Immune checkpoint inhibitors targeting the programmed cell death protein 1 (PD-1)/programmed cell death protein ligand 1 (PD-L1) axis have been remarkably successful in inducing tumor remissions in... Show moreImmune checkpoint inhibitors targeting the programmed cell death protein 1 (PD-1)/programmed cell death protein ligand 1 (PD-L1) axis have been remarkably successful in inducing tumor remissions in several human cancers, yet a substantial number of patients do not respond to treatment. Because this may be partially due to the mechanisms giving rise to high PD-L1 expression within a patient, it is highly relevant to fully understand these mechanisms. In this study, we conduct a bioinformatic analysis to quantify the relative importance of transcription factor (TF) activity, microRNAs (miRNAs) and mutations in determining PD-L1 (CD274) expression at mRNA level based on data from the Cancer Genome Atlas. To predict individual CD274 levels based on TF activity, we developed multiple linear regression models by taking the expression of target genes of the TFs known to directly target PD-L1 as independent variables. This analysis showed that IRF1, STAT1, NFKB and BRD4 are the most important regulators of CD274 expression, explaining its mRNA levels in 90-98% of the patients. Because the remaining patients had high CD274 levels independent of these TFs, we next investigated whether mutations associated with increased CD274 mRNA levels, and low levels of miRNAs associated with negative regulation of CD274 expression could cause high CD274 levels in these patients. We found that mutations or miRNAs offered an explanation for high CD274 levels in 81-100% of the underpredicted patients. Thus, CD274 expression is largely explained by TF activity, and the remaining unexplained cases can largely be explained by mutations or low miRNA abundance. Show less
This thesis describes i) the function of an alternatively spliced coagulation factor in hemostasis, ii) the contribution of coagulation factors on cancer progression, and iii) expands our view... Show moreThis thesis describes i) the function of an alternatively spliced coagulation factor in hemostasis, ii) the contribution of coagulation factors on cancer progression, and iii) expands our view on cancer-associated thrombosis. Inhibition of Tissue Factor (TF) signaling with the antibody (Mab-10H10) resulted in decreased tumor initiating capacity and metastasis in a triple negative breast cancer (TNBC) cell line. Since this is a tumor type that is difficult to treat, and has high relapse-rates, it would be of interest to target TF signaling. Dual treatment of TNBC with conventional chemotherapy and Mab-10H10 could result in a positive treatment strategy as both highly proliferative and cancer stem cells are targeted. Furthermore, we provided a proof-of-principle study to search for novel biomarkers in patients with cancer-associated thrombosis in an unbiased manner. Up till now it is challenging to accurately predict those cancer patients with elevated risk of thrombosis. Furthermore, patients with cancer-associated thrombosis have poorer survival. Expansion of this study to validation cohorts and other tumor types will give insights in the underlying molecular mechanism of cancer-associated thrombosis. Eventually, this will aid a better prediction model to select those cancer patients with high risk of thrombosis and those who might benefit from thromboprophylaxis. Show less
Wijdeven, R.H.; Pang, B.X.; Assaraf, Y.G.; Neefjes, J. 2016
