Research Senada Koljenovic

Abstract

Cholangiocarcinoma (CCA), an aggressive cancer of the epithelial cells of the bile ducts, is unfortunately often diagnosed in the late stage, leading to limited treatment options and subsequently to poor prognosis (5-year overall survival rates of 7-20%). Late-stage, unresectable disease is typically tested for FGFR2 fusions in tissue samples. However, diagnostic tissue samples often fail to capture the heterogeneity of the disease and may be inaccessible or risky to obtain. Liquid biopsies offer a promising minimally invasive alternative. While existing molecular techniques for gene fusion detection, such as FISH, RT-qPCR, and targeted RNA sequencing, have shown efficacy, they possess limitations in terms of speed, cost, multiplexing (i.e., simultaneous detection of different markers in the same sample), technical complexity and adaptability to liquid biopsies. To address these challenges, we propose a novel enzyme-free approach utilizing a singlet oxygen-based photoelectrochemical (1O2-PEC) platform for the fusion partner-agnostic detection of FGFR2 fusions in CCA patients. This platform offers high sensitivity, rapidity, ease-of-use, possibility for multiplexing, and is cost-effective. During the project, we will develop highly specific probes, evaluate their performance and determine the minimal sample preparation for tissue and liquid biopsies as a first push towards the routine clinical practice.

Researcher(s)

• Promoter: Koljenovic Senada
• Co-promoter: De Wael Karolien
• Co-promoter: Vandamme Timon
• Fellow: Arnouts Jorine

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

Surgery is the mainstay of treatment for oral cavity squamous cell carcinoma (OCSCC). Adequate resection margins (i.e. a minimum distance of 5 mm between the tumor and the surface of the resection specimen) are crucial for local disease control and prognosis. Inadequate tumor resection necessitates adjuvant (chemo) radiation or re-operation. Despite such adjuvant treatment the prospects of the patient are definitely diminished by inadequate margins. In addition, both radiation and chemotherapy may significantly affect the decreased quality of life. Unfortunately, the current rate of adequate OCSCC surgical results is only 15%. Clearly, the combination visual inspection and palpation with pre-operative imaging (e.g. CT, MRI), is insufficient to warrant adequate resections. To compensate this, a common intraoperative procedure for surgeons is to take tissue samples from the surgical wound bed for intraoperative pathological assessment of the resection margin. However, this so called frozen section procedure has many limitations; only a small proportion of the resection margin can be inspected in this way and the samples may not be representative. Moreover, here is no measurement of margin length, so close margins cannot be detected. More importantly, frozen section of the wound bed has not been unambiguously demonstrated to improve outcome. Intraoperative assessment of resection margins (IOARM) of OCSCC resection specimen has been proven to be the way forward. This approach has led to an immediate increase in the number of adequate resections from 15% to more than 50%. However, it is not realistic to expect that such laborious intraoperative assessment requiring a well-trained dedicated team of specialists can be widely adopted to become a standard of care. Therefore, an objective easy-to-use technique is needed, to accurately assess all resection margins intraoperatively. In this project, we propose the development of such a technique based on Raman spectroscopy. Raman spectroscopy is a non-destructive optical technique, which provides detailed information of the biochemical composition of a tissue, without the use of labels, dyes or reagents. Because malignant transformation is associated with changes in the biochemical composition of tissues, Raman spectroscopy can be used to distinguish a normal tissue from tumor. Recently, we have clearly shown that tissue water content is a powerful biomarker for discrimination between OCSCC and uninvolved oral structures. We have found the water concentration in OCSCC to be consistently higher than in the surrounding tissue. This new finding opens the way to new opportunities in intraoperative assessment of resection margins, in an objective and time-efficient manner.

Researcher(s)

• Promoter: Koljenovic Senada
• Co-promoter: Peeters Marc
• Co-promoter: Smits Evelien
• Co-promoter: Vanderveken Olivier

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

The complexity of critical illness in intensive care essentially requires a precision approach. Organ failure and sepsis are key detrimental factors in critical illness, and fundamentally driven by an auto-amplifying loop of cell death and inflammation. This process feeds dynamic disease fluctuations and heterogeneity in critical care, which might partially explain inconsistent translatability. Patients with similar clinical presentations typically have different cellular and molecular responses due to individual differences and co- morbidities. To deal with this form of heterogeneity, innovative biomarkers with predictive value are needed to allow determining subtypes of clinically similar patients. There is a growing list of circulating detrimental biomolecules related to some forms of regulated non-apopoptic cell death (i.e. so-called ferroptotic and pyroptotic cell death), which are druggable and allow stratifying critically ill patients. Actually, we discovered that therapeutic targeting ferroptosis or pyroptosis respectively increased survival in experimental models of multi organ failure or septic shock. To allow follow-up of clinical intervention studies, real-time diagnostics for these detrimental factors are needed. Dynamic monitoring of a panel of cytokines in critically ill patients showed prognostic value for 30-day survival, septic shock and organ injury. To level up our proof of concept, we want to conduct a translational study in critically ill patients by using real-time immunodiagnostics to detect ferroptosis and pyroptosis; which should allow quick stratification for the linked targeted therapies thereby preventing organ/systemic dysfunction and mortality. To detect general tissue injury due to excess cell death, we also optimized a procedure to episequence plasma cell free DNA (cfDNA) using real-time Oxford Nanopore Technology. As a potential future complementary diagnostic tool, we want to determine the diagnostic power of nanopore episequencing to detect tissue specific cell death. To process the clinical and molecular fingerprint of the critically ill determined in biofluids, we additionally use big data mining approaches in these phenotypically well-characterized patients. Precision intervention based on innovative real-time molecular diagnostics and stratification could bring diagnostics in intensive care into the 21st century and pinpoint which patients are likely to benefit from a certain treatment.

Researcher(s)

• Promoter: Vanden Berghe Tom
• Co-promoter: Jorens Philippe
• Co-promoter: Koljenovic Senada

Research team(s)

• Cell death signaling (CDS)

Project type(s)

• Research Project

Abstract

Cancer is a leading cause of death worldwide, accounting for nearly 10 million deaths in 2020. SOCan will contribute to the (early) diagnosis and follow up of cancer via a new disruptive detection platform, i.e. singlet oxygen-based photoelectrochemical detection of cancer biomarkers. Those biomarkers are increasingly discovered and validated, but the detection necessitates rapid, accurate and sensitive devices. To achieve this, the combined use of electrochemical detection with light-triggered sensor technology for the specific and sensitive detection of pre-selected DNA and RNA cancer biomarkers is proposed. The application of this technology on tissue and liquid biopsy samples will be a major contribution to the early detection of cancer. SOCan aligns with the EU Mission on Cancer and will lead to an affordable and sensitive diagnosis of cancer, reducing the time to result which allows faster and specific treatment, and thereby saving lives.

Researcher(s)

• Promoter: Peeters Marc
• Co-promoter: Koljenovic Senada

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

Inspired by the mission of the EU commission, this project commits to tackle a major societal challenge, i.e. fighting cancer. A striking target for 2030 has been set by the EU: more than 3 million lives saved, living longer and better, achieve a thorough understanding of cancer, prevent what is preventable, optimize diagnosis and treatment, support the quality of life of all people exposed to cancer, and ensure equitable access to the above across Europe. This project contributes to (early) diagnosis and follow up of the disease. More and more biomarkers are discovered and validated for cancer and the highly precise determination thereof is high on the priority list, necessitating analytical devices that allow rapid and accurate analysis with high sensitivity. Electrochemical biochips are an emerging tool for point-of-care diagnostic systems due to their inherent high sensitivity and cost and time effectiveness. We propose the combined use of electrochemical detection with a light-triggered sensing technology for the specific and selective photoelectrochemical detection of low concentrations of cancer biomarkers (i.e. KRAS mutations), also allowing us to detect a panel of cancer biomarkers. Detection and quantification of the selected target sequences will be performed in tissue and liquid biopsies, to ensure the translation from a lab technology to a device for clinicians and even patients.

Researcher(s)

• Promoter: De Wael Karolien
• Co-promoter: Koljenovic Senada
• Co-promoter: Peeters Marc
• Co-promoter: Van Camp Guy

Research team(s)

• Antwerp engineering, PhotoElectroChemistry & Sensing (A-PECS)

Project type(s)

• Research Project

Abstract

Melanocytic skin lesions can either be benign or malignant. Although pathologic examination often provides a final diagnosis, in a number of cases the morphology is ambiguous and the malignant potential of the lesion cannot be determined. This uncertainty of the diagnosis has important consequences for the patients and the community. In case patients are incorrectly diagnosed with melanoma instead of a benign lesion, they will be subjected to unnecessary clinical examinations, psychological pressure and social disadvantages. On the other hand, patients with an incorrect diagnosis of a benign lesion instead of melanoma are insufficiently treated leading to a high risk of developing deadly metastatic disease. In this project we aim to technically verify and clinically validate a molecular assay to predict the malignant potential of ambiguous melanocytic lesions for which proof-of-concept has ready been established. This assay is based on genome-wide copy number variation (CNV) analysis. In a first phase we will finetune and standardize the proof-of-concept assay using a training set of 106 cases, enriched with ambiguous cases. The diagnostic accuracy and ideal cut-off will be determined and the performance of the assay will be verified in an independent test set of 76 ambiguous cases. The resulting assay, hereafter named AMELA assay (assay for Ambiguous MELanocytic skin lesions Analysis), will be validated in the second phase of the study. In a second phase a prospective, observational multicenter study will be conducted. Samples of 552 patients with ambiguous lesions will be included. The clinical performance (accuracy, sensitivity and specificity) of the assay will be determined based on adverse events during 2 years of follow-up. In addition, the robustness of the assay and the potential financial impact on the society will be assessed

Researcher(s)

• Promoter: Koljenovic Senada

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

Inspired by the mission of the EU commission, this project commits to tackle a major societal challenge, i.e. fighting cancer. A striking target for 2030 has been set by the EU: more than 3 million lives saved, living longer and better, achieve a thorough understanding of cancer, prevent what is preventable, optimise diagnosis and treatment, support the quality of life of all people exposed to cancer, and ensure equitable access to the above across Europe. This project contributes to (early) diagnosis and follow up of the disease. More and more biomarkers are discovered and validated for cancer and the highly precise determination thereof is high on the priority list, necessitating analytical devices that allow rapid and accurate analysis with high sensitivity. Electrochemical biochips are an emerging tool for point-of-care diagnostic systems due to their inherent high sensitivity and cost and time effectiveness. We propose the combined use of electrochemical detection with a light-triggered sensing technology for the specific and selective photoelectrochemical detection of low concentrations of cancer biomarkers (i.e. KRAS mutations). In this project we will focus on the development of a multiplexed 96-well plate-based detection of a panel of cancer biomarkers. Detection and quantification of the selected target sequences will be performed in liquid biopsies, to ensure the translation from a lab technology to a device for clinicians and even patients.

Researcher(s)

• Promoter: De Wael Karolien
• Co-promoter: Koljenovic Senada
• Co-promoter: Peeters Marc
• Co-promoter: Van Camp Guy

Research team(s)

Project type(s)

• Research Project