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Projects / Programmes source: ARIS

Minimally invasive diagnostic approaches in brain tumours using circulating cell-free nucleic acids

Research activity

Code Science Field Subfield
3.03.00  Medical sciences  Neurobiology   

Code Science Field
3.01  Medical and Health Sciences  Basic medicine 
Keywords
Central nervous system tumours, gliomas, circulating nucleic acids, liquid biopsy, mutation detection, tumour classification, epigenetics, non-coding RNA expression profiles, methylation profiles, digital PCR, new generation sequencing, molecular biomarkers.
Evaluation (rules)
source: COBISS
Researchers (21)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  33147  PhD Luka Bolha  Biochemistry and molecular biology  Researcher  2020 - 2023  26 
2.  10511  PhD Roman Bošnjak  Neurobiology  Researcher  2020 - 2023  416 
3.  39127  PhD Ana Dolinar  Chemistry  Junior researcher  2020  20 
4.  35916  PhD Barbara Faganel Kotnik  Human reproduction  Researcher  2020 - 2023  155 
5.  39128  PhD Gašper Grubelnik  Microbiology and immunology  Junior researcher  2020 - 2021  31 
6.  50799  Arne Jeglič  Interdisciplinary research  Researcher  2020 - 2023  10 
7.  19130  PhD Jera Jeruc  Microbiology and immunology  Researcher  2020 - 2023  164 
8.  19257  PhD Lidija Kitanovski  Oncology  Researcher  2020 - 2023  156 
9.  52857  Danijela Kolenc    Researcher  2020  52 
10.  29321  PhD Rok Košir  Cardiovascular system  Researcher  2020 - 2022  90 
11.  35428  PhD Alenka Matjašič  Oncology  Researcher  2020 - 2023  35 
12.  20251  PhD Boštjan Matos  Neurobiology  Researcher  2020 - 2023  46 
13.  26058  PhD Jože Pižem  Oncology  Head  2020 - 2023  170 
14.  07090  PhD Mara Popović  Neurobiology  Retired researcher  2020 - 2023  306 
15.  28382  PhD Uršula Prosenc Zmrzljak  Public health (occupational safety)  Researcher  2020 - 2023  89 
16.  32723  PhD Marija Skoblar Vidmar  Medical sciences  Researcher  2020 - 2023  77 
17.  20176  PhD Uroš Smrdel  Oncology  Researcher  2020 - 2023  119 
18.  34912  Milica Stefanović  Oncology  Researcher  2020 - 2023  13 
19.  51957  PhD Ana Unkovič  Medical sciences  Junior researcher  2020 - 2021 
20.  28143  PhD Andrej Zupan  Oncology  Researcher  2020 - 2023  53 
21.  51028  PhD Margareta Žlajpah  Oncology  Researcher  2020 - 2022  17 
Organisations (4)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0381  University of Ljubljana, Faculty of Medicine  Ljubljana  1627066  48,404 
2.  0302  Institute of Oncology Ljubljana  Ljubljana  5055733000  15,485 
3.  0312  University Medical Centre Ljubljana  Ljubljana  5057272000  77,691 
4.  2802  LABENA trgovina, svetovanje in proizvodnja laboratorijske opreme d.o.o. (Slovene)  Ljubljana  5699479  392 
Abstract
Introduction. Tumours of the central nervous system (CNS) are a group of tumours that develop in the brain and spinal cord, including the meninges, pituitary gland, pineal gland and optic nerve. The majority of primary CNS tumours are aggressive neoplasms, which despite radical treatment (usually a combination of surgery, radiotherapy and chemotherapy) frequently recur, often in a more malignant form. Advances in the molecular characterization of primary brain tumours have led to an extensive revision of the WHO classification of CNS tumours and to an update of the neuropathological assessment of brain tumours, which integrates histopathological features and molecular genetic tests for classification, prediction of biological behaviour and treatment decisions. One of the main problems in the management of patients with primary brain tumours is the lack of effective strategies that could detect the disease at an early stage. In addition, these tumours are clinically and molecularly extremely heterogeneous. Often several genes are altered, both at the genomic and transcriptomic level. Due to high tumour heterogeneity, the correct diagnosis and therapy selection can therefore be difficult and inadequate, and may lead to poor prognosis. Currently, CNS tumour diagnostics require surgical removal of the tumour, a highly invasive procedure, which sometimes needs to be performed repeatedly (for primary and recurrent tumours), and, on the other hand, is not always possible due to the tumour location or patient’s general condition. Objectives. The main goal of the proposed research project is the implementation of minimally invasive diagnostics of brain tumours in adults and children by analysing cell-free tumour DNA and RNA in plasma and cerebrospinal fluid (liquid biopsy). We will also compare detailed genetic data from patients' tumour tissue and fluids to study the heterogeneity and evolution of tumours. By using a next-generation sequencing panel, we will try to identify and monitor acquired treatment resistance and the efficiency of treatment. Moreover, with the use of ultrasensitive digital droplet PCR, we will monitor minimal residual disease and recurrence. We aim that the results will provide us with standardised tests and techniques needed for an early diagnosis/recurrence of brain tumours and for determining the response to treatment and follow-up. Patients and methods. For the study, we will prospectively recruit 150-200 patients with primary brain tumour and follow them from the initial diagnostic phase, through the treatment phase and during the monitoring phase. In each phase, we will collect plasma and cerebrospinal fluid (when available) samples, together from 4-6 samples (before surgery, before radiation and/or chemotherapy and then at 3-6 months’ intervals). Surgically removed brain tumour samples will be used for standard histopathological diagnostic procedures and analysed by next-generation sequencing panels. We will develop new methods, such as digital droplet PCR-based custom assays for the ultrasensitive detection of cell-free tumour DNA and RNA in the plasma and cerebrospinal fluid of the patient. For a broader biomarker detection in plasma and cerebrospinal fluid, we will use a method of next-generation sequencing pan-cancer panel. In addition, we will perform non-coding RNA and methylation profiling on tissue samples using RNA sequencing and methylation array profiling.
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