Research Timon Vandamme

Abstract

Colorectal cancer (CRC) is the third most common malignancy, accounting for approximately 10% of all cancer cases (i.e. 1.2 million CRC patients each year), and is the second leading cause of cancer-related deaths worldwide. Current treatment options such as chemotherapy and targeted/immunotherapies are insufficient due to resistance development and limited efficacy. Personalized medicine, focusing on novel prognostic and predictive biomarkers to identify patients that will respond to treatment, is crucial to increase the success rate and the patient's quality of life. One of the hallmark features of CRC adenocarcinomas is aberrant mucin (MUC) expression which drives the transition from inflammation towards cancer and has been linked to initiation, progression, and poor prognosis. Adenocarcinomas also overexpress transmembrane mucins to exploit their role in promoting tumour cell death resistance, as previously shown for MUC1, MUC4 and MUC13. Furthermore, mucins undergo extensive splicing. Mucins are highly polymorphic and gene polymorphisms affecting mucin gene expression have been reported to influence susceptibility towards CRC. The presence of genetic differences, including single nucleotide polymorphisms (SNPs), in mucin genes can give rise to a large repertoire of structurally diverse mRNA isoforms via alternative splicing. While most mRNA isoforms produced from the same mucin gene locus encode similar biological functions, others can have the potential to alter protein function resulting in the progression towards disease. Such cancer-associated mucin mRNA isoforms can thus be essential players in protecting CRC cells from death and in this way impacting the efficacy of CRC treatment. In this project, we will first unravel the mucin mRNA isoform landscape and its alternative splicing machinery that associate with the marked heterogeneity in CRC and investigate its potential to predict the malignant transformation in patients with precancer stadia. Thereafter, we will investigate the functional link between the CRC-associated mucin mRNA isoform signatures driving cell death resistance and their potential to predict the optimal therapy. These research objectives will be approached using established high-throughput next-generation sequencing and organoid models derived from CRC patients.

Researcher(s)

• Promoter: De Winter Benedicte
• Co-promoter: Sleegers Kristel
• Co-promoter: Smet Annemieke
• Co-promoter: Vandamme Timon

Research team(s)

• Laboratory Experimental Medicine and Pediatrics (LEMP)

Project type(s)

• Research Project

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

COVID-19, a disease caused by an infection with SARS-CoV-2, has a broad range of clinical presentations varying from asymptomatic to severe bilateral pneumonia and even death. The risk to develop severe COVID-19 as well as the mortality is the highest in the elderly and in people with a pre-existing condition such as cancer. Hence, cancer patients were prioritized for COVID-19 vaccination even though data on the effectiveness and safety was not available as immunocompromised patients, like cancer patients, were excluded from vaccine approval trials. Since the approval of different COVID-19 vaccines, our group as well as many others performed studies to map the immunological responses of cancer patients after vaccination. In general cancer patients have reduced humoral immune responses after COVID-19 vaccination, nevertheless the vaccines are well-tolerated. As COVID-19 is evolving to be an endemic virus, it is important to map all parts of the vaccination-induced immune response. While most studies report IgG levels and neutralizing antibodies when investigating the humoral immunity, IgA antibodies are important for mucosal immunity and eliminate pathogens immediately at the point of entry (e.g. respiratory system). In the context of influenza, IgA serum levels have been correlated with influenza vaccine efficacy and influenza-specific IgA has been shown to be more effective in preventing infections in mice and humans compared with influenza-specific IgG. Therefore the level of IgA in serum may serve as an indicator of host immune response and might possible be a better predictor for protection against respiratory viruses compared to IgG, but studies on IgA production upon COVID-19 vaccination are lacking. Additionally, studies assessing the role of innate immune cells in vaccination-induced immune response are scarce. A recent study provided the first hints towards the predictive capacity of NK cells -innate lymphocytes that are crucial for mediating anti-viral responses- for vaccine-induced immunity in both healthy individuals and immunocompromised patients without cancer. This is in line with other research highlighting the potential of the activity level of NK cells to serve as a biomarker for a functional immune response, but as NK cells are involved in anti-tumor responses and might be affected by anti-neoplastic treatment, it is currently unknown if these findings can be applied in a cancer population. Hence, the aim of the current study is to gain a more in depth understanding of the different aspects of vaccination-induced immunity against SARS-CoV-2 in cancer patients focusing on both IgA levels and NK cells. This will help guiding COVID-19 vaccination strategies for cancer patients during future endemic outbreaks by providing knowledge on the state of the immune system of cancer patients and their response upon vaccination. Furthermore, the obtained insights can be used to improve vaccination strategies for cancer patients for other viruses as well as when novel viral pathogens emerge.

Researcher(s)

• Promoter: Vandamme Timon
• Co-promoter: Van Audenaerde Jonas
• Fellow: Debie Yana

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

Inspired by the European Union (EU) commission, this project aims to address a major societal challenge: fighting cancer. The EU has ambitious goals, such as saving more than three million lives and improving diagnosis and treatment for everyone in Europe. MutArray will contribute to achieve them by providing fast, affordable and reliable diagnosis and monitoring for colorectal cancer (CRC), which is the second leading cause of cancer deaths globally. Accurate detection of clinical biomarkers is a priority, requiring analytical devices that enable rapid analysis with high specificity and sensitivity. Electrochemical bioplatforms are emerging tools for diagnostic systems thanks to their inherent simplicity, cost and time effectiveness, which are the limitations of current clinical technologies. MutArray will focus on the development of a 96-well plate multiplexed bioplatform based on the use of the singlet oxygen-mediated photoelectrochemistry, locked nucleic acids (LNA) probes and the CRISPR/Cas system for the specific detection of CRC biomarkers, such as single nucleotide variations (SNVs). Both solid (tissue) and liquid (plasma) biopsies from CRC patients will be analyzed and clinically validated for SNV detection in the KRAS oncogene. This novel approach can be used to detect any nucleic acid biomarker and will ensure the translation from a laboratory technology to a benchtop device for clinicians and hospital settings that positively impacts the fight against cancer.

Researcher(s)

• Promoter: De Wael Karolien
• Co-promoter: Vandamme Timon
• Fellow: Valverde De La Fuente Alejandro

Research team(s)

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

Project type(s)

• Research Project

Abstract

In Belgium, yearly approximately 1600 patients are diagnosed with mCRC, and have a 5-year overal survival (OS) rate below 20%. Therapy generally consists of chemotherapy and targeted therapy, and the response to therapy is evaluated every 8 weeks using imaging techniques (i.e., CT scans) and tumor markers. However, this follow-up method is not optimal and delays detection of progressive disease (PD). This poses challenges in care for these patients given their poorer prognosis as compared to other common cancer types. Late detection of PD delays the switch from the current therapy to a new therapy. In this case, the optimal therapeutic window for the new therapy is missed and there is longer exposure to unwanted toxicities of the current therapy. These factors contribute to a worse Quality of Life (QoL) both directly and indirectly, and thus impact patient outcomes. Novel biomarkers like circulating tumor DNA (ctDNA) have shown promise in mitigating these shortcomings of the current follow-up techniques. These biomarkers are obtained through LBs, which harbor ctDNA that originates directly from the tumor. The analysis of ctDNA has shown its utility in various settings in oncology, and specifically for mCRC, pilot studies, including our research, indicate that follow-up of patients with NPY methylation-based ctDNA analysis can detect PD earlier than conventional techniques. One such pilot study is the FOLICOLOR lead-in study, which showed that LBs can detected PD earlier than the current techniques (manuscript in preparation). The NPY methylation-based ctDNA analysis was validated during this study, and optimal cut-off for PD detection was determined. Within the randomized FOLICOLOR trial, this promising NPY methylation-based ctDNA analysis is applied to compare treatment follow-up via LBs to follow-up through the current techniques. We hypothesize that earlier PD detection will lead to earlier identification of patients who do not respond to the current line of therapy, which will prompt earlier switch to a new line of therapy. This will prevent unnecessary toxicities from the current therapy and allows the start of a new line of therapy in a more suitable therapeutic window leading to enhanced treatment efficacy, potentially improving OS and QoL. Frequent follow-up will also empower patients and will stimulate true joint decision-making on therapy decisions. In the prospective, randomized, open-label, multicentric, phase II FOLICOLOR trial, 150 mCRC patients starting 1st line therapy are randomized to one of the two study arms: the control arm (with follow-up through CT scans and CEA every 8 weeks as part of the standard of care (SOC)) or the study arm (with follow-up through LBs every 4 weeks, while still receiving CT scans and CEA every 8 weeks as part of the SOC). As the aim of this project is to reduce the overall toxicity in these patients, in order to improve QoL, the primary endpoint is to assess the difference in time to deterioration (TTD) in both arms. Secondary endpoints include difference between both arms in terms of progression-free survival (PFS), 3-year OS, toxicity, and long-term QoL. Finally, exploratory endpoints like comparison of ctDNA and CEA in PD prediction, association of ctDNA and PFS, and the development of a decision aid are included.

Researcher(s)

• Promoter: Vandamme Timon
• Co-promoter: Op de Beeck Ken
• Co-promoter: Peeters Marc
• Co-promoter: Prenen Hans
• Co-promoter: Van Camp Guy

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

Neuroendocrine neoplasms (NENs) require regular assessment of tumor growth and treatment response. However, adequate, non-invasive tumor markers are currently lacking. Recently, we demonstrated that sequential genome-wide copy number alteration (CNA) profiling of circulating cell-free DNA (ccfDNA) could serve as novel, non-invasive biomarker in NEN patients. Expanding upon these findings, we will explore and benchmark a new analytical approach, GIPXplore, against the current gold standard for ccfDNA CNA analysis (ichorCNA). Moreover, aberrant methylation in ccfDNA will be analyzed using the novel, highly sensitive MSRE-smMIP-seq technology. Both methods for detection and quantification of tumoral DNA will be correlated to clinical outcomes in an extensive prospectively collected cohort of 250 NEN patients. This cohort will be established through the international collaboration between the Belgian ENETS CoEs and Dutch FORCE initiative. In doing so, we will validate the potential added value of ccfDNA analysis for clinical decision-making in NEN patients and facilitate clinical implementation.

Researcher(s)

• Promoter: Vandamme Timon

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

Digestive neoplasms include include a wide range of tumortypes in the upper and lower digestive tract. In Belgium, 12740 new cases of digestive neoplasms were reported (16% of total new reported cancer diagnoses) (source: Belgian Cancer Registry). A large proportion of these tumors is diagnosed at an advanced stage, resulting in high morbidity and mortality rates as the ideal therapeutic window is missed. Despite their high incidence and prevalance, there is a lack of (1) tools for early diagnosis, and lack of (2) good quality follow-up tools tot detect progressive disease (PD) earlier. There is urgent requirement of developement of accurate non-invasive biomarkers to answer to these unmet needs. Neuroendocrine neoplasms (NENs) form a group of relatively rare malignancies, and originate frequently from organs of the digestive tract. In Belgium, more than 1000 new NEN cases were reported in 2018 and the 5-year prevalence of all NEN cases was estimated at 3400 patients (Belgian Cancer Registry). Because of their relatively indolent nature, long-term follow-up is necessary to assess tumor growth and response to treatment. Currently, follow-up is performed using techniques based on imaging and evaluation of protein biomarkers, neither of which is ideal. The development of accurate noninvasive biomarkers in NEN patients represents one of the most important unmet needs according to the European Neuroendocrine Tumor Society (ENETS). Recently, we demonstrated that sequential genome-wide copy number alteration (CNA) profiling of circulating cell-free DNA (ccfDNA) could serve as a new, non-invasive biomarker for follow-up of patients with metastatic NEN. Additionally literature shows that similar principle of analysis of ccfDNA in digestive neoplasms, has great potential too as a non-invasive biomarker for early diagnosis of these tumors, and better follow-up of patients with metastatic disease. Moreover, it was revealed that even ccfDNA without apparent CNAs contains informative genomic signatures, that allow for better differentiation between healthy individuals and cancer patients. Additionally, preliminary studies already revealed great potential for methylation profiling of ccfDNA as a biomarker in NENs and digestive neoplasms. However, investigating the potential clinical impact of ccfDNA in extensive cohorts of NEN patients and patients with digestive neoplams, given clinical implementation remains difficult due to restricted numbers of patients and/or incomplete datasets. The project aims to investigate the potential impact of ccfDNA on clinical decision-making and facilitate the implementation of ccfDNA assays in a clinical setting, with the ultimate goal of improving care and outcome of patients with NENs and digestive neoplasms. To achieve this, we pursue these objectives: 1. Setting up a systematic collection of liquid biopsies and clinical data from a large population of patients with NENs and digestive neoplasms to achieve an adequate sample size for ccfDNA analysis. 2. Validating two novel ccfDNA analyzing techniques for assessment of the presence and quantification of circulating tumor DNA (ctDNA) in liquid biopsies derived from an extensive cohort of patients with NENs and digestive neoplasms. 3. Monitoring tumor fraction (i.e. ctDNA quantities) over time in sequential plasma samples from NEN patients using two ccfDNA assays and correlating this with time to progression (according to RECIST 1.1 criteria) to explore the predictive efficacy of ccfDNA analysis and thereby evaluate its biomarker potential for patient follow-up.

Researcher(s)

• Promoter: Prenen Hans
• Promoter: Vandamme Timon

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

Neuroendocrine neoplasms (NENs) exhibit clinical and biological heterogeneity, making diagnosis extremely challenging. Moreover, NENs tend to progress slowly necessitating long-term follow-up to monitor tumor growth and response to therapy. Current modalities for diagnosis and follow-up of NENs are primarily based on imaging and (repeated) tissue biopsies, but these suffer from several shortcomings which has a direct impact on patients' lives. Over the past few years, liquid biopsies have gained interest as a minimallyinvasive way for rapid tumor detection and collection of molecular information of the tumor with circulating tumor DNA (ctDNA) as one of the most promising new markers. This ctDNA is the fraction of cellfree DNA (cfDNA) released by the tumor, that reflects both the genetic and epigenetic alterations of the tumor. Consequently, this project aims to leverage liquid biopsies to improve diagnostic accuracy in NENs and enable real-time monitoring of NEN patients. For this purpose, NEN-specific molecular alterations namely copy number alterations and differentially methylated CpGs will be identified and selected to enable detection and quantification of ctDNA. Since the gold standard detection methods, shallow whole genome sequencing and methylation arrays, respectively, are not capable to detect very low concentrations of ctDNA, two alternative and highly sensitive multiplex assays based on DNA sequencing and photoelectrochemistry, respectively, will be employed.

Researcher(s)

• Promoter: Vandamme Timon
• Fellow: Vandamme Timon

Research team(s)

• Center for Oncological Research (CORE)

Project type(s)

• Research Project

Abstract

T-cells are not only crucial actors in our defense against microbes but play an important role in protecting us from cancer. T-cells recognize their targets via its T-cell Receptor (TCR), which consists of a TCRa and TCRb chain. It has been shown that the cancer tissue TCR repertoire holds capacity in predicting which cancer patients will respond to checkpoint-inhibitor therapy, thereby supporting the concept that the tissue-specific TCR repertoire may be considered a stratification biomarker. Decoding the paired TCRab repertoire from the routinely obtained FFPE tissue, necessitates the development of a new single cell workflow method that will allow FFPE tissue paired TCRab sequencing. This would potentially represent a revolution, not only in oncology, but in autoimmunity diseases too where rogue Tcells could be found in affected tissues. In this project, we will create, develop and validate an experimental protocol to obtain paired TCRab data from FFPE tissue.

Researcher(s)

• Promoter: Ogunjimi Benson
• Co-promoter: Vandamme Timon

Research team(s)

• Centre for Health Economics Research and Modelling of Infectious Diseases (CHERMID)

Project type(s)

• Research Project