Introduction: Intraperitoneal tumor seeding is a common form of recurrence after surgery for GI tumours. Early diagnosis and treatment may influence the course of disease. Hypothesis and objectives of the work The finding of free tumor cells and / or elevation of tumor markers in peritoneal fluid predicts intraperitoneal tumor recurrence. The results of these tests can be used to indicate HIPEC. Aim of this work is to determine the sensitivity and specificity of cytology and tumor markers levels and importance of these tests for early diagnosis and prognosis of recurrence. Another objective was to confirm the applicability of RT PCR for identification of free tumor cells. Patients and methods . Materials are sourced both during initial surgery (220 patients) and by the dispensary controls (25 patients). The peritoneal fluid was examined cytologically and biochemically too. 50 samples was exemined by RT PCR. Results Elevation of tumor markers or finding of free intraperitoneal tumor cells predicts recurrence. The prognosis of these patients corresponds to stage IV TNM classification, regardless of other parameters TNM. Low sensitivity of these tests (34% for cytology, 53% for tumor markers) does not allow its use as an indicator of HIPEC. Due to degradation of RNA we did not confirm the value of RT...

Abstract Cancers of the alimentary tract include many common cancer types, some of which have well-established treatment protocols and relatively good prognosis, such as colorectal cancer, and others, which have generally very poor prognosis. The gastrointestinal canal is colonized by a multitude of bacteria, the effects of which are currently poorly understood. Toll-like receptor 9 (TLR9) in cells of the alimentary tract recognizes the bacterial DNA-fragments and regulates immune functions in the host and the cancer. This thesis examines the function and prognostic significance of Toll-like receptor 9 in oral and esophageal squamous cell carcinoma as well as in esophageal, gastric and colorectal adenocarcinoma. The studies were made using tissue samples from patient cohorts and various cell culture techniques. Our data indicate that high expression of Toll-like receptor 9 in cancer cells associates with metastatic properties in oral and esophageal cancers and poor prognosis in esophageal adenocarcinoma and oral squamous cell carcinoma. Cell culture studies further suggest that TLR9 is functional in alimentary tract cancers and mediates cellular invasion when activated. Based on the results, TLR9 is active in alimentary tract cancers and its expression is related to poor cancer prognosis. Thus, TLR9 may represent a novel therapeutic target in alimentary tract cancers and might provide a link between bacteria and oral and gastrointestinal cancer. / Tiivistelmä Ruuansulatuskanavan syöpiin lukeutuu useita yleisiä syöpätyyppejä, kuten kohtalaisen hyväennusteinen paksusuolen syöpä, jonka hoitokäytäntö on vakiintunut. Toisissa ruuansulatuskanavan syövissä puolestaan ennuste on hyvin huono. Mahasuolikanavaa asuttavat moninaiset bakteerikannat, joiden vaikutuksia ymmärretään vielä kehnosti. Tollinkaltainen reseptori 9 (TLR9) tunnistaa näiden bakteerien DNA-rakenteita ja vaikuttaa yksilön ja syövän immuunivasteeseen. Tämä väitöstutkimus selvittää TLR9:n toimintaa ja ennustevaikutusta suun ja ruokatorven levyepiteelisyövissä, sekä ruokatorven, mahalaukun ja paksusuolen adenokarsinoomassa. Tutkimus toteutettiin käyttäen syöpäpotilaiden kudosnäytteitä sekä soluviljelytekniikoita. Tuloksemme osoittavat, että TLR9:n lisääntynyt ilmentyminen syöpäsoluissa yhdistyy metastasointiin suu- ja ruokatorvisyövissä, sekä korkeaan kuolleisuuteen suun levyepiteelisyövässä ja ruokatorven adenokarsinoomassa. Soluviljelykokeidemme tuloksiin nojaten TLR9 toimii ruuansulatuskanavan syövissä ja sen aktivaatio saa aikaan solujen invasoitumisen. Tutkimustuloksiimme vedoten TLR9 on aktiivinen ja toimiva ruuansulatuskanavan syövissä ja sen ilmentyminen liittyy huonoon ennusteeseen. TLR9 saattaa osoittautua uudeksi syöpähoitojen kohteeksi tai yhdistäväksi tekijäksi syövän ja bakteerien välillä ruuansulatuskanavan syövissä tulevaisuudessa.

Objective: We aimed to assess the prognostic value of circulating tumor cells (CTC) in patients with advanced gastric and gastroesophageal adenocarcinomas. Methods: The presence of CTC was evaluated in 62 patients with advanced gastric and gastroesophageal adenocarcinomas before systemic therapy and at follow-up through immunomagnetic enrichment for mucin 1- and epithelial cell adhesion molecule (EpCAM)-positive cells, followed by real-time RT-PCR of the tumor-associated genes KRT19 , MUC1 , EPCAM , CEACAM5 and BIRC5 . Results: The patients were stratified into groups according to CTC detection (CTC negative: with all marker genes negative; CTC positive: with at least 1 of the marker genes positive). Patients who were CTC positive at baseline had a significantly shorter median progression-free survival (PFS; 3.5 months, 95% CI: 2.9–4.2) and overall survival (OS; 5.8 months, 95% CI: 4.5–7.0) than patients lacking CTC (PFS 10.7 months, 95% CI: 6.9–14.4, p < 0.001; OS 13.3 months, 95% CI: 8.0–18.6, p = 0.003). Alterations in the marker profile during the course of chemotherapy were not predictive of clinical outcome or response to therapy. Yet, a favorable clinical response depended significantly on CTC negativity (p = 0.03). Conclusion: Our data suggest that the presence of CTC is a major predictor of outcome in patients with gastric and gastroesophageal malignancies.

Utilisation of New Biomarkers for the Optimalization of Diagnostics and Therapy of Tumors of the Gastrointestinal Tract Introduction: Tumor markers are standard diagnostic tools. They are mainly used to monitor the course of the disease and to check the efficacy of the treatment. It is important to observe dynamics. Changing the level of the biomarker can prevent clinical manifestation and lead to early diagnosis of relapse, which in turn means improving the quality of life, including prolonging survival. Recently, we have encountered a number of diagnostic algorithms that suggest algorithms for estimating the risk of tumor presence or the risk of progression of cancer, using statistical methods. Objectives: The aim of this work is to verify new biomarkers for the diagnosis of gastric cancer and to develop an optimal algorithm for their use. Further, to evaluate the importance of cytokeratin markers - Tissue Polypeptide Antigen (TPA) and Tissue Polypeptide Specific Antigen (TPS) for the diagnosis of metastatic colorectal carcinoma in the liver. To carry out a pilot study of FGF23 levels in people with colorectal carcinoma and other gastrointestinal tumors. Methods and patients: Patient samples were analyzed using immunoradiometric, chemiluminescence and fluorescence assays. For each solved problem,...

Eines der prävalentesten humanen Pathogene ist das Magenbakterium Helicobacter pylori, welches ca. die Hälfte der Weltbevölkerung infiziert. Die Persistenz geht mit einer chronischen Gastritis einher, welche bis zu Magenkrebs fortschreiten kann. H.pylori bedient sich diverser Mechanismen um sich der Erkennung des Immunsystems zu entziehen und somit eine chronische Infektion zu ermöglichen. Erhöhte Expression des Immunzellinhibitors PD-L1 wurde in Magenepithelzellen gefunden, welche mit diesem Gram-negativen Erreger infiziert wurden. In dieser Arbeit wurde die Regulation auf in vitro Ebene untersucht, wobei zwei unterschiedliche Mechanismen identifiziert wurden. Ursächlich für die frühe PD-L1-Induktion ist die ADP-heptose/ALPK1 Signalkaskade. Der bakterielle Metabolit ADP-heptose, welcher für die Bildung von LPS benötigt wird, wurde als PAMP identifiziert, welcher durch das Sekretionssystems cagT4SS in die infizierte transportiert und anschließend von der Host Kinase ALPK1 erkannt wird. Gegensätzlich hierzu, wurde festgestellt, dass die zweite PD-L1-Hochregulation auf der metabolischen Reprogrammierung des Wirts beruht. Ein Merkmal von H. pylori ist dessen Bedarf an Cholesterin, welches es aus dem Medium oder aus membranösen Lipidregionen des Wirts extrahiert wird. Es konnte bewiesen werden, dass dieser Sterol-Abbauprozess zu einer erhöhten Stoffwechselaktivität führt, die spezifisch mit einer Zunahme der Glykolyse verbunden ist und mit einer Expressionsverschiebung des ersten Glykolyseenzyms Hexokinase von der Isoform 1 zu 2 einhergeht. Knockdown und Knockout- Experimente wiesen auf einen Zusammenhang mit der Regulation des Immunzellinhibitoren PD-L1 hin. / One of the most prevalent bacteria is the gastric bacterium Helicobacter pylori, which infects half of the world’s population. Persistence is accompanied with chronic gastritis which can progress towards gastric cancer. Several strategies are used by H.pylori to evade the immune system, enabling chronic infection. Heightened expression of the immune cell inhibitor PD-L1 was found in gastric epithelial cells, infected with this Gram-negative pathogen. Within this thesis, upregulation was studied in in vitro models, revealing two distinct mechanism. Causative for early PD-L1 induction is the ADP heptose/ALPK1 signaling axis. The bacterial metabolite ADP heptose, which is needed for LPS synthesis, was identified as PAMP, which is transported through the secretion system cagT4SS into the infected cell and is recognized by the host kinase ALPK1. In contrast, late upregulation of PD-L1 was found to be linked to metabolic reprogramming upon infection. Characteristic to H.pylori is its need of cholesterol, which it has to extract from the surrounding medium or lipid-rich regions within the host membrane. It could be shown that this sterol extraction process is accompanied with an increased metabolic activity which is linked with enhanced glycolysis and an expression shift of the glycolytic enzyme hexokinase isoform 1 to 2. Knockdown and knockout experiments showed a link between HK2 and regulation of the immune checkpoint PD-L1.

Hypothesis testing has long been a formal and standardized process. Hypothesis generation, on the other hand, remains largely informal. This thesis assess whether eXplainable AI (XAI) can aid in the standardization of hypothesis generation through its utilization as a hypothesis generating tool for medical research. We produce XAI heat maps for a Convolutional Neural Network (CNN) trained to classify Microsatellite Instability (MSI) in colon and gastric cancer with four different XAI methods: Guided Backpropagation, VarGrad, Grad-CAM and Sobol Attribution. We then compare these heat maps with pathology annotations in order to look for differences to turn into new hypotheses. Our CNN successfully generates non-random XAI heat maps whilst achieving a validation accuracy of 85% and a validation AUC of 93% – as compared to others who achieve a AUC of 87%. Our results conclude that Guided Backpropagation and VarGrad are better at explaining high-level image features whereas Grad-CAM and Sobol Attribution are better at explaining low-level ones. This makes the two groups of XAI methods good complements to each other. Images of Microsatellite Insta- bility (MSI) with high differentiation are more difficult to analyse regardless of which XAI is used, probably due to exhibiting less regularity. Regardless of this drawback, our assessment is that XAI can be used as a useful hypotheses generating tool for research in medicine. Our results indicate that our CNN utilizes the same features as our basic pathology annotations when classifying MSI – with some additional features of basic pathology missing – features which we successfully are able to generate new hypotheses with.

Utilisation of New Biomarkers for the Optimalization of Diagnostics and Therapy of Tumors of the Gastrointestinal Tract Introduction: Tumor markers are standard diagnostic tools. They are mainly used to monitor the course of the disease and to check the efficacy of the treatment. It is important to observe dynamics. Changing the level of the biomarker can prevent clinical manifestation and lead to early diagnosis of relapse, which in turn means improving the quality of life, including prolonging survival. Recently, we have encountered a number of diagnostic algorithms that suggest algorithms for estimating the risk of tumor presence or the risk of progression of cancer, using statistical methods. Objectives: The aim of this work is to verify new biomarkers for the diagnosis of gastric cancer and to develop an optimal algorithm for their use. Further, to evaluate the importance of cytokeratin markers - Tissue Polypeptide Antigen (TPA) and Tissue Polypeptide Specific Antigen (TPS) for the diagnosis of metastatic colorectal carcinoma in the liver. To carry out a pilot study of FGF23 levels in people with colorectal carcinoma and other gastrointestinal tumors. Methods and patients: Patient samples were analyzed using immunoradiometric, chemiluminescence and fluorescence assays. For each solved problem,...