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Simple Summary: The tyrosine kinase TYK2 was assessed in this study using digital image analysis of archived formalin-fixed paraffin-embedded blocks. The immunohistochemical expression of TYK2 was significantly weaker in cancer than in normal control tissues, and its high predictive value allowed its use as a biomarker in the diagnosis of CRC. The obtained results were additionally verified by other molecular methods, which confirmed the presence of a higher protein level of the kinase TYK2 and a higher TYK2 fluorescence intensity in normal colonic mucosa than in CRC tissue. Independently assessed TYK2 immunoreactivity in fresh colonic biopsies from CRC and ulcerative colitis (UC) patients showed that the kinase distribution was greater in UC than in cancer. Background/Objectives: The aim of this study was to examine the expression of TYK2 in colorectal cancer (CRC) and to determine the potential diagnostic and prognostic significance of this kinase. Methods: Digital image analysis was performed to assess immunohistochemical TYK2 reactivity. Results: There were significant differences for all positive pixels between CRC and normal colonic mucosa, with higher TYK2 expression levels observed in surgical margins than in adenocarcinomas (p = 0.0004). Paired t tests showed elevated immunoreactivity for overall TYK2 expression in matched pairs of CRC with adjacent surgical margins (p < 0.0001). Higher percentages of weak (p < 0.0001) and strong pixels (p = 0.0260) were detected in normal colonic mucosa than in cancer tissues. To distinguish cancer from normal intestinal mucosa, the following cutoffs for the TYK2 immune score were found: 29.5% for all cases and 31% for matched pairs. Tumor budding (Bd) was negatively correlated with the percentage of strong pixels for TYK2 (ρ = −0.270, p = 0.0096). The percentage of strong pixels was significantly elevated for the T parameter (p = 0.0428). There was a positive correlation between the number of involved lymph nodes and weak pixels (ρ = 0.239, p = 0.0242). Immunofluorescence staining showed significantly higher signal intensities in colonic mucosa than in CRC. The protein level of TYK2 was significantly higher in controls than in cancer tissues. TEM imaging showed lower levels of TYK2 in cancer than in ulcerative colitis. Conclusions: TYK2 protein expression may bring diagnostic value in patients diagnosed with CRC. [ABSTRACT FROM AUTHOR]

Selection of optimal control samples is crucial in expression profiling tumor samples. To address this issue, we performed microarray expression profiling of control samples routinely used in head and neck squamous cell carcinoma studies: human bronchial and tracheal epithelial cells, squamous cells obtained by laser uvulopalatoplasty and tumor surgical margins. We compared the results using multidimensional scaling and hierarchical clustering versus tumor samples and laryngeal squamous cell carcinoma cell lines. A general observation from our study is that the analyzed cohorts separated according to two dominant factors: "malignancy", which separated controls from malignant samples and "cell culture-microenvironment" which reflected the differences between cultured and non-cultured samples. In conclusion, we advocate the use of cultured epithelial cells as controls for gene expression profiling of cancer cell lines. In contrast, comparisons of gene expression profiles of cancer cell lines versus surgical margin controls should be treated with caution, whereas fresh frozen surgical margins seem to be appropriate for gene expression profiling of tumor samples. [ABSTRACT FROM AUTHOR]