Despite various treatment attempts, the heterogenous group of soft tissue sarcomata (STS) with more than 100 subtypes still shows poor outcomes. Therefore, effective biomarkers for prognosis prediction and personalized treatment are of high importance. The Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase (PLOD) gene family, which is related to multiple cancer entities, consists of three members which encode important enzymes for the formation of connective tissue. The relation to STS, however, has not yet been explored. In this study, data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases were used to analyze the role of PLOD1–3 in STS. It was found that an overexpression of PLOD family members correlates with poor prognosis, which might be due to an increased infiltration of immune-related cells in the tumor microenvironment. In STS, the expression of PLOD genes could be a novel biomarker for prognosis and a personalized, more aggressive treatment in these patients.

Simple Summary Soft tissue sarcomas (STS) are a group of rare malignant tumors with high tissue heterogeneity and poor prognosis, and which are still without effective individualized immunotherapy approaches. In this study, four potential tumor antigens, six STS immune subtypes, and six functional gene modules were identified. The different immune subtypes have different molecular, cellular, and clinical characteristics. The superiority of mRNA vaccine therapies has been demonstrated during the current pandemic as well as in tumor vaccine studies, and the present study provides guidance for future mRNA vaccine development. Furthermore, in future individualized immunotherapies for STS, it is possible to select different immunotherapies based on the different immune subtypes identified in this study. In fact, the immune subtypes identified in this study explain, to some extent, the failure of immunotherapy for certain STS subtypes in previous clinical trials, and facilitate further understanding of strategy selection for the immunotherapy of STS. To our knowledge, this is the first study to address STS mRNA vaccine development and immunophenotyping. This study provides a theoretical framework for STS mRNA vaccine development and the selection of patients for vaccination and provides a reference for promoting individualized immunotherapy. Abstract Soft tissue sarcomas (STS) are a rare disease with high recurrence rates and poor prognosis. Missing therapy options together with the high heterogeneity of this tumor type gives impetus to the development of individualized treatment approaches. This study identifies potential tumor antigens for the development of mRNA tumor vaccines for STS and explores potential immune subtypes, stratifying patients for immunotherapy. RNA-sequencing data and clinical information were extracted from 189 STS samples from The Cancer Genome Atlas (TCGA) and microarray data were extracted from 103 STS samples from the Gene Expression Omnibus (GEO). Potential tumor antigens were identified using cBioportal, the Oncomine database, and prognostic analyses. Consensus clustering was used to define immune subtypes and immune gene modules, and graph learning-based dimensionality reduction analysis was used to depict the immune landscape. Finally, four potential tumor antigens were identified, each related to prognosis and antigen-presenting cell infiltration in STS: HLTF, ITGA10, PLCG1, and TTC3. Six immune subtypes and six gene modules were defined and validated in an independent cohort. The different immune subtypes have different molecular, cellular, and clinical characteristics. The immune landscape of STS reveals the immunity-related distribution of patients and intra-cluster heterogeneity of immune subtypes. This study provides a theoretical framework for STS mRNA vaccine development and the selection of patients for vaccination, and provides a reference for promoting individualized immunotherapy.

Melanoma is a highly malignant neoplasia with high rates of metastasis in humans and dogs. Regardless of being considered a highly immunogenic neoplasm, the function of the immune system is hampered by the expression of immune checkpoint molecules by the cancer cells. In contrast, soft tissue sarcomas are poorly immunogenic, as Tumor infiltrating Lymphocytes are lacking, or when present they are usually at the periphery of the tumor. Still, soft tissue sarcomas are considered immunosuppressed. Checkpoint molecules from the PD-axis are overexpressed in numerous human malignant neoplasia and have recently gained attention with a few reports in canine tumors. Immunotherapies against these checkpoint molecules have shown great efficacy in humans, but in order to determine translational approaches into canine patients, more research is needed. Here we determined the gene expression of Programed Death receptor-1, and its ligands PD-L1 and PD-L2 in canine tumors with two distinct immune profiles. Our results show that regardless of their immune profiles, melanoma versus soft tissue sarcoma, checkpoint molecules expression was higher in malignant tumors with a higher grade. Additionally, we evaluated the expression of these molecules in a set of patients that received histotripsy, which is a non-invasive and non-thermal ultrasound focused therapy that induces mechanical stress to the cells, leading to liquefactive necrosis. Here we reported a focal decrease of the expression of these checkpoint molecules in tissue sections obtain at the treatment interface, compared to those taken from untreated areas of the tumor. In addition, a positive relationship was noticed between the infiltration of CD3+ T lymphocytes and the expression of these checkpoint molecules in both canine melanoma, and soft tissue sarcoma. Our findings demonstrate that immunotherapies targeting these checkpoint molecules have a great potential for efficacy in canine neoplasia, along or combined with tumor ablation therapies that increased immune cell infiltration in poorly immunogenic neoplasia. / Doctor of Philosophy / Melanoma is a highly malignant tumor and very resistant to therapy for humans and dogs. At the same time, this neoplasia is usually highly infiltrated by cells from the immune system. However, this immune infiltration is often inhibited by molecules expressed by the melanoma cells. In contrast, soft tissue sarcoma is considered poorly immunogenic, as they often contain low levels of immune cell infiltrates but are still considered immune suppressed. In this study, we determined the expression of molecules that inhibit the effect of T lymphocytes, specifically Programed cell death receptor-1, PD-Ligand 1, and PD-Ligand 2 for these neoplasms with distinct immune profiles. We encounter that despite their immune profiles, the expression of these molecules is higher in malignant tumors. Additionally, we evaluated the expression of these molecules in a set of patients that received histotripsy, which is a non-invasive and non-thermal focused ultrasound therapy that induces mechanical stress to the cancerigenous cells, leading to its death (necrosis). Here we reported a focal decrease of the expression of these checkpoint molecules in tissue sections obtain at the treatment interface, compared to those taken from untreated areas of the tumor. In addition, a positive relationship was noticed between the infiltration of T lymphocytes and the expression of these checkpoint molecules in both canine melanoma, and soft tissue sarcoma. Our findings demonstrate that immunotherapies targeting these checkpoint molecules have a great potential for efficacy in canine neoplasms, along or combined with tumor ablation therapies that increased immune cell infiltration in poorly immunogenic neoplasia.

Soft tissue sarcoma (STS) patients with pulmonary metastases (PM) experience a significant decrease in 5-year survival rates, ranging from 15 % to 50 % compared to 81 % without metastases. Despite this clinical challenge, there is a lack of consensus regarding the optimal treatment approach for PM in STS. To address this, a convolutional neural network (CNN) was developed, utilising transfer learning from a MED3D base model with added custom layers. The CNN aimed to predict surgical treatment response and extract relevant radiological parameters via attribution maps from the CT images of PMs.  The CNN demonstrated promising performance with a balanced distribution of true positive and true negative predictions, giving precision, recall and F1-scores of 0.8. However, the limited size of the data set calls for caution in interpreting the statistical validity of these results.  The evaluation of the attribution maps revealed the classifier assigning significance to regions lacking anatomical relevance, except for one region – the dorsal lobe near a metastasis – showing lower blood vessel density. Nonetheless, no definitive pathological conclusions can be drawn from this observation currently.  In conclusion, this study presents a CNN-based approach for predicting surgical treatment response in STS patients with PMs. However, the small data set warrants further validation and exploration of clinical implications associated with the identified regions of significance.

Objective: Epithelioid sarcoma (ES) presents unique clinical features in comparison to other sarcoma subtypes. Data regarding the benefits of chemotherapy are very limited. Combination regimens using gemcitabine and docetaxel (Gem/Doce) have proven to be effective, especially in uterine and nonuterine leiomyosarcoma. Yet, there is no available data on the efficacy of Gem/Doce in ES. Methods: A retrospective analysis of the three participating institutions was performed. Twenty-eight patients with an ES diagnosis presented at one of the participating institutions between 1989 and 2012. Of this group, 17 patients received chemotherapy. Results: Patients’ median overall survival (OS) after the beginning of palliative chemotherapy was 21 months, and the 1-year OS was 87%. Twelve patients received Gem/Doce with a clinical benefit rate of 83%. The median progression-free survival (PFS) was 8 months for all patients receiving Gem/Doce. The best response was complete remission in 1 patient and partial remission in 6 patients. All 6 patients receiving Gem/Doce as a first-line treatment showed measurable responses with a median PFS of 9 months. Conclusions: In this retrospective study, Gem/Doce was an effective chemotherapeutic regimen for ES. Prospective studies are needed to better assess the effects of this combination drug therapy.

The tumor microenvironment (TME) comprising immune cells and stromal components, such as fibroblasts and vessels, emerged as one of the most significant predictors of patient survival in a variety of solid tumors. With T cells representing the major cellular effector cells of the adaptive immune system and B cells orchestrating the humoral immune response, both cell types acquire crucial roles in the antitumor immune response. Thus, a high abundance of tumor-infiltrating CD8+ T cells and B cells has been generally associated with longer survival, while immunosuppressive subsets such as regulatory T cells (Treg) and M2-polarized macrophages are frequently linked to poor prognosis. Besides the frequency, also the spatial organization emerged as a clinically relevant parameter. Hence, the formation of T and B cells in tertiary lymphoid structures (TLS) was found to favor improved clinical outcome of patients. It was further reported that besides the prognostic value, the baseline immune architecture harbors the ability to predict the response to immunotherapies such as immune checkpoint inhibitor treatment and even chemotherapy. In turn, standard cytotoxic treatment regimens like radio- and chemotherapy, as well as novel immunotherapeutic or targeted approaches, exhibit distinct effects on various immune cells. Depending on the tumor entity, therapy, and immune cell subsets, differing modulation of infiltrating immune cells after therapy was observed. While previous studies mainly investigated an altered abundance of T and B cells, changes in functional orientation and composition of lymphocyte populations are gaining increasing relevance. In this thesis, the aim was to uncover the phenotype, frequency, composition, spatial distribution, clinical significance, and therapeutic modulation of the T cell compartment in soft tissue sarcoma (STS), and B cell populations in pancreatic ductal adenocarcinoma (PDAC). Due to the low incidence and heterogeneous nature of STS, detailed analyses of distinct CD8+ and CD4+ T cell subsets are lacking. To assess the effect of multimodal treatment, comprising radiotherapy and locoregional hyperthermia with or without chemotherapy, on the immune architecture, the patient cohort included matched pre- and post-therapy tissue samples. By assessing both the peritumoral and intratumoral region, additional information about the spatial distribution of STS-infiltrating T cells was gained. In PDAC, the T cell compartment and its therapeutic modulation has been explored in detail recently, but equivalent insight into the B cell landscape is missing. Going beyond the abundance of pan B cells, the aim was to identify proliferating B and T cells, germinal center (GC) B cells, plasmablasts, and plasma cells to investigate their modulation by neoadjuvant chemo(radio)therapy (NeoTx). Further insight into the spatial composition was gained by analyzing different regions (intratumoral and peritumoral) and tissue compartments (epithelial, stromal, TLS). To achieve this, three novel multiplex immunohistochemistry panels were established enabling simultaneous staining of six markers plus DAPI. For CD4+ T helper (Th) cells, the master transcription factors for Th1 (T-box expressed in T cells), Th2 (GATA-binding protein 3), Th17 (retinoic acid receptor-related orphan receptor T), and Treg (Forkhead box protein 3) were included in addition to CD3 and the proliferation marker Ki67. The CD8+ T cell panel comprised the phenotypic marker CD8, the immune checkpoint molecules programmed cell death protein 1 and lymphocyte-activation gene 3 as well as the activation-associated molecules granzyme B and 4-1BB, in addition to Ki67. It was thus found that post-treatment STS samples displayed moderately reduced frequencies of both CD8+ and CD3+ T cells in comparison to the pretreatment biopsy. The Th cell landscape was dominated by Th2 cells, whose density was significantly reduced upon multimodal therapy and a moderate redistribution favoring Th1 and Th17 cells was observed. While high frequencies of CD3+ and CD8+ T cells in the posttreatment tissues were associated with significantly longer disease-free survival, these populations held no prognostic value in the biopsy obtained prior to treatment, suggesting a reshaping of the TME upon therapy. Furthermore, the spatial distribution, reflected by the ratio of intra- to peritumoral CD8+ T cells, emerged as an independent prognostic factor for the risk of recurrence. In PDAC, B cell subsets were identified by staining for CD3, CD20, Ki67, the transcription factor B cell lymphoma 6, and the plasma cell markers CD38 and CD138. While CD3+ T cells were unaffected, significantly lower frequencies of proliferating B cells, GC B cells, plasmablasts, and plasma cells were observed in the NeoTx group compared to patients undergoing primary resection (PR). Furthermore, neoadjuvant-treated patients exhibited a significantly lower abundance of TLS, which was validated in an independent cohort. These results indicate that NeoTx differentially affects distinct immune cell subsets, and that B cellmediated antitumor immunity may be inhibited by chemo(radio)therapy. Spatial analysis further revealed that plasma cell accumulations frequently localized close to TLS, being accompanied by C-X-C motif chemokine ligand 12-expressing fibroblasts. Furthermore, patients with TLS exhibited significantly higher plasma cell frequencies, suggesting that TLS can foster the generation of plasma cells whose migration is then guided by fibroblastic tracks. Lastly, a prognostic value of pan T and B cells was observed only in the PR group, while these populations provided no clinical significance in neoadjuvant-treated patients. However, proliferating Ki67+CD20+ B cells emerged as an independent prognostic factor for a lower risk of death in the NeoTx group, suggesting a restorative post-treatment TME in these patients. Altogether, this thesis provided novel insights into the TME of STS and PDAC and its therapeutic alteration. Spatial analyses further enabled an improved understanding of the immune architecture and potential cell-cell interactions within the TME. In addition, strong associations with patient survival highlight the enormous significance of the TME and may guide future therapy development. Although the results do not encourage a concomitant application of cytotoxic therapy regimens and immunotherapy, patients may benefit from sequential combination treatments. An enhanced understanding of the immunomodulatory effects of NeoTx is pivotal for overcoming the immunosuppressive TME of STS and PDAC by refining existing treatment regimens and developing novel therapy approaches in order to improve the long-term outcome of patients.

Objective: Soft tissue sarcomas (STS) and gastrointestinal stromal tumours (GIST) are a group of rare malignant tumours with a high and heterogenous disease burden. As evidence is scarce, we analysed the prevalence of increased emotional distress and identified distress‐associated factors in these patients. - Methods: The PROSa‐study (Burden and medical care of sarcoma) was conducted between 2017 and 2020 in 39 study centres. Cross‐sectional data from adult STS and GIST patients were analysed. Distress was measured with the Patient Health Questionnaire (PHQ‐4). The relation of socioeconomic and clinical factors with distress was explored in adjusted logistic regression models. - Results: Among 897 patients, 17% reported elevated anxiety and 19% reported depression. Unemployed patients (odds ratio [OR] 6.6; 95% CI 2.9–15.0), and those with a disability pension (OR 3.1; 95% CI 1.9–5.0) were more likely to experience distress compared to employed patients. Also, patients with a disability pass had higher odds of increased distress than those without (OR 1.8; 95% CI 1.2–2.7). Lowest distress was observed in patients 2 to <5 years and ≥5 years after diagnosis (comparison: <6 months) (OR 0.4; 95% CI 0.2–0.6) and (0.3; 95% CI 0.2–0.6). Patients with thoracic STS (vs. lower limbs) had twice the odds to experience distress(OR2.0;95%CI 1.1–3.6). Distress was seen almost twice as often in patients with progressive disease (vs. complete remission) (OR 1.7; 95% CI 1.1–2.8). - Conclusion: The prevalence of elevated distress in STS and GIST patients is high. In unemployed patients, in those with a disability pension and in newly diagnosed patients a noticeable increase was observed. Clinicians should be aware of these factors and consider the social aspects of the disease.