HNSCC progression.

Nutrition and Cancer Prevention

Cancer cells invade surrounding tissues and metastasize to distant sites. Diet high in fat is a strong link to, and perhaps causes, a high incidence of tumours. Trans-fatty acid might impair the function and it could be involved in the development of cancer. Cholesterol is also strongly suspected to be involved in the development of tumours, therefore it is important for everyone to eat well, especially for people with cancer to prevent the body tissues from breaking down and helping to rebuild the normal tissue that may have been affected by the treatments. Factors secreted by adipocytes and macrophages such as TNF-alpha and other inflammatory proteins are involved in inflammation in cancer. In addition, MCSF which up-regulates adipocyte tissue is also important for the stimulation of fat cell proliferation and is expressed by human adipocytes. Many cytokines, such as IL-1, IL-6, IL-8, IL-32, IL-33 and MCP-1, are biomarkers for cancer and chronic diseases along with transcription factors NFkB and AP-1; these last two factors are important bioactive substances on the molecular mechanism of the control of genes which in turn affect cellular metabolism. In this paper we revisit the interrelationship between cancer and metabolism.