Joint MSc programme “Applied Biochemistry: Clinical Chemistry, Biotechnology, Evaluation of Pharmaceutical Products”                      

MSc Thesis Presentation

Name: Angeliki Natsiou

Title: “Exploring collagen fiber organization and extracellular matrix architecture in atherosclerotic plaques”

Supervisor: Dr. Chrysostomi Gialeli, Researcher, University of Lund, Sweden

Date: 21/07/2025

Time: 11:00

Zoom link:

https://upatras-gr.zoom.us/j/98403186871?pwd=2V44oOA1JG15IU8PIRaHVUpq1J3YTr.1

Abstract

Atherosclerosis is the primary contributor to cardiovascular disease (CVD), the leading cause of mortality worldwide. It is initiated by endothelial dysfunction and progresses through lipid accumulation, thinning of the fibrous cap, calcification, and uncontrolled inflammation, ultimately leading to vessel narrowing and rupture. The structure, composition and turnover of the vascular extracellular matrix

(ECM) are crucial for the development of atherosclerotic plaques. Among the various ECM components, collagens are essential for maintaining plaque stability by forming the fibrous cap. As atherosclerosis progresses, collagen degradation leads to fibrous cap thinning, rendering plaques more prone to rupture. While collagen amount is important for structural integrity, research suggests that collagen type, orientation, structural organization and cross-linking are equally important for plaque stability.

The present study investigates the organization of the atherosclerotic ECM, emphasizing the spatial distribution and structural characteristics of collagen to identify patterns that contribute to plaque instability.

Histochemical staining was performed on human atherosclerotic carotid plaques to visualize collagen. ECM architecture was quantified using the FIJI macro TWOMBLI, which evaluates matrix alignment, fiber length, branching, endpoints, gaps, fractal dimension, curvature, and fiber thickness distribution. TWOMBLI analysis revealed that rupture-prone regions display a unique ECM organization pattern, characterized by lower fiber density and thickness, and a loosely packed, random ECM, where collagen fibers lack uniform orientation.

The strong correlation between TWOMBLI-derived metrics and visual histological assessment supports the utility of this method for quantifying ECM architecture. Importantly, these findings highlight the critical role of ECM organization – and specifically collagen structure –in determining plaque stability. Distinct collagen organizational patterns may serve as indicators of rupture-prone plaques, offering potential biomarkers for risk assessment.

 Angeliki Natsiou - MSc Thesis presentation

                                                   Παρουσίαση Μ.Δ.Ε.

Ονοματεπώνυμο: Τσιαντής Ευάγγελος

Θέμα: Μελέτη της επίδρασης των μορίων του εξωκυττάριου χώρου στον καρκίνο του μαστού

Επιβλέπων: Καθηγητής Νίκος Καραμάνος

Ημερομηνία: 16 Ιουλίου 2025

Ώρα: 5μμ

Τόπος:

https://upatras-gr.zoom.us/j/92459480059?pwd=UIHlY7s4Fr0qHJHzbXHh7DB9Kwhaqe.1

                                                         Περίληψη

Ο καρκίνος του μαστού αποτελεί μια από τις πιο συνηθισμένες μορφές καρκίνου στις γυναίκες. Καθοριστικό ρόλο στην ανάπτυξη, εξέλιξη και εξάπλωση του παίζουν τα οιστρογόνα και κυρίως η 17β-οιστραδιόλη, η οποία ασκεί τη δράση της μέσω των σηματοδοτικών μοναπατιών των οιστρογονικών υποδοχέων ERα και ERβ και την αναδιαμόρφωση του εξωκυττάριου διακυτταρικού δικτύου (ECM). Μεταξύ των κύριων συστατικών του ECM συμπεριλαμβάνονται τα πρωτεολυτικά ένζυμα μεταξύ των οποίων πρωτεύοντα ρόλο παίζουν οι μεταλλοπρωτεϊνάσες (MMPs), οι οποίες συμμετέχουν στην αναδιαμόρφωση του ECM, ενώ τα αυξημένα επίπεδα έκφρασης τους συνδέονται κατά κανόνα με αυξημένη επιθετικότητα και κακή πρόγνωση. Η αναδιαμόρφωση του ECM συνδέεται με την ενεργοποίηση σηματοδοτικών μονοπατιών τα οποία επηρεάζουν σε μεγάλο βαθμό και τo μεταστατικό δυναμικό των καρκινικών κυττάρων.

Στην παρούσα διπλωματική εργασία διερευνήθηκε αρχικά με τη βοήθεια προγραμμάτων βιοπληροφορικής η συσχέτιση της έκφρασης των MMP1, MMP2, MMP9, MMP7 και MMP14 με τα επίπεδα έκφρασης των ERs (Kaplan Meier Plotter, TNM Plotter). Σε επόμενο στάδιο μελετήθηκε η έκφραση αυτών των πέντε MMPs συγκριτικά σε διαφορετικά είδη καρκίνου μαστού με τη χρήση των βάσεων δεδομένων (UALCAN, GEPIA2). Επίσης διερευνήθηκε η προγνωστική τους αξία ως βιοδείκτες μέσω προγράμματος μετα-ανάλυσης (ROC Plotter). Τέλος μελετήθηκε η αλληλεπίδραση άμεση και έμμεση των MMPs και άλλων μορίων του ECM μέσω  της βάσης δεδομένων (STRING), καθώς και η πολυγονιδιακή ανάλυση για εκτίμηση βιοδεικτών μέσω μελέτης για τις γονιδιακές τους εκφράσεις.

Τα αποτελέσματα της εργασίας αυτής σηματοδοτούν τον επαναπροσδιορισμό της προγνωστικής αξίας των MMPs μέσω του συνδυαστικού ρόλου που παίζουν στην ανάπτυξη, εξάπλωση και μεταστατική ικανότητα των καρκινικών κυττάρων μαστού με την αναδιαμόρφωση του μικροπεριβάλλοντος του όγκου.

_______________________

Nikos Karamanos, PhD, ERT

Professor of Biochemistry

E-mail:

Board Member: ISMB [1]  I HSBMB [2]

Series editor: Biology of ECM [3]

Book editor: ECM Pathobiology & Signaling  [4]

Editor: FEBS J  [5]I Mol Bio Rep Section ECM Biology [6] Associate Editor: Cellular & Molecular Oncology  [7](Frontiers [8]) I Cancers [9]

Profiles:  Dept website  [10]I Google Scholar [11] I ResearchGate [12] I Orcid [13] I https://research.com/u/nikos-k-karamanos

Web of Science_Highly Cited researcher 2022 [14]

Dear all,

Please, find attached the September examination schedule of Academic Year 2024-2025 of the JMSc Programme «Applied Biochemistry: Clinical Chemistry, Biotechnology, Evaluation of Pharmaceutical Products».

Best wishes,

D. Vynios

September 2024-2025 Exams

Dear All,

Please, find attached the abstract of the seminar of Rami Babas, post-graduate student of the JMSC Programme in Applied Biochemistry: "Biotechnology, Clinical Chemistry, evaluation of pharmaceutical products", which will take place on Friday, June 27, 2025, at 14.00.

Sincerely,

D. H. Vynios

 R. Babas - Abstract

Dear all,

Please, find attached the abstracts of the seminars of the Post-graduate students of JMSc Programme in Applied Biochemistry: "Biotechnology, Clinical Chemistry, Evaluation of Pharmaceutical products", D.I. Zafeirakopoulos (27/06/25, 13.00), P. Megremi (27/06/25, 13.30),  and L. Delivoria (01/07/25, 10.00).

Sincerely,

D. H. Vynios

Dimitrios-Ilias Zafeirakopoulos - Abstract

P. Megremi - Abstract

Lygeri Delivoria - Abstract

Πληροφορίες στα επισυναπτόμενα.

Προκήρυξη του ΔΠΜΣ «Εφαρμοσμένη Βιοχημεία: Κλινική Χημεία, Βιοτεχνολογία, Αξιολόγηση Φαρμακευτικών Προϊόντων» 2025-2026

Announcement of the Join Post Graduated Programme in Applied Biochemistry - 2025-2026

Ονοματεπώνυμο: Ραπασάρδου Διονυσία

Θέμα: Επίδραση σιμβαστατίνης παρουσία ορμονών στην έκφραση πρωτεογλυκανών σε κύτταρα τριπλά αρνητικού καρκίνου του μαστού.

Επιβλέπων: Δημήτριος Βύνιος, Καθηγητής

Ημερομηνία: Τετάρτη 11 Ιουνίου 2025

Ώρα: 10:00

Τόπος: https://upatras-gr.zoom.us/j/98403186871?pwd=2V44oOA1JG15IU8PIRaHVUpq1J3YTr.1

ΠΕΡΙΛΗΨΗ

Ο καρκίνος του μαστού είναι ο πιο συχνός τύπος καρκίνου στις γυναίκες παγκοσμίως, με τον τριπλά αρνητικό καρκίνο (TNBC) να αποτελεί έναν ιδιαίτερα επιθετικό υπότυπο, καθώς δεν εκφράζει υποδοχείς οιστρογόνων, προγεστερόνης ή HER2. Λόγω της απουσίας στοχευμένων θεραπειών και της κακής πρόγνωσης, η έρευνα έχει στραφεί τα τελευταία χρόνια στην αναζήτηση νέων θεραπευτικών προσεγγίσεων.

Σκοπός της εργασίας ήταν η διερεύνηση της επίδρασης της σιμβαστατίνης — μιας στατίνης με γνωστή αντικαρκινική δράση — στην έκφραση πρωτεογλυκανών και των ενζυμών που σχετίζονται με τη βιοσύνθεση γλυκοζαμινογλυκανών, σε κυτταρικά μοντέλα TNBC (MDA-MB-231 και Hs578T). Παράλληλα, εξετάστηκε και η δράση των στεροειδών ορμονών 17β-οιστραδιόλης και προγεστερόνης, είτε μόνες είτε σε συνδυασμό με τη σιμβαστατίνη.

Τα αποτελέσματα έδειξαν διαφοροποιημένη ρύθμιση των ενζύμων CHPF, CHPF2, CHSY1 και CHSY3, ανάλογα με τη συγκέντρωση της σιμβαστατίνης, την παρουσία ορμονών και τον κυτταρικό τύπο. Ιδιαίτερο ενδιαφέρον παρουσίασε η πρωτεογλυκάνη decorin, η οποία εμφάνισε μείωση σε επίπεδο mRNA αλλά αύξηση σε επίπεδο πρωτεΐνης, γεγονός που πιθανόν σχετίζεται με μετα-μεταφραστικές τροποποιήσεις ή μειωμένη αποικοδόμηση. Η έκφραση της versican παρουσίασε μεταβολές που δεν ήταν απόλυτα ξεκάθαρες, αλλά φαίνεται να επηρεάζεται από την παρουσία ορμονών και τη δόση της σιμβαστατίνης.

Επιπλέον, μελετήθηκε η επίδραση της σιμβαστατίνης στην ανάπτυξη σφαιροειδών από τα κύτταρα. Παρατηρήθηκαν αλλαγές στη μορφή και την κυκλικότητα των σφαιροειδών, που υποδεικνύουν μείωση της κυτταρικής συνοχής και πιθανή διαφοροποίηση του φαινοτύπου.

Συνολικά, τα ευρήματα δείχνουν ότι η σιμβαστατίνη επηρεάζει τη σύνθεση και τη σταθερότητα του εξωκυττάριου μικροπεριβάλλοντος στον TNBC, ενισχύοντας την πιθανή της χρησιμότητα ως συμπληρωματική θεραπευτική επιλογή.

ABSTRACT

Breast cancer is the most common cancer type in women worldwide, with triple-negative breast cancer (TNBC) representing one of its most aggressive subtypes, lacking expression of estrogen, progesterone, and HER2 receptors. Due to the absence of targeted therapies and its poor prognosis, research has increasingly focused on identifying novel therapeutic strategies.

This study aimed to investigate the effects of simvastatin — a statin with known anticancer activity — on the expression of proteoglycans and enzymes involved in glycosaminoglycan biosynthesis, using TNBC cell lines (MDA-MB-231 and Hs578T). In parallel, the potential modulatory role of the steroid hormones 17β-estradiol and progesterone was assessed, either alone or in combination with simvastatin.

Our findings revealed differential regulation of CHPF, CHPF2, CHSY1, and CHSY3 depending on simvastatin concentration, hormonal context, and cell type. The proteoglycan decorin showed reduced mRNA expression but increased protein levels, possibly due to post-translational modifications or decreased degradation. Versican expression also varied, although no consistent pattern was observed, and appeared to be hormone- and dose-dependent. In addition, the effect of simvastatin on spheroid formation was studied. Morphological changes in spheroid structure and circularity were detected, suggesting reduced cell cohesion and potential phenotypic alteration.

Overall, our results indicate that simvastatin affects extracellular matrix dynamics in TNBC models, supporting its potential role as an adjuvant therapeutic agent.

Name: Chrisavgi Gourdoupi

Title: Evaluation of EGFR and IGF-IR signaling in the expression of matrix macromolecules and cell functional properties for conventional 2D cell cultures and spheroids

Supervisor: Professor Nikos K. Karamanos

Date: 04/06/2025

Time: 10 am

Zoom link: https://upatras-gr.zoom.us/j/99967801031?pwd=VuhPwGQLaoQ54ZX6IHyai2BYuIsWIS.1

Cancer is one of the most serious diseases in humans in developed countries. Statistical studies show that they are the second most common cause of death after heart disease. Breast cancer is a disease characterized by significant phenotypic and genotypic heterogeneity, which is reflected in the remodeling of the extracellular matrix (ECM).

The ECM is a highly dynamic macromolecular network that constantly changes in normal and pathological conditions. The action of the various matrix effectors may alter ECM macromolecular composition, a process associated with cancer progression. On the other hand, receptor tyrosine kinases (RTKs) are critical signaling effectors for gene expression and cell functional properties. Among RTKs, epidermal growth factor receptor

(EGFR) and insulin-like growth factor receptor (IGF-IR) are considered important players in breast cancer diagnosis and treatment since they are implicated in tumor growth and invasiveness potential. These RTKs affect the composition of ECM in health and disease. Evaluating the changes that ECM undergoes following inhibition of EGFR and IGF-IR is an emerging area in cancer research and pharmacological targeting. Notably, crosstalk between EGFR and IGF-IR plays a significant role in regulating the behavior and morphology of breast cancer cells, including MDA-MB-231 (highly aggressive) and MCF-7 (low invasive hormone-dependent) cell lines. It is noted that up-to-date studies are focused on the well-known 2D cell culture models where cells grow on a polystyrene plate and have been used for many years to study the net effects of signaling molecules and receptors. However, 2D models fail to mimic the dynamics of the tumor microenvironment in respect to true three-dimensional tumor development, growth, and spreading. To this end, the recently developed 3D cell culture models are considered as a more closely related condition regarding the biochemical properties and cell-cell interactions of tumors as compared to conventional 2D platforms.

For that reason, this study aims to utilize 3D cell platforms as to evaluate, through quantitative RT-PCR analysis, and wetting experiments the effect of agents inhibiting the EGFR and IGF-IR pathways (alone or in combination) in the expression of ECM key components and the functional properties of breast cancer cells (proliferation, migration, spreading), comparing new 3D cell models with the traditional 2D ones.

Our results indicated the crosstalk between IGF-IR and EGFR,  and the effect of each on the proliferation and migration capacity. Moreover, phenotypic alterations emerged between 2D and 3D conditions that were related to the expression of important molecules such as MMPs.

Additionally, this research confirmed basic features of the two cell lines, both in 2D and 3D conditions, but also indicated new properties and responses dependent on the environment of the cell culture. Overall, our findings are indeed promising, both in advancing the understanding of RTKs signaling, with particular emphasis on the intricate crosstalk between EGFR and IGF-IR pathways, and in demonstrating the utility of 3D models as effective tools for unraveling the biological processes governing the distinct breast cancer phenotypes.

Name: Spyros Kremmydas

Title: The impact of EGF and IGF-Ι receptors’ inhibition on extracellular matrix modulation in 2D and 3D cancer cell cultures

Supervisor: Nikos K. Karamanos, Professor

Date: 02/06/2025

Time: 11:00

Zoom link: https://upatras-gr.zoom.us/j/96516568158?pwd=bbhcVOhnjiDkYcHAn8ZzQNxPCgnA5e.1

Among solid tumors, breast cancer (BC) remains the most frequently diagnosed cancer in women globally and the leading cause of cancer-related mortality in females. Triple-negative breast cancer

(TNBC) is a highly aggressive and heterogeneous BC subtype, which accounts for approximately 90% of BC-related deaths. Receptor tyrosine kinases (RTKs), including EGFR and IGF-IR, are crucial regulators of cell proliferation, survival, and differentiation, and their dysregulation has been closely linked to therapy resistance in TNBC. The inhibition of RTKs, using small chemical molecules or monoclonal antibodies, has emerged as a promising therapeutic strategy in previous years. However, recent research has shifted to the development of novel preclinical models that closely resemble the tumor microenvironment (TME). The development and progression of cancer are directly influenced by microenvironmental signals, including those from the extracellular matrix (ECM). Traditional two-dimensional (2D) cell cultures, while widely used in early preclinical studies, fail to replicate the structural and biochemical characteristics of TME three-dimensional (3D) nature. To this end, advanced 3D cell culture models that can simulate the growth and initial progression of solid tumors represent a promising approach.

The aim of the present study is to address this research gap by employing both 2D and spheroid-based 3D cell culture models to investigate the effects of EGFR and IGF-IR inhibition, individually and in combination, on two TNBC cell lines: Hs578T and shERβ MDA-MB-231 (ERβ-suppressed).

The results indicated that both EGFR and IGF-IR are key regulators of the functional properties in TNBC cells, such as cell proliferation and migration, as well as the expression of EMT markers and matrix metalloproteinases (MMPs). Using 3D spheroid-based models, additional functional properties like spheroid growth rate and dissemination were accessible for evaluation, with inhibition of both receptors leading to a reduction in treatment-dependent manners. Additionally, gene expression and functional properties of spheroid-derived cells were compared with their respective 2D cell cultures under treatment conditions. Interestingly, spheroid-derived cells of both cell lines exhibit different responses on their migratory capacity and on gene expression of MMPs and cell surface proteoglycans (PGs) upon inhibition of the two receptors. Conclusively, this dual-model approach underscores the importance of 3D systems in cancer research and provides new insights into RTKs’ regulatory role in TNBC.

Name: Nikolaos Koletsis

Title: Functional properties and differential expression of key matrix components in three dimensional breast cancer spheroids

Supervisor: Nikos Karamanos, Professor

Date: 02/06/2025

Time: 10.00 am

Zoom link: https://upatras-gr.zoom.us/j/96516568158?pwd=bbhcVOhnjiDkYcHAn8ZzQNxPCgnA5e.1

Tumor microenvironment dynamic interactions play critical roles in premetastatic niche, cancer cells invasion and metastatic potential. The three-dimensional (3D) extracellular matrices (ECMs) structural networks are capable of modulating cell functional properties. Traditional 2D cultures have offered valuable insights in cellular behavior, although lacking the ability of accurately representing the complex matrix microenvironment structure in vivo. Thus, developing in vitro cell models that could mimic the 3D morphological aspects of solid tumors in vivo, could improve our understanding on tumor growth and progression.

This study focuses on the development of three-dimensional cell culture models, particularly on breast cancer derived spheroids utilizing two breast cancer cell lines, shERβ MDA-MB-231 (derived from the highly aggressive MDA-MB-231 ERbeta-positive cell line) and Hs578T. Estrogen receptors (ERs) have pivotal roles in breast cancer growth and progression. Even though the contribution of ERα in the modulation of breast cancer cells' behavior is thoroughly studied, the biological functions of its isoform, ERβ, are less elucidated.

The aim of this study is to examine possible morphological alterations in the formation of the different cell line 3D-spheroids, accompanied by variations in the expression of ECM macromolecules implicated in cancer progression comparatively to the respective cell lines grown in 2D culture flasks in the presence and absence of matrix macromolecules.

To this end, total RNA was extracted, and 3D spheroid formation and behavior was evaluated as to examine the 3D-spheroids functional properties. The obtained data revealed significant variations in the expression of ECM macromolecules, mesenchymal markers, receptors, proteases in 3D cell models, as compared with respective 2D cell cultures. Ultimately, this study underscores the importance of focusing on 3D cultures, as these more innovative cell culture models offer deeper insights into breast cancer research.