Periostin splice variants in pancreatic cancer

Introduction: Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest solid tumours, with 5-year survival of less than 5%. The aggressive nature of the tumour, the tumour-supportive environment (stroma), delayed diagnosis and poor chemotherapy response lead to poor patient prognosis. The tumour-stroma is a dynamic network of immune, mesenchymal, and endothelial stromal cells surrounded by an extracellular matrix rich in matricellular and architectural proteins. Periostin (POSTN), a matricellular protein primarily secreted by stromal cells, is often associated with cell proliferation and migration. POSTN overexpression has been observed in many tumour types, however downregulation in bladder carcinoma rises some questions. POSTN is an alternatively sliced gene, that encodes multiple different isoforms, whose function in PDAC is still unknown. The aim of this study is to isolate and clone these isoforms in order to produce recombinant proteins for further investigation. Methods: The transcript variants were extracted from PS1 cells (a pancreatic stromal cell line), converted to cDNA and amplified by RT-PCR. The synthesised DNA was ligated with plasmid vectors and cloned by traditional cloning into E.coli cells. Single colonies were sequenced and analyses, determining the transcript variant being cloned. The plasmids ligated with the variants of interest were isolated and transfected into PS1 cells. The recombinant proteins synthesised by the PS1 cells were then purified. Results: Multiple isoforms of POSTN were cloned in E.coli. Sequencing analysis revealed the exons present in each sample of the cloned colonies and the isoforms were identified. The plasmids of interest were successfully extracted from the colonies by using purification technique appropriate for subsequent mammalian cell transfection. Substantial progress was made in producing recombinant POSTN proteins. Conclusion: In this study the isolation of three cloned POSTN transcript variants were achieved. These variants are POSTN-202, 209 and 201-b

A Multidisciplinary Hyper-Modeling Scheme in Personalized In Silico Oncology: Coupling Cell Kinetics with Metabolism, Signaling Networks, and Biomechanics as Plug-In Component Models of a Cancer Digital Twin.

The massive amount of human biological, imaging, and clinical data produced by multiple and diverse sources necessitates integrative modeling approaches able to summarize all this information into answers to specific clinical questions. In this paper, we present a hypermodeling scheme able to combine models of diverse cancer aspects regardless of their underlying method or scale. Describing tissue-scale cancer cell proliferation, biomechanical tumor growth, nutrient transport, genomic-scale aberrant cancer cell metabolism, and cell-signaling pathways that regulate the cellular response to therapy, the hypermodel integrates mutation, miRNA expression, imaging, and clinical data. The constituting hypomodels, as well as their orchestration and links, are described. Two specific cancer types, Wilms tumor (nephroblastoma) and non-small cell lung cancer, are addressed as proof-of-concept study cases. Personalized simulations of the actual anatomy of a patient have been conducted. The hypermodel has also been applied to predict tumor control after radiotherapy and the relationship between tumor proliferative activity and response to neoadjuvant chemotherapy. Our innovative hypermodel holds promise as a digital twin-based clinical decision support system and as the core of future in silico trial platforms, although additional retrospective adaptation and validation are necessary

A multidisciplinary hyper-modeling scheme in personalized in silico oncology : coupling cell kinetics with metabolism, signaling networks, and biomechanics as plug-in component models of a cancer digital twin

The massive amount of human biological, imaging, and clinical data produced by multiple and diverse sources necessitates integrative modeling approaches able to summarize all this information into answers to specific clinical questions. In this paper, we present a hypermodeling scheme able to combine models of diverse cancer aspects regardless of their underlying method or scale. Describing tissue-scale cancer cell proliferation, biomechanical tumor growth, nutrient transport, genomic-scale aberrant cancer cell metabolism, and cell-signaling pathways that regulate the cellular response to therapy, the hypermodel integrates mutation, miRNA expression, imaging, and clinical data. The constituting hypomodels, as well as their orchestration and links, are described. Two specific cancer types, Wilms tumor (nephroblastoma) and non-small cell lung cancer, are addressed as proof-of-concept study cases. Personalized simulations of the actual anatomy of a patient have been conducted. The hypermodel has also been applied to predict tumor control after radiotherapy and the relationship between tumor proliferative activity and response to neoadjuvant chemotherapy. Our innovative hypermodel holds promise as a digital twin-based clinical decision support system and as the core of future in silico trial platforms, although additional retrospective adaptation and validation are necessary

Exploiting Clinical Trial Data Drastically Narrows the Window of Possible Solutions to the Problem of Clinical Adaptation of a Multiscale Cancer Model

The development of computational models for simulating tumor growth and response to treatment has gained significant momentum during the last few decades. At the dawn of the era of personalized medicine, providing insight into complex mechanisms involved in cancer and contributing to patient-specific therapy optimization constitute particularly inspiring pursuits. The in silico oncology community is facing the great challenge of effectively translating simulation models into clinical practice, which presupposes a thorough sensitivity analysis, adaptation and validation process based on real clinical data. In this paper, the behavior of a clinically-oriented, multiscale model of solid tumor response to chemotherapy is investigated, using the paradigm of nephroblastoma response to preoperative chemotherapy in the context of the SIOP/GPOH clinical trial. A sorting of the model's parameters according to the magnitude of their effect on the output has unveiled the relative importance of the corresponding biological mechanisms; major impact on the result of therapy is credited to the oxygenation and nutrient availability status of the tumor and the balance between the symmetric and asymmetric modes of stem cell division. The effect of a number of parameter combinations on the extent of chemotherapy-induced tumor shrinkage and on the tumor's growth rate are discussed. A real clinical case of nephroblastoma has served as a proof of principle study case, demonstrating the basics of an ongoing clinical adaptation and validation process. By using clinical data in conjunction with plausible values of model parameters, an excellent fit of the model to the available medical data of the selected nephroblastoma case has been achieved, in terms of both volume reduction and histological constitution of the tumor. In this context, the exploitation of multiscale clinical data drastically narrows the window of possible solutions to the clinical adaptation problem

E2F1 and its role in Hodgkin lymphoma

Hodgkin’s lymphoma (HL) was first described by Sir Thomas Hodgkin in 1832, from which it took its name. It is considered up to now, in most cases, a B-cell lymphoma without excluding cases of T-cell origin. It constitutes 30% of all lymphomas. The basic diagnostic feature of HL is the presence of rare neoplastic multinucleated Reed-Sternberg and mononuclear Hodgkin cells (HRS cells) within an inflammatory reactive environment of T and B lymphocytes, admixed with plasma cells, macrophages, eosinophils, mast cells and fibroblasts. It seems that the microenvironment interacts with the tumor cells and somehow ensures their survival.The E2F-1 transcriptional factor is the first and best described member of the E2F family. It consists of an N terminal binding site of DNA and one C final position for binding “pocket” proteins. The E2F1 selectively binds to Retinoblastoma protein (pRb). This connection is the first and most important interaction between E2F factors and "pocket" proteins. E2F-1 appears on the G1-S phase of interphase. Molecules such as proteins ATM / ATR and chk2 directly phosphorylate E2F1 in Ser positions 31 and Ser 364 respectively during DNA repair process and thus E2F1 participates in the DNA damage response pathway (DDR).Its role is rather surprising, as it has been proven to promote proliferation or apoptosis in different tissues, events that are by nature opposed processes. The role of E2F1 in HL has not been elucidated and its effect on the development and course of this entity remains unknown.The purpose of our study was to examine the immunohistochemical expression of E2F-1 in HL and to correlate it with proliferation and apoptosis of the tumor, clinicopathological parameters and patient outcome, as well as with the expression of the downstream molecules p53 and p21.E2F-1 showed a median value of 80 %. A significant positive correlation was found between expression of E2F-1 and p53 (p= 0.034). Following stratification of our cases, within the group harboring functional p53, a statistically significant inverse correlation was identified between E2F-1 and Topo IIa (p= 0.019).E2F-1 is upregulated in the context of HL and its expression is inversely associated with proliferation. It seems that functional p53 can modulate the relationship between E2F-1 expression and tumor kinetics in HL. E2F-1 is likely capable of leading to apoptosis, acting thus as a tumor suppressor gene in HL.Το λέμφωμα Hodgkin (ΛΗ) περιγράφτηκε για πρώτη φορά από τον Sir Thomas Hodgkin το 1832, από τον οποίο πήρε και το όνομά του. θεωρείται σήμερα, στην πλειοψηφία των περιπτώσεων, λέμφωμα Β-κυτταρικής αρχής χωρίς να αποκλείονται περιπτώσεις Τ-κυτταρικής προελεύσεως. Βασικό διαγνωστικό χαρακτηριστικό της νόσου είναι η παρουσία των κυττάρων Reed-Sternberg, που αποτελούν τα τυπικά νεοπλασματικά κύτταρα του λεμφώματος, καθώς και των μονοπύρηνων κυττάρων Hodgkin. Σημαντικό ρόλο για τη διάγνωση της νόσου έχει το περιβάλλον στο οποίο εμφανίζονται τα νεοπλασματικά κύτταρα, ένα υπόστρωμα φλεγμονώδους διήθησης μη νεοπλασματικής φύσης αποτελούμενο από ηωσινόφιλα, λεμφοκύτταρα, ιστιοκύτταρα και άλλα βοηθητικά κύτταρα. Φαίνεται πως το μικροπεριβάλλον αυτό αλληλεπιδρά με τα νεοπλασματικά κύτταρα και κατά κάποιο τρόπο εξασφαλίζει την επιβίωση τους.Ο παράγοντας E2F-1 αποτελεί τον πρώτο και πιο καλά μελετημένο παράγοντα της οικογένειας των E2F. Περιλαμβάνει στο μόριό του μία Ν τελική θέση πρόσδεσης του DNA και μία C τελική θέση για την πρόσδεση των πρωτεϊνών “ pocket. Ο E2F1 συνδέεται εκλεκτικά με την πρωτείνη του ρετινοβλαστώματος (pRb). Η σύνδεση αυτή αποτελεί την πρώτη και πιο σημαντική αλληλεπίδραση μεταξύ παραγόντων E2F και “pocket” πρωτεϊνών Ο παράγοντας E2F-1 εμφανίζεται στη φάση G1-S της μεσόφαση. Μόρια όπως οι πρωτεΐνες ATM/ATR και chk2 φωσφορυλιώνουν απευθείας το E2F1 στις θέσεις Ser 31 και Ser 364 αντίστοιχα κατά τη διαδικασία αποκατάστασης βλαβών του DNA, συμμετέχοντας με τον τρόπο αυτό ο E2F1 στο μονοπάτι της απάντησης σε βλάβη του DNA (DNA damage response pathway, DDR).Ο ρόλος του είναι παράδοξος, καθώς έχει αποδειχθεί ότι μπορεί να ευοδώνει τον πολλαπλασιασμό, ή να προάγει την απόπτωση σε διαφορετικούς ιστούς, γεγονότα που αποτελούν από τη φύση τους αντίθετες διαδικασίες. Ο ρόλος του E2F1 στο ΛΗ δεν έχει μελετηθεί και άγνωστη παραμένει η επίδρασή του στην εξέλιξη και πορεία αυτής της νοσολογικής οντότητας.Στόχος της παρούσας διατριβής είναι η μελέτη της ανοσοϊστοχημικής έκφρασης του E2F-1 στο ΛH και η συσχέτισή του με τον πολλαπλασιασμό και την απόπτωση, με τις κλινικοεργαστηριακές παραμέτρους και την επιβίωση των ασθενών, καθώς και με την έκφραση άλλων μορίων όπως της p53 και της p21 που συμμετέχουν σε βασικά μονοπάτια των κινητικών παραμέτρων του όγκου.Η έκφραση του E2F-1 εμφάνισε διάμεση τιμή 80% και θετική συσχέτιση με την έκφραση της πρωτείνης p53 (p= 0.034). Ακολουθώντας μια διαστρωμάτωση των περιπτώσεων με βάση τη λειτουργική p53, στην ομάδα των ασθενών που δημιουργήθηκε προέκυψε μια στατιστικώς σημαντική αντίστροφη συσχέτιση μεταξύ της έκφρασης του E2F-1 και ενός δείκτη του πολλαπλασιασμού, της TopoIIa (p= 0.019). Καμιά στατιστικώς σημαντική συσχέτιση δεν προέκυψε μεταξύ της έκφρασης του E2F-1 και των κλινικοεργαστηριακών παραμέτρων ή την επιβίωση των ασθενών.Ο παράγοντας E2F-1 υπερεκφράζεται στο ΛΗ και η έκφρασή του σχετίζεται αντίστροφα με τον πολλαπλασιασμό. Φαίνεται ότι η λειτουργική p53 μπορεί να ρυθμίσει τη σχέση του E2F-1 με τις κινητικές παραμέτρους του όγκου

Bilateral hypoplasia of the internal carotid artery and ectasia of the internal jugular vein

Hypoplasia of the internal carotid artery and internal jugular vein ectasia are rare congenital abnormalities, whose diagnosis and treatment are not uniformly described. A 32-year-old neurologically asymptomatic woman with renal failure had a carotid artery duplex ultrasound scan as part of an evaluation for renal transplantation and was found to have bilateral internal carotid artery hypoplasia. Computed tomography angiography confirmed congenital bilateral internal carotid artery stenosis and left internal jugular vein ectasia. She had no neurologic deficits. She underwent antiplatelet treatment

A Modular Repository-based Infrastructure for Simulation Model Storage and Execution Support in the Context of Oncology and Medicine

The plethora of available disease prediction models and the ongoing process of their application into clinical practice – following their clinical validation – have created new needs regarding their efficient handling and exploitation. Consolidation of software implementations, descriptive information, and supportive tools in a single place, offering persistent storage as well as proper management of execution results, is a priority, especially with respect to the needs of large healthcare providers. At the same time, modelers should be able to access these storage facilities under special rights, in order to upgrade and maintain their work. In addition, the end users should be provided with all the necessary interfaces for model execution and effortless result retrieval. We therefore propose a software infrastructure, based on a tool, model and data repository that handles the storage of models and pertinent execution-related data, along with functionalities for execution management, communication with third-party applications, user-friendly interfaces to access and use the infrastructure with minimal effort and basic security features