\nAluminum (Al) toxicity represents an important limitation to worldwide crop production, occurring in upwards of 50 % of the world’ arable land The most evident symptom and important consequence of Al toxicity is root growth inhibition Additionally, Al influences phosphorus (Pi) availability, eventually resulting in nutritional deficiency in shoots and leaves Recently, we have identified through a chemical genomics screen in Arabidopsis thaliana a compound (nominated C43) that confers Al resistance, being a potential Casein Kinase 2 (CK2) inhibitor Our preliminary data indicate that CK2 grants Al toxicity resistance through phosphorylation of the SOG1 transcription factor, being an essential regulator arresting cell cycle progression in response to DNA damage Strikingly, C43 also grants growth under low Pi conditions, suggesting that Pi-deficiency and Al-toxicity converge via the CK2-SOG1 pathway Within this project, we aim to test this hypothesis through a detailed structural-functional analysis in combination with physiological experiments In particular, the interactions between C43, CK2 and SOG1 will be studies at the biochemical, biophysical and structural level Additionally, the obtained structural data will be correlated with growth experiments under conditions of Al toxicity and Pi depletion\n\n
","iweto_id":"3G036020","start_date":"2020-01-01","title":"Functional-structural analysis of Casein Kinase 2 and SOG1 in response to Al-induced DNA damage and phosphate starvation","gismo_id":"4896f6d6-225c-11ea-9b15-d7676230cb7f","end_date":"2023-12-31"}],"volume":"54","abstract_full":[{"lang":"eng","text":"Liquid-liquid phase separation is a key phenomenon in the regulation of transcription in eukaryotes, leading to the formation of so-called membraneless organelles. While transcription factors take part in several types of membraneless organelles, it remains unclear how specific DNA binding, multivalent interactions with DNA/RNA, and condensation are interlinked. Here, we show that the NAC domain of suppressor of gamma response 1 (SOG1) (SOG1NAC), a transcription factor that is central to the DNA damage response in plants, can undergo liquid-liquid phase separation in vitro in the presence of both RNA or double-stranded DNA. This behaviour and the ability of SOG1NAC to bind DNA in a sequence-specific manner are dependent on its potential to form homodimers and the presence of a cluster of positive charges in its DNA-binding site. Short double-stranded DNA fragments containing the sequence motif that is specifically recognized by SOG1NAC inhibit RNA-mediated phase separation, suggesting overlapping binding sites for DNA and RNA. This may reflect a complex interplay between DNA and RNA binding that could control the formation of condensates at transcription sites."}],"author":[{"first_name":"Kim","name_last_first":"Mignon, Kim","name":"Kim Mignon","last_name":"Mignon"},{"name":"Rani Van der Eecken","last_name":"Van der Eecken","first_name":"Rani","name_last_first":"Van der Eecken, Rani"},{"ugent_id":["000191693218","802003463441","974677734262"],"orcid_id":"0000-0002-1095-5957","biblio_id":"4527cdc0-b1af-11ea-8258-8ff63b5ed74c","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE09"}],"ugent_id":"WE09"}],"name":"Margot Galle","name_last_first":"Galle, Margot","first_name":"Margot","last_name":"Galle","_id":"4527cdc0-b1af-11ea-8258-8ff63b5ed74c"},{"name_last_first":"Demulder, Manon","first_name":"Manon","last_name":"Demulder","name":"Manon Demulder"},{"last_name":"Van Lindt","name":"Joris Van Lindt","name_last_first":"Van Lindt, Joris","first_name":"Joris"},{"_id":"F4C04C64-F0ED-11E1-A9DE-61C894A0A6B4","last_name":"De Veylder","ugent_id":["801000929338","978299444177"],"orcid_id":"0000-0003-1150-4426","biblio_id":"F4C04C64-F0ED-11E1-A9DE-61C894A0A6B4","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE09"}],"ugent_id":"WE09"}],"name":"Lieven De Veylder","name_last_first":"De Veylder, Lieven","first_name":"Lieven"},{"last_name":"De Greve","name":"Henri De Greve","name_last_first":"De Greve, Henri","first_name":"Henri"},{"first_name":"Remy","name_last_first":"Loris, Remy","name":"Remy Loris","last_name":"Loris"}],"date_created":"2026-01-26 11:17:32","external":0,"doi":["10.1093/nar/gkaf1522"],"subject":["Biology and Life Sciences"],"biblio_id":"01KFX0BWVWEK66706ZB0AFAD9K","status":"public","abstract":["Liquid-liquid phase separation is a key phenomenon in the regulation of transcription in eukaryotes, leading to the formation of so-called membraneless organelles. While transcription factors take part in several types of membraneless organelles, it remains unclear how specific DNA binding, multivalent interactions with DNA/RNA, and condensation are interlinked. Here, we show that the NAC domain of suppressor of gamma response 1 (SOG1) (SOG1NAC), a transcription factor that is central to the DNA damage response in plants, can undergo liquid-liquid phase separation in vitro in the presence of both RNA or double-stranded DNA. This behaviour and the ability of SOG1NAC to bind DNA in a sequence-specific manner are dependent on its potential to form homodimers and the presence of a cluster of positive charges in its DNA-binding site. Short double-stranded DNA fragments containing the sequence motif that is specifically recognized by SOG1NAC inhibit RNA-mediated phase separation, suggesting overlapping binding sites for DNA and RNA. This may reflect a complex interplay between DNA and RNA binding that could control the formation of condensates at transcription sites."],"type":"journalArticle","article_number":"gkaf1522","handle":"http://hdl.handle.net/1854/LU-01KFX0BWVWEK66706ZB0AFAD9K","title":"DNA binding and dimerization of the SOG1 NAC domain are functionally linked with its ability to undergo liquid–liquid phase separation","_id":"01KFX0BWVWEK66706ZB0AFAD9K","issue":"2","article_type":"original","page":{"count":"16"},"file":[{"_id":"01KFX0SF60M4BTG0Q0VBTB6K5P","size":"1699158","thumbnail_url":"https://biblio.ugent.be/publication/01KFX0BWVWEK66706ZB0AFAD9K/file/01KFX0SF60M4BTG0Q0VBTB6K5P/thumbnail.png","publication_version":"acceptedVersion","kind":"fullText","access":"private","sha256":"d5823b94bc13c89bae52f8ab832b351b60769e413695237fe5e8ab374e798ef8"},{"thumbnail_url":"https://biblio.ugent.be/publication/01KFX0BWVWEK66706ZB0AFAD9K/file/01KFX0X48KDH202XGAK9TG0DHN/thumbnail.png","url":"https://biblio.ugent.be/publication/01KFX0BWVWEK66706ZB0AFAD9K/file/01KFX0X48KDH202XGAK9TG0DHN.pdf","content_type":"application/pdf","_id":"01KFX0X48KDH202XGAK9TG0DHN","size":"6359554","access":"open","sha256":"5bfb95242e0fb99f37381f676c1f015d9145736db00e44011c4166524eafb4d6","publication_version":"publishedVersion","kind":"fullText","name":"Mignon et al. (2026)Nucleic Acids Research 54, gkaf1522.pdf"}],"classification":"A1","issn":["0305-1048","1362-4962"],"language":["eng"],"year":"2026","parent":{"title":"NUCLEIC ACIDS RESEARCH","short_title":"Nucleic Acids Res."},"copyright_statement":"Creative Commons Attribution-NonCommercial 4.0 International Public License (CC BY-NC 4.0)"},{"date_updated":"2026-04-02 10:37:41","cite":{"bof":"The current study introduces novel methodologies in forensic and diagnostic science, notably the isothermal amplification of STR loci via Recombinase Polymerase Amplification (RPA) and the development of RPA-compatible, probe-based genotyping. At the heart of this research is the isothermal mechanism of RPA, which facilitates STR amplification at a constant temperature, thus eliminating the need for the thermal cycling required in traditional Polymerase Chain Reaction (PCR) methods. Moreover, this study replaces the conventional requirement for allele detection, typically achieved through electrophoresis or massively parallel sequencing, with a lab-on-a-chip compatible, probe-based quantitative RPA (qRPA) detection method. This advancement reduces the need for extensive equipment, enhancing the feasibility of implementing this technology in field-deployable, disposable microfluidic lab-on-a-chip systems. Such an innovation holds significant potential for transformative applications, particularly in situations demanding rapid decision-making. Its utility extends to a range of fields, including rapid diagnostics, urgent crime scene investigations, immediate disaster victim identification, and critical food safety assessments.
","_id":"1S02625N"}],"volume":"16","abstract_full":[{"text":"Forensic DNA profiling commonly relies on polymerase chain reaction (PCR) amplification followed by capillary electrophoresis (CE) or massively parallel sequencing (MPS), which requires expensive, laboratory-based equipment that depends on a stable power supply and is unsuitable for field applications. Here, we present a proof-of-concept assay that uses recombinase polymerase amplification (RPA) combined with exo probe detection for rapid, isothermal genotyping of insertion-deletion (InDel) markers. To the best of our knowledge, this study represents the first demonstration of forensic DNA typing using RPA coupled with exo probes. The reaction proceeds at 39 degrees C and combines amplification and detection in a single 20 min step. Thirteen DNA samples were genotyped in triplicate across eight InDel loci using allele-specific fluorescent probes. Genotypes were derived from differential endpoint fluorescence between matched and mismatched probes. Compared with benchmark genotyping, 97.07% of genotypes (n = 307) were correct at 1 ng DNA input. Accurate profiles were reliably obtained for DNA inputs as low as 250 pg, and partial profiles were still detectable at 31 pg. The results demonstrate that RPA-based InDel genotyping is fast, sensitive, and reproducible. With further optimization, such as refined probe design and selection of robust loci, the assay has clear potential to achieve complete accuracy and to be integrated into portable lab-on-a-chip platforms for rapid, field-deployable forensic identification.","lang":"eng"}],"publication_status_sort":2,"keyword":["recombinase polymerase amplification","InDel genotyping","forensic genetics","DNA probes","lab-on-a-chip","ASSAY"],"wos_type":"Article","publication_status":"published","date_updated":"2026-03-31 05:30:24","cite":{"chicago-author-date":"Three to five percent of people who are confronted with cancer will be diagnosed with Cancer of Unknown Primary (CUP); a metastasized cancer of which the tissue-of-origin cannot be determined. If possible, a biopsy of the tumor will be taken for pathological examination, but this can take up to two weeks to plan, execute and analyze. Diagnosis usually requires multiple rounds of immunostaining, a slow and costly method that leaves about 34% of CUPs without definite diagnosis. Because treatment options are limited to aspecific chemotherapy, CUP is the fourth most common cause of cancer death.\n\nThe tumor DNA methylation pattern is a unique ‘fingerprint’ that can be used to determine the tissue-of-origin in CUPs. A novel technique, called cfRRBS, developed at the UGent-VIB allows the identification of the methylation profile starting from minimal amounts of highly fragmented DNA. With this technique not only DNA extracted from paraffin-embedded tumor tissue can be used, but also cell-free DNA isolated from liquid biopsies such as blood.\n\nIn this research project, cfRRBS will be turned into a clinically applicable protocol. A computational analysis pipeline with reference data sets will be built to classify tumors according to their methylation profile. The processing of patient samples and sequencing data will be optimized to achieve a flexible and reliable classifier. The performance of this classifier will then be prospectively validated as a diagnostic tool for CUPs.
","iweto_id":"3S010820","_id":"3S010820"}],"abstract_full":[{"lang":"eng","text":"Accurate tumor classification is essential for guiding clinical management, yet remains\nchallenging in cases with limited, degraded, or highly heterogeneous DNA material. This\ndissertation investigates the potential of a novel technique called cfRRBS, developed at the\nUGent-VIB, as a cost-efficient and low-input method for DNA methylation profiling. The\noverarching goal is to evaluate whether cfRRBS can support reliable cancer diagnosis in both\nformalin-fixed paraffin-embedded (FFPE) tissue and liquid biopsies, with a particular focus on\ncancers of unknown primary (CUP) and central nervous system (CNS) tumors.\nThe first part of this dissertation focuses on optimizing cfRRBS for cancers of unknown primary\n(CUP) by establishing standardized sample workflows for plasma, ascites, and pleural effusion\nsamples, followed by assessment of circulating cell-free DNA (cfDNA) quality and integrity. To\nenable cfRRBS-based tumor classification, existing public resources such as The Cancer\nGenome Atlas (TCGA) were found to have limited CpG site overlap with cfRRBS. Consequently,\nthe development of a custom cfRRBS-based reference dataset covering 16 tumor entities and\nhealthy plasma samples became a central component of this work. Entity-specific methylation\nregions were defined for each entity to build a classifier based on nonnegative least squares\ndeconvolution.\nMethylation profiling on FFPE-derived DNA is already routinely performed in clinical practice for\nCNS tumor diagnostics. The second part of this dissertation addresses the benchmarking of\ncfRRBS against the current clinical gold standard—the Illumina Infinium MethylationEPIC array\nand its associated Heidelberg classifier for CNS tumor classification. To enable compatibility\nwith array-based references, a cfRRBS-specific classifier for CNS tumors was constructed using\na classification strategy adapted from the CUP workflow, using only CpG clusters shared\nbetween platforms. Sensitivity was assessed through in silico dilutions and reproducibility\nthrough inter- and intrarun comparisons.\nAcross both applications, cfRRBS showed strong potential for accurate tumor classification,\neven from fragmented or low-quantity DNA. This work highlights cfRRBS as a versatile and\naccessible technique for methylation-based cancer diagnostics on both FFPE tissue and liquid\nbiopsies."}],"classification":"D1"},{"author":[{"_id":"4a3a6332-168c-11f1-8219-b18bd7f88a7a","last_name":"Peymen","name_last_first":"Peymen, Anouk","first_name":"Anouk","credit_role":["first_author"],"ugent_id":["000241878186","802005080715"],"biblio_id":"4a3a6332-168c-11f1-8219-b18bd7f88a7a","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE31"}],"ugent_id":"GE31"}],"name":"Anouk Peymen"},{"last_name":"Valverde","name":"Alejandro Valverde","name_last_first":"Valverde, Alejandro","first_name":"Alejandro"},{"first_name":"Thijs","name_last_first":"Van der Snickt, Thijs","orcid_id":"0000-0001-9865-0367","affiliation":[{"ugent_id":"GE31","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE31"}]}],"biblio_id":"1BA56604-4B75-11E5-A422-DA3AB5D1D7B1","name":"Thijs Van der Snickt","ugent_id":["000150620990","802003388063","973554499625"],"_id":"1BA56604-4B75-11E5-A422-DA3AB5D1D7B1","last_name":"Van der Snickt"},{"name":"Elise Daems","last_name":"Daems","first_name":"Elise","name_last_first":"Daems, Elise"},{"name_last_first":"Mestdagh, Pieter","first_name":"Pieter","ugent_id":["802000056519","978002813228"],"name":"Pieter Mestdagh","orcid_id":"0000-0001-7821-9684","biblio_id":"F86E58A6-F0ED-11E1-A9DE-61C894A0A6B4","affiliation":[{"ugent_id":"GE31","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE31"}]}],"last_name":"Mestdagh","_id":"F86E58A6-F0ED-11E1-A9DE-61C894A0A6B4"},{"name":"Karolien De Wael","last_name":"De Wael","first_name":"Karolien","name_last_first":"De Wael, Karolien"}],"date_created":"2026-03-10 07:19:30","external":0,"keyword":["Photoelectrochemistry","Biosensor","Locked nucleic acid (LNA)","Double-stranded DNA","KRAS G12C mutation","Singlet oxygen","Cancer diagnostics","BIOSENSOR","DESIGN"],"wos_type":"Article","publication_status":"published","publication_status_sort":2,"project":[{"start_date":"2023-01-01","title":"A new photoelectrochemical singlet oxygen-based detection platform for a panel of cancer biomarkers in tissue and liquid biopsies (SOCAN)","gismo_id":"4633e20b-8108-11ed-9393-1d2a5b1ada47","end_date":"2026-12-31","_id":"01IB5223","iweto_id":"01IB5223","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 detection paradigm, 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 game-changing technology on tissue and liquid biopsy samples will be a major contribution to the early detection of cancer. SOCAN will lead to an affordable and sensitive diagnosis of cancer, reducing the time to result which allows faster and specific treatment, potentially saving lives on the longer term which is in line the EU mission regarding fighting cancer.
"}],"volume":"193","abstract_full":[{"lang":"eng","text":"The accurate detection of double-stranded DNA (dsDNA) cancer biomarkers remains a critical challenge in biosensing technologies, as native strand pairing hampers probe hybridization. While photoelectrochemical (PEC) biosensors hold promise for rapid and cost-effective nucleic acid diagnostics, their application has largely been confined to synthetic single-stranded DNA (ssDNA), limiting their clinical applicability. Here, we introduce an enzyme-free PEC biosensing strategy that directly detects DNA targets within their native double-stranded form by integrating locked nucleic acid (LNA) probes into a singlet oxygen (1O2)-based PEC assay. Using KRAS G12C as a dsDNA model, systematic probe engineering identified a 17-nucleotide capture probe with three LNA modifications flanking the mutation site as the optimal design for the capture probe. The biosensor achieved a limit of detection of 20 pM for KRAS-mutated dsDNA, a discrimination efficiency of 92.9% against KRAS wild-type (WT) sequences, and reliable detection of 1% variant allele frequency (VAF) in a WT background, closely reflecting clinical scenarios. This study represents the first use of LNA-modified probes in PEC biosensing and offers a robust strategy for enzyme-free detection of dsDNA targets, with broad potential for precision oncology and point-of-care applications."}],"created_by":{"last_name":"Van der Snickt","_id":"1BA56604-4B75-11E5-A422-DA3AB5D1D7B1","first_name":"Thijs","name_last_first":"Van der Snickt, Thijs","affiliation":[{"ugent_id":"GE31","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE31"}]}],"biblio_id":"1BA56604-4B75-11E5-A422-DA3AB5D1D7B1","orcid_id":"0000-0001-9865-0367","name":"Thijs Van der Snickt","ugent_id":["000150620990","802003388063","973554499625"]},"affiliation":[{"name":"Department of Biomolecular Medicine","ugent_id":"GE31","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE31"}]}],"jcr":{},"cite":{"fwo":"Edible insects are one of the solutions for Europe’s growing dependency on imported protein. Because of their ability to convert organic lowgrade residual streams into a nutritional rich product they can be used as a sustainable and locally produced high quality protein source.
\nDespite the legal approval, the use of edible insects is almost nonexistent in food for dogs and cats. The implementations of edible insects are fairly new in Europe, hence there are still some fundamental questions before the widespread application will kick off. The focus of Petsect is gathering knowledge about the fundamental baselines of the use of insects as ingredients for pet food and novel health applications, such as processing techniques, nutritional value, digestibility and especially the effect on immune system. More research is necessary to develop a palatable insect-based pet food with a high nutritional value. Petsect will focus on the use of yellow mealworms (YMW) and black soldier fly larvae (BSFL) as these production processes are currently the furthest developed which has a direct impact on the mass availability and the price.
\nThe overall goal of Petsect is to create a nutritional balanced food, with an extra benefit for gastrointestinal health, for both cats and dogs with insect larvae (fractions) as main protein source or functional (chitin, lipid or protein based) ingredient. The leveled ingredient approach for selecting promising feed ingredients comprises 1) nutritional analyses 2) in vitro digestibility & bioactivity evaluation. 3) in vivo digestibility and palatability with 4) monitoring of gastrointestinal health effects by means of microbiome and metabolome analyses. Additionally, the sustainability of the whole process from farming the insects up to the development of the pet food will be assessed to ensure a sustainable end product.
\n","iweto_id":"3S001922"}],"defense":{"location":"Gent : Campus Schoonmeersen (lokaal GSCH.C.0.125)","date":"2026-04-28"},"publication_status":"published","file":[{"thumbnail_url":"https://biblio.ugent.be/publication/01KS7E4JP5YBZYP9MH5TGE9EBR/file/01KQJZWCZQGPTF4SPNBTKM2ZQZ/thumbnail.png","content_type":"application/pdf","url":"https://biblio.ugent.be/publication/01KS7E4JP5YBZYP9MH5TGE9EBR/file/01KQJZWCZQGPTF4SPNBTKM2ZQZ.pdf","_id":"01KQJZWCZQGPTF4SPNBTKM2ZQZ","size":"8418877","access":"restricted","sha256":"eebadd125bfb57b4f4c0d1bb296d60a7e1c53308178a4b9f76322a44def3a22c","publication_version":"publishedVersion","name":"10792.pdf","kind":"fullText"}],"page":{"count":"224"},"isbn":["9789493542099"],"alternative_title":["Nutritionele en technologische aspecten van zwarte soldaten vlieg en meelworrm in huisdiervoeding"],"year":"2026","external":0,"date_created":"2026-05-22 08:51:53","copyright_statement":"No license (in copyright)","language":["eng"],"promoter":[{"biblio_id":"F8F4AE24-F0ED-11E1-A9DE-61C894A0A6B4","affiliation":[{"ugent_id":"LA23","path":[{"ugent_id":"UGent"},{"ugent_id":"LA"},{"ugent_id":"LA23"}]}],"orcid_id":"0000-0002-8537-5084","name":"Mia Eeckhout","ugent_id":["802000193834","919014292548"],"first_name":"Mia","name_last_first":"Eeckhout, Mia","_id":"F8F4AE24-F0ED-11E1-A9DE-61C894A0A6B4","last_name":"Eeckhout"},{"_id":"F52858F4-F0ED-11E1-A9DE-61C894A0A6B4","last_name":"Hesta","ugent_id":["801001127479"],"name":"Myriam Hesta","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI11"}],"ugent_id":"DI11"}],"orcid_id":"0000-0001-9423-9765","biblio_id":"F52858F4-F0ED-11E1-A9DE-61C894A0A6B4","name_last_first":"Hesta, Myriam","first_name":"Myriam"}],"author":[{"first_name":"Elias","name_last_first":"Leocadio dos Santos Neto, Elias","biblio_id":"28a331b7-7b3a-11ed-9d28-cd7f23b577ed","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"LA"},{"ugent_id":"LA23"}],"ugent_id":"LA23"}],"name":"Elias Leocadio dos Santos Neto","ugent_id":["000221594880","802004251666"],"last_name":"Leocadio dos Santos Neto","_id":"28a331b7-7b3a-11ed-9d28-cd7f23b577ed"}],"status":"public","type":"dissertation","abstract":["Accurate tumor classification is essential for guiding clinical management, yet remains\nchallenging in cases with limited, degraded, or highly heterogeneous DNA material. This\ndissertation investigates the potential of a novel technique called cfRRBS, developed at the\nUGent-VIB, as a cost-efficient and low-input method for DNA methylation profiling. The\noverarching goal is to evaluate whether cfRRBS can support reliable cancer diagnosis in both\nformalin-fixed paraffin-embedded (FFPE) tissue and liquid biopsies, with a particular focus on\ncancers of unknown primary (CUP) and central nervous system (CNS) tumors.\nThe first part of this dissertation focuses on optimizing cfRRBS for cancers of unknown primary\n(CUP) by establishing standardized sample workflows for plasma, ascites, and pleural effusion\nsamples, followed by assessment of circulating cell-free DNA (cfDNA) quality and integrity. To\nenable cfRRBS-based tumor classification, existing public resources such as The Cancer\nGenome Atlas (TCGA) were found to have limited CpG site overlap with cfRRBS. Consequently,\nthe development of a custom cfRRBS-based reference dataset covering 16 tumor entities and\nhealthy plasma samples became a central component of this work. Entity-specific methylation\nregions were defined for each entity to build a classifier based on nonnegative least squares\ndeconvolution.\nMethylation profiling on FFPE-derived DNA is already routinely performed in clinical practice for\nCNS tumor diagnostics. The second part of this dissertation addresses the benchmarking of\ncfRRBS against the current clinical gold standard—the Illumina Infinium MethylationEPIC array\nand its associated Heidelberg classifier for CNS tumor classification. To enable compatibility\nwith array-based references, a cfRRBS-specific classifier for CNS tumors was constructed using\na classification strategy adapted from the CUP workflow, using only CpG clusters shared\nbetween platforms. Sensitivity was assessed through in silico dilutions and reproducibility\nthrough inter- and intrarun comparisons.\nAcross both applications, cfRRBS showed strong potential for accurate tumor classification,\neven from fragmented or low-quantity DNA. This work highlights cfRRBS as a versatile and\naccessible technique for methylation-based cancer diagnostics on both FFPE tissue and liquid\nbiopsies.","Een accurate tumorclassificatie is cruciaal voor het bepalen van de juiste klinische aanpak, maar\nblijft uitdagend in gevallen met beperkt, gedegradeerd of sterk heterogeen DNA. Dit proefschrift\nonderzoekt het potentieel van een nieuwe techniek, cfRRBS, ontwikkeld aan UGent-VIB, als een\nkostenefficiënte methode voor DNA-methylatieprofilering. Het hoofddoel is evalueren of op\nbasis van cfRRBS een betrouwbare kankerdiagnose kan bekomen worden, bij zowel\nformaline-gefixeerd paraffine-ingebed (FFPE) weefsel als vloeibare biopsies, met bijzondere\naandacht voor primaire tumor onbekend (PTO)-tumoren en tumoren van het centraal\nzenuwstelsel (CZS).\nHet eerste deel van dit proefschrift richt zich op het optimaliseren van cfRRBS voor\nPTO-diagnostiek door gestandaardiseerde procedures op te zetten voor de verzameling van\nplasma-, ascites- en pleuravochtstalen, gevolgd door een evaluatie van de kwaliteit en integriteit\nvan circulerend celvrij DNA (cfDNA). Om cfRRBS-gebaseerde tumorclassificatie mogelijk te\nmaken, bleken de bestaande publieke datasets zoals The Cancer Genome Atlas (TCGA) slechts\nbeperkte overlap te vertonen met cfRRBS. Daarom werd de ontwikkeling van een op cfRRBS\ngebaseerde referentiedataset voor 16 tumortypes en gezonde plasmastalen een essentieel\nonderdeel van dit werk. Per entiteit werden specifieke methylatiemerkers geselecteerd om een\nclassificator te bouwen met behulp van “non-negative least squares” deconvolutie.\nMethylatieprofilering op DNA uit FFPE-weefsel wordt in de klinische praktijk al routinematig\ntoegepast voor de diagnose van CZS-tumoren. Het tweede deel van dit proefschrift vergelijkt\ncfRRBS met de huidige klinische gouden standaard: de Illumina Infinium MethylationEPIC-array\nen de bijbehorende Heidelberg- classificator voor CZS-tumorclassificatie. Om compatibiliteit\nmet array-gebaseerde referenties mogelijk te maken, werd een cfRRBS-specifieke CZSclassificator ontwikkeld volgens een classificatiestrategie gebaseerd op de PTO-werkwijze,\nwaarbij enkel gedeelde CpG-groepen tussen beide platforms werden gebruikt. De gevoeligheid\nwerd beoordeeld via in silico verdunningen en de reproduceerbaarheid via inter- en intrarun\nvergelijkingen.\nIn beide toepassingen toont cfRRBS een sterk potentieel voor nauwkeurige tumorclassificatie,\nzelfs bij gefragmenteerd of zeer beperkt DNA. Dit werk toont cfRRBS als een veelzijdige en\ntoegankelijke techniek voor methylatie-gebaseerde kankerdiagnostiek op zowel FFPE-weefsel\nals vloeibare biopsies."],"subject":["Biology and Life Sciences"],"biblio_id":"01KS7E4JP5YBZYP9MH5TGE9EBR","publisher":{"name":"Ghent University. Faculty of Bioscience Engineering","location":"Ghent, Belgium"},"cite":{"apa":"
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 detection paradigm, 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 game-changing technology on tissue and liquid biopsy samples will be a major contribution to the early detection of cancer. SOCAN will lead to an affordable and sensitive diagnosis of cancer, reducing the time to result which allows faster and specific treatment, potentially saving lives on the longer term which is in line the EU mission regarding fighting cancer.
","iweto_id":"01IB5223"}],"abstract_full":[{"text":"Background\nThe detection of actionable DNA biomarkers in liquid biopsies is essential for advancing precision oncology. While conventional techniques such as PCR and NGS are highly accurate, their high cost, complexity, and slow turnaround time limit widespread clinical applications. Electrochemical biosensors present a promising alternative through their portability, affordability, and rapid analysis capabilities.\nObjective\nThis systematic review evaluates the current status and potential clinical adoption of electrochemical biosensors for detecting cancer DNA biomarkers in liquid biopsies, focusing on their sensitivity and specificity compared to standard PCR-based methods.\nMethods\nA comprehensive search across PubMed, Scopus, and Web of Science was conducted up to August 2025, yielding 1723 articles. After applying PRISMA guidelines with strict inclusion and exclusion criteria, 31 studies were selected. The quality of the selected studies was assessed using the SURE checklist. Data on biosensor design, amplification strategies, detection limits, and clinical applicability were extracted.\nResults\nMost biosensors achieved femtomolar to attomolar detection limits (LODs), reaching the required sensitivity limits for germline and somatic mutations respectively These LODs were achieved primarily via signal amplification strategies using redox mediators, nanomaterials, and strand displacement assays. Target amplification was less common and did not demonstrate consistent superiority. Specificity was enhanced through modified probes, enzymatic cleavage, magnetic separation, and blocking agents, though assessment methods varied. In general, covalently immobilized probes improved stability and sensitivity. However, most assays were validated in buffer with synthetic DNA, limiting clinical relevance.\nConclusions\nWith respect to their performance, electrochemical biosensors exhibit considerable potential for clinical integration. In particular when integrating different signal amplification strategies, such as a synergistic approach of redox mediators and nanocomposites, or combining target and signal amplification to reach the required sensitivity limits. Nonetheless, their clinical integration requires evaluation in complex biological samples, more thorough selectivity studies, and rigorous validation on patient samples. When standard validation assays can be provided and performed, electrochemical biosensing assays hold great promise for the detection of cancer DNA biomarkers in liquid biopsies.","lang":"und"}],"volume":"304","publication_status_sort":2,"author":[{"last_name":"Peymen","_id":"94c8b99a-8f5b-11f0-906f-c69827b9fe37","name":"Anouk Peymen","biblio_id":"94c8b99a-8f5b-11f0-906f-c69827b9fe37","affiliation":[{"path":[{"ugent_id":"UGent"}],"ugent_id":"UGent","name":"Ghent University"}],"ugent_id":["974654318967"],"credit_role":["first_author"],"first_name":"Anouk","name_last_first":"Peymen, Anouk"},{"credit_role":["first_author"],"first_name":"Thijs","name_last_first":"Van der Snickt, Thijs","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE31"}],"ugent_id":"GE31"}],"biblio_id":"1BA56604-4B75-11E5-A422-DA3AB5D1D7B1","orcid_id":"0000-0001-9865-0367","name":"Thijs Van der Snickt","ugent_id":["000150620990","802003388063","973554499625"],"last_name":"Van der Snickt","_id":"1BA56604-4B75-11E5-A422-DA3AB5D1D7B1"},{"name_last_first":"Valverde, Alejandro","first_name":"Alejandro","last_name":"Valverde","name":"Alejandro Valverde"},{"last_name":"Ailliet","_id":"D188A138-FEB7-11E1-A24A-69BD10BDE39D","name":"Scott Ailliet","biblio_id":"D188A138-FEB7-11E1-A24A-69BD10BDE39D","affiliation":[{"ugent_id":"GE31","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE31"}]}],"orcid_id":"0000-0003-0589-6988","ugent_id":["000120708416","802004506290","976982859743"],"first_name":"Scott","name_last_first":"Ailliet, Scott"},{"name":"Karen Zwaenepoel","last_name":"Zwaenepoel","first_name":"Karen","name_last_first":"Zwaenepoel, Karen"},{"_id":"F86E58A6-F0ED-11E1-A9DE-61C894A0A6B4","last_name":"Mestdagh","first_name":"Pieter","name_last_first":"Mestdagh, Pieter","name":"Pieter Mestdagh","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE31"}],"ugent_id":"GE31"}],"orcid_id":"0000-0001-7821-9684","biblio_id":"F86E58A6-F0ED-11E1-A9DE-61C894A0A6B4","ugent_id":["802000056519","978002813228"]},{"first_name":"Karolien","name_last_first":"De Wael, Karolien","name":"Karolien De Wael","last_name":"De Wael"}],"date_created":"2026-02-10 16:01:01","external":0}],"size":10,"limit":10,"total":5442,"start":0}