The Transcription Factor Twist1 Has a Significant Role in Mycosis Fungoides (MF) Cell Biology: An RNA Sequencing Study of 40 MF Cases

SIMPLE SUMMARY: Mycosis fungoides (MF) is the most common variety of cutaneous T-cell lymphoma. Our previous studies showed that the epithelial–mesenchymal transition (EMT) transcription factors (TFs) Twist1 and Zeb1 have prognostic value in MF. The main objective of the present study was to gain better knowledge about the biological mechanisms behind this phenomenon. The RNA of 40 skin tumor biopsies (from 40 patients) was sequenced and analyzed. Twist1 protein expression seemed to classify MF cases into different groups based on their global RNA expression. Additionally, high Twist1 protein expression was associated with several genes and pathways known to have roles in aggressive tumor biology. For Zeb1, similar results were not found. Our results suggest Twist1 to be a central transcription factor and pathway regulator in the disease progression of MF. Twist1 might be an interesting object for developing targeted therapies for MF. ABSTRACT: The purpose of this RNA sequencing study was to investigate the biological mechanism underlying how the transcription factors (TFs) Twist1 and Zeb1 influence the prognosis of mycosis fungoides (MF). We used laser-captured microdissection to dissect malignant T-cells obtained from 40 skin biopsies from 40 MF patients with stage I–IV disease. Immunohistochemistry (IHC) was used to determinate the protein expression levels of Twist1 and Zeb1. Based on RNA sequencing, principal component analysis (PCA), differential expression (DE) analysis, ingenuity pathway analysis (IPA), and hub gene analysis were performed between the high and low Twist1 IHC expression cases. The DNA from 28 samples was used to analyze the TWIST1 promoter methylation level. In the PCA, Twist1 IHC expression seemed to classify cases into different groups. The DE analysis yielded 321 significant genes. In the IPA, 228 significant upstream regulators and 177 significant master regulators/causal networks were identified. In the hub gene analysis, 28 hub genes were found. The methylation level of TWIST1 promoter regions did not correlate with Twist1 protein expression. Zeb1 protein expression did not show any major correlation with global RNA expression in the PCA. Many of the observed genes and pathways associated with high Twist1 expression are known to be involved in immunoregulation, lymphocyte differentiation, and aggressive tumor biology. In conclusion, Twist1 might be an important regulator in the disease progression of MF.