Background and purpose: Contouring oropharyngeal primary tumors in radiotherapy is currently done manually which is time-consuming. Autocontouring techniques based on deep learning methods are a... Show moreBackground and purpose: Contouring oropharyngeal primary tumors in radiotherapy is currently done manually which is time-consuming. Autocontouring techniques based on deep learning methods are a desirable alternative, but these methods can render suboptimal results when the structure to segment is considerably smaller than the rest of the image. The purpose of this work was to investigate different strategies to tackle the class imbalance problem in this tumor site.Materials and methods: A cohort of 230 oropharyngeal cancer patients treated between 2010 and 2018 was retrospectively collected. The following magnetic resonance imaging (MRI) sequences were available: T1 -weighted, T2-weighted, 3D T1-weighted after gadolinium injection. Two strategies to tackle the class imbal-ance problem were studied: training with different loss functions (namely: Dice loss, Generalized Dice loss, Focal Tversky loss and Unified Focal loss) and implementing a two-stage approach (i.e. splitting the task in detection and segmentation). Segmentation performance was measured with Sorensen-Dice coefficient (Dice), 95th Hausdorff distance (HD) and Mean Surface Distance (MSD). Results: The network trained with the Generalized Dice Loss yielded a median Dice of 0.54, median 95th HD of 10.6 mm and median MSD of 2.4 mm but no significant differences were observed among the different loss functions (p-value > 0.7). The two-stage approach resulted in a median Dice of 0.64, median HD of 8.7 mm and median MSD of 2.1 mm, significantly outperforming the end-to-end 3D U-Net (p-value < 0.05).Conclusion: No significant differences were observed when training with different loss functions. The two-stage approach outperformed the end-to-end 3D U-Net. Show less
HPV has evolved mechanisms to resist immune attack. I showed that HPV impaired necroptosis induced by IFNγ and TNFα by down-regulation of RIPK3 expression. Methyltransferase inhibitor DZNeP... Show moreHPV has evolved mechanisms to resist immune attack. I showed that HPV impaired necroptosis induced by IFNγ and TNFα by down-regulation of RIPK3 expression. Methyltransferase inhibitor DZNeP restored the expression of RIPK3 in HPV+ keratinocytes, and increased the necroptosis in HPV+ keratinocytes. Simultaneously, hrHPV effectively inhibited IFNγ/TNFα-mediated arrest of cell growth by down-regulating IFITM1. Then I studied HPV associated oropharyngeal squamous cell cancer (OPSCC). The OPSCC infiltrating HPV specific CD4+ Tcells produce cytokines such as IFNγ and TNFα. I found that HPV16-positive tumor cells lacked expression of RIPK3, which were not sensitive to the necroptosis induced by IFNγ /TNFα. I also showed that a combination of IFNγ and TNFα with cisplatin synergized in killing tumor cells. Last but not least I showed that combination of the clinically applied EGFR inhibitor Cetuximab and IFNγ/TNFα increased gene expression of multiple cytokines, including CXCL9, CXCL10 and CCL5, which may attract more lymphocytes to the tumor site. By using the inhibitors of the targets downstream of EGFR, I found that JNK and MEK1 played major role in mediating the suppression of CCL5, CXCL9 and CXCL10 expression. Show less
Arts, T.; Breedveld, S.; Jong, M.A. de; Astreinidou, E.; Tans, L.; Keskin-Cambay, F.; ... ; Hoogeman, M.S. 2017
In this thesis, several aspects and cellular players involved in the immune response to (HPV-induced) tumors were investigated. In chapter 2 a detailed analysis of HPV-specific immunity in a large... Show moreIn this thesis, several aspects and cellular players involved in the immune response to (HPV-induced) tumors were investigated. In chapter 2 a detailed analysis of HPV-specific immunity in a large group of patients with HPV-induced cervical cancer (CxCa) in relation to HLA-types and prognostic factors was performed. In 30% of the tested patients, circulating HPV specific T cells were found, most often in patients with deeply infiltrating tumors. In this group, patients with HPV specific proliferative immunity displayed better disease free survival. It was shown earlier by Piersma et al [69] that only in 30% of TIL populations, HPV specific T cells were found. In chapter 3 an in depth analysis of the breadth and type of HPV specific T-cell populations in tumor infiltrating T cell (TIL) cultures or LN cells from HPV 16 or 18 positive CxCa patients was performed. We found that if patients displayed a HPV-specific T cell response, this was surprisingly broad. Despite recognition, a number of cells did not produce type 1 cytokines and therefore we tested what TLR-agonist was able to support cytokine induction by these T cells. In chapter 4 we asked the question whether HPV-specific T cells play a role in HPV-induced HNSCC. We hypothesize that HPV-induced tumors are more immunogenic and stimulate strong T-cell reactivity to the viral oncoproteins in contrast to HPV-negative tumors. We set up a pilot study to investigate whether HPV is present in HNSCC in the Dutch patient population and at which anatomical site. Accordingly, blood and tumor infiltrating T cells were analyzed for the presence of functional HPV specific T cells. The lack of T cell responses in CxCa patients and the __poised__ function of tumor-antigen specific T cells could be a lack of proper priming by DC. Therefore we investigated in chapter 5A the effects of CxCa produced soluble factors on the differentiation of antigen presenting cells (APC). Several tumor cell lines hampered DC differentiation or even skewed monocyte differentiation into tolerogenic tumor promoting M2 macrophages. We identified the factors responsible for this and investigated the outcome of the interaction of HPV specific T-cell clones with these macrophages. Since patients with advanced or recurrent disease are treated with platinum based chemotherapy we investigated the immune-modulating effect of this therapy on tumor cells, tumor-modulated APC and subsequent interaction with T cells. This ongoing work is summarized in chapter 5B. Therapeutic vaccination is being developed for treatment of chronic infections and cancer, and aims to generate protective T-cell immunity. Although some clinical successes have been reported, particularly in the field of cancer vaccination, there is still much to be gained in terms of efficacy [91,92]. Especially the adjuvant used and the route of administration of vaccines are critical factors that determine the type and memory of the resulting T-cell response. Intradermal vaccination is an attractive method for diseases in the skin such as HPV induced tumors and melanomas since the induced T cells get skin-homing instructions. In chapter 5 we showed already that highly pure DC can become activated by the addition of several different TLR agonists in vitro. To assess the effect of these TLR agonists on the APC present in the dermis, a human skin-explant model was used to analyze the phenotype and function of the APC migrating out the skin upon TLR-injection. These results are described in chapter 6. Surprisingly, only few TLR-agonists turned out to induce activation of the migrating cells. The current treatment of patients with advanced colorectal cancer consists of chemotherapy together with the MAb bevacizumab that blocks soluble VEGF. The addition of a second antibody that targets tumor expressed EGFR (cetuximab) to this treatment did not result in the expected disease free survival benefit in a large randomized phase III study (CAIROII). Analysis of gene polymorphisms in the Fc__Receptors revealed that patients with the high affinity FCGR3A polymorphism did significantly worse upon addition of cetuximab to the standard treatment. As colon cancers are generally infiltrated with macrophages we tested the hypothesis that membrane bound antibodies could activate tumor promoting M2 macrophages and that this would happen more efficiently in patients with high affinity FCGRIIIA in chapter 7. In chapter 8 the work of this thesis is discussed in light of recent literature. Show less
