Umweltmedizin am IUK

Aim of the project:

To generate new knowledge about the epigenetic changes during cancer therapy and to use this knowledge to develop improved diagnostic and therapeutic strategies for better patient outcome.

Project description:

Our project is a part of nanodiag_BW Cluster4Future that brings together multidisciplinary research teams from academic institutions and industry in Baden-Württemberg. The cluster aims to enhance existing and develop new nanopore technologies for the detection of protein post-translational modifications (PTMs) in clinical samples. Our group investigates epigenetic biomarkers, such as DNA methylation and PTMs in extracellular vesicles (EVs), which are applicable as liquid biopsy biomarkers, and have a potential to improve identification of resistance by immune and epigenetic therapies in cancer patients. The vision of the project is to establish a basis for the application of nanopore technology in liquid biopsy.

Funding and collaborators:

Aim of the project:

Our main goal is to explore EVs as biomarkers for cardiovascular disease, on the one hand as predictors of clinical progression, e.g. after a heart attack, and on the other hand to distinguish between different classes and stages of cardiovascular disease. Let's take the vesicles from bench to bedside.

Project description:

My project is about cardiovascular diseases. I want to know how certain cardiovascular diseases affect the production of extracellular vesicles (EVs) in the blood and their effects on other cells, as well as on the progression of the disease. EVs are produced by all cell types, but with cell- and disease-specific configurations. Changes in their release, size, cargo and function can be observed between different pathologies and cell types. Interestingly, EVs are loaded with different contents (proteins, nucleic acids, etc.) in specific and non-specific ways by their host cell. By analysing the phenotypes of circulating EVs in the blood (liquid biopsy), we can estimate the origin of these EVs. They could have been secreted by endothelial cells, immune cells, platelets etc. The specific surface markers such as receptors on the EVs also allow us to infer which cells might be a target of EVs.

Funding and collaborators:

Aim of the project:

To develop next-generation liquid biopsy assay for early diagnosis of prostate cancer utilizing molecular signatures on extracellular vesicles

Project description:

The early detection of cancer and the identification of therapy resistance are crucial for improving the chances of survival for affected individuals. The EV-Surf project is currently investigating a new approach to cancer diagnosis using extracellular vesicles (EVs) isolated form the blood of patients.

By leveraging advancements in protein analytics, such as miniaturization through microfluidics, digital assay technology, and AI-based protein pattern recognition, the project aims to develop a highly accurate diagnostic assay. This innovative technique focuses on analyzing EVs, which carry specific cancer-related proteins on their surface. The initial focus is on prostate cancer, serving as an illustrative example to demonstrate how the limitations of current blood-based assays can be overcome through digital analysis of EVs.

Once successful for prostate cancer, the EV-Surf technology can be extended to other diseases. For patients, the introduction of the EV-Surf blood test eliminates the need for painful tissue biopsies. In the event of a positive test, it enables the immediate identification of the specific subtype of cancer, facilitating prompt initiation of effective treatment.

Funding and collaborators:

Project Aim:

Differentiate between EV and non-EV particles in biofluids by using fluorescence mode by Nanoparticle Tracking Analysis.

Project description:

My project focuses on developing an innovative method for distinguishing between extracellular vesicles (EVs) and non-EV particles in blood samples using nanoparticle tracking analysis (NTA). Blood samples are a convenient and reliable way to gain insights into both healthy and pathological conditions. However, a significant challenge in analyzing blood samples is differentiating EVs from other vesicles, such as lipoproteins (HDL, LDL, VLDL, and chylomicrons), which share similar size and density characteristics with EVs. To ensure accurate results, we are currently working on quantifying them using NTA. By employing specific markers and antibodies labeled with fluorophores, we can differentiate and measure distinct populations of EVs and lipoproteins as separate entities.

In summary, our project aims to isolate EVs from the blood of both healthy individuals and patients with prostate cancer using SEC. We then characterize these particles using NTA, allowing us to discriminate between EVs and non-EV particles. This advancement holds promise for optimizing diagnostics in prostate cancer.

In the frame of my upcoming PhD thesis, I will implement the gained knowledge for the validation of prostate cancer biomarkers identified on extracellular vesicles as indicators of castration and therapy resistance.

Funding and collaborations:   

Dr. Gerhard Pütz - Institute for Clinical Chemistry and Laboratory Medicine

Project Aims:

1. Investigate the role of Müller cell-derived extracellular vesicles in retinal vasoproliferative diseases

2. Characterize the EV-profile of blood samples from patients suffering from diabetic retinopathy

Project description:

My PhD thesis focusses on the pathophysiology of retinal vasoproliferative diseases, especially on the involvement of extracellular vesicles. I am mainly working with two sample types: Müller cells (funded by the Else-Kröner-Fresenius Foundation) and blood samples from diabetic patients (funded by Bayer – Förderprogramm für Augenheilkunde).

Project 1: Müller cells, the major glial cells in the retina, interact with various retinal cell types, playing a crucial role in retinal function and health. However, how Müller cells communicate with other retinal cells is not well understood. We are researching the role of extracellular vesicles (EVs), which can transport proteins, nucleic acids, and lipids between cells, in mediating this communication in both healthy and diseased retinas.

Project 2: Diabetic retinopathy (DR) is one leading cause of vision loss in patients suffering from diabetes mellitus. Since many patients do not show any symptoms until later stages of the disease, biomarkers that help to detect ophthalmologic complications early in the disease progression could improve treatment strategies. Therefore, we aim to investigate the EV-profile of blood samples from patients suffering from different stages of DR.

Funding and collaborations:   

PD Dr. Felicitas Bucher – https://www.uniklinik-freiburg.de/augenklinik/fol/expo/agbucher.html

Aim of the project:

To understand the molecular and genetic changes that occur in response to second-line therapy in prostate cancer, with the ultimate goal of identifying biomarkers that can guide treatment decisions and improve patient outcomes.

Project description:

My project aims to identify biomarkers that correlate with the response to second-line therapy in prostate cancer. To achieve this, we analyse extracellular vesicles (EVs) released from organoids and circulating in the blood of mice with human prostate cancer xenografts. These organoids are treated with Enzalutamide and Dihydrotestosterone, and the EVs will be studied for their surface proteins, RNA, and DNA content.

Funding and collaborators:

Project Aim:

I am working on a comparison of different methods for isolating extracellular vesicles (EVs) from patient samples (plasma) to find out which is best suited for clinical application. To evaluate the isolates, I am using several analytical methods commonly used in EV research.

Project Description:  

Isolation and analysis of extracellular vesicles (EVs) from body fluids can provide information about their origin and possible pathological conditions. EVs used for further analysis are often retrieved from blood samples since blood carries EVs from all kind of tissues and organs. However, plasma is a complex body fluid containing many lipoproteins and other proteins that are difficult to separate from EVs as they share similar properties such as size and density. This leads to inaccuracies in the analysis of isolates due to, for example, an overestimation of EV numbers and steric hindrances in immunoassays. Because of the enormous potential that EV specific information holds with regard to pathological findings and further research, there is great interest in highly purified EVs.

The project I am working on, which is a collaboration between the research group Nazarenko and Hahn-Schickard (https://www.hahn-schickard.de), aims to compare different EV isolation methods in terms of clinical applicability. I compare already established methods for the isolation of EVs from plasma to newly developed methods and methods that are still under development. For that, I use different analytical methods such as NTA, DLS, BCA and ELISA, which give an indication of the purity and yield of the isolates.

Funding and collaborations:

Aim of the project:

Isolation and characterization of EVs from human fibrosarcoma cell lines using NTA

Project Description:

Extracellular vesicles (EVs) are involved in intercellular communication; transferring their contents to recipient cells and modulating changes in these cells. They contain membrane proteins (e.g. teraspanins – Tspan8, CD63, CD9, and CD81) implicated in EV formation and in a wide range of human cancers. These proteins produce expression patterns that can provide useful information on the stages of a tumour, therefore, therapeutic intervention could be developed to block specific membrane proteins responsible for EV formation, hence preventing tumour metastasis.

Due to the heterogeneity of EVs in biological fluids, isolation of EVs from fibrosarcoma cells in culture and its characterisation using single particle optical techniques such as a nanoparticle tracking analysis (NTA) and nanoflow cytometry, provides scientific insight into the various size distribution of these vesicles, including target membrane proteins. NTA requires standard reference materials which mimics the properties of EVs and is capable of measuring EV epitope, size, refractive index and concentration. I am therefore also working on the establishment and optimization of standard operating procedures for the use of NTA in scatter mode, using silica(iv)oxide beads as reference material.

Funding and collaborations:

Role description:

Tanja holds a master degree in biology and is the main pillar for efficient functioning in our research group.  She trains and mentors students and lab staff as well as enforcing standard and safety regulations for sample handling. She manages group coordination within Uniklinik research groups and our external research collaborators.

She also oversees the smooth operation in the laboratory, handling tasks like staff scheduling and safety protocols. She is maintaining a safe and efficient lab environment. Her responsibilities include employee and student supervision, supply management and documentation.

Tanja is also heavily involved in teaching master students of Molecular Medicine, in their offered module Exosome and Tumour Biology.