showResults({"hits":[{"handle":"http://hdl.handle.net/1854/LU-01KFX0BWVWEK66706ZB0AFAD9K","_id":"01KFX0BWVWEK66706ZB0AFAD9K","author":[{"first_name":"Kim","name":"Kim Mignon","name_last_first":"Mignon, Kim","last_name":"Mignon"},{"name":"Rani Van der Eecken","first_name":"Rani","name_last_first":"Van der Eecken, Rani","last_name":"Van der Eecken"},{"biblio_id":"4527cdc0-b1af-11ea-8258-8ff63b5ed74c","last_name":"Galle","_id":"4527cdc0-b1af-11ea-8258-8ff63b5ed74c","name_last_first":"Galle, Margot","ugent_id":["000191693218","802003463441","974677734262"],"orcid_id":"0000-0002-1095-5957","first_name":"Margot","name":"Margot Galle","affiliation":[{"ugent_id":"WE09","path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE09"}]}]},{"last_name":"Demulder","name_last_first":"Demulder, Manon","name":"Manon Demulder","first_name":"Manon"},{"last_name":"Van Lindt","first_name":"Joris","name":"Joris Van Lindt","name_last_first":"Van Lindt, Joris"},{"name":"Lieven De Veylder","first_name":"Lieven","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE09"}],"ugent_id":"WE09"}],"ugent_id":["801000929338","978299444177"],"orcid_id":"0000-0003-1150-4426","_id":"F4C04C64-F0ED-11E1-A9DE-61C894A0A6B4","name_last_first":"De Veylder, Lieven","biblio_id":"F4C04C64-F0ED-11E1-A9DE-61C894A0A6B4","last_name":"De Veylder"},{"name":"Henri De Greve","first_name":"Henri","name_last_first":"De Greve, Henri","last_name":"De Greve"},{"last_name":"Loris","name_last_first":"Loris, Remy","first_name":"Remy","name":"Remy Loris"}],"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."],"article_type":"original","biblio_id":"01KFX0BWVWEK66706ZB0AFAD9K","abstract_full":[{"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.","lang":"eng"}],"jcr":{},"classification":"A1","subject":["Biology and Life Sciences"],"cite":{"chicago-author-date":"  <div class=\"csl-entry\">Mignon, Kim, Rani Van der Eecken, Margot Galle, Manon Demulder, Joris Van Lindt, Lieven De Veylder, Henri De Greve, and Remy Loris. 2026. “DNA Binding and Dimerization of the SOG1 NAC Domain Are Functionally Linked with Its Ability to Undergo Liquid–Liquid Phase Separation.” <i>NUCLEIC ACIDS RESEARCH</i> 54 (2). https://doi.org/10.1093/nar/gkaf1522.</div>\n","mla":"  <div class=\"csl-entry\">Mignon, Kim, et al. “DNA Binding and Dimerization of the SOG1 NAC Domain Are Functionally Linked with Its Ability to Undergo Liquid–Liquid Phase Separation.” <i>NUCLEIC ACIDS RESEARCH</i>, vol. 54, no. 2, 2026, doi:10.1093/nar/gkaf1522.</div>\n","bof":"  <div class=\"csl-entry\">Mignon, Kim, Rani Van der Eecken, Margot Galle, Manon Demulder, Joris Van Lindt, Lieven De Veylder, Henri De Greve, and Remy Loris. 2026. “DNA Binding and Dimerization of the SOG1 NAC Domain Are Functionally Linked with Its Ability to Undergo Liquid–Liquid Phase Separation.” <i>NUCLEIC ACIDS RESEARCH</i> 54 (2). doi:10.1093/nar/gkaf1522.</div>\n","vancouver":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">1. </div><div class=\"csl-right-inline\">Mignon K, Van der Eecken R, Galle M, Demulder M, Van Lindt J, De Veylder L, et al. DNA binding and dimerization of the SOG1 NAC domain are functionally linked with its ability to undergo liquid–liquid phase separation. NUCLEIC ACIDS RESEARCH. 2026;54(2).</div>\n   </div>\n","ieee":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">[1]</div><div class=\"csl-right-inline\">K. Mignon <i>et al.</i>, “DNA binding and dimerization of the SOG1 NAC domain are functionally linked with its ability to undergo liquid–liquid phase separation,” <i>NUCLEIC ACIDS RESEARCH</i>, vol. 54, no. 2, 2026.</div>\n  </div>\n","apa":"  <div class=\"csl-entry\">Mignon, K., Van der Eecken, R., Galle, M., Demulder, M., Van Lindt, J., De Veylder, L., … Loris, R. (2026). DNA binding and dimerization of the SOG1 NAC domain are functionally linked with its ability to undergo liquid–liquid phase separation. <i>NUCLEIC ACIDS RESEARCH</i>, <i>54</i>(2). https://doi.org/10.1093/nar/gkaf1522</div>\n","fwo":"  <div class=\"csl-entry\">Mignon, Kim, Rani Van der Eecken, Margot Galle, Manon Demulder, Joris Van Lindt, Lieven De Veylder, Henri De Greve, and Remy Loris. 2026. “DNA Binding and Dimerization of the SOG1 NAC Domain Are Functionally Linked with Its Ability to Undergo Liquid–Liquid Phase Separation.” <i>NUCLEIC ACIDS RESEARCH</i> 54 (2). doi:10.1093/nar/gkaf1522.</div>\n"},"project":[{"iweto_id":"3G036020","_id":"3G036020","start_date":"2020-01-01","end_date":"2023-12-31","gismo_id":"4896f6d6-225c-11ea-9b15-d7676230cb7f","title":"Functional-structural analysis of Casein Kinase 2 and SOG1 in response to Al-induced DNA damage and phosphate starvation","abstract":"<p>\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</p>"}],"publication_status_sort":2,"parent":{"title":"NUCLEIC ACIDS RESEARCH","short_title":"Nucleic Acids Res."},"page":{"count":"16"},"date_updated":"2026-03-31 15:26:12","title":"DNA binding and dimerization of the SOG1 NAC domain are functionally linked with its ability to undergo liquid–liquid phase separation","doi":["10.1093/nar/gkaf1522"],"created_by":{"name_last_first":"Bleys, Annick","_id":"F68A8C76-F0ED-11E1-A9DE-61C894A0A6B4","last_name":"Bleys","biblio_id":"F68A8C76-F0ED-11E1-A9DE-61C894A0A6B4","affiliation":[{"ugent_id":"WE09","path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE09"}]}],"name":"Annick Bleys","first_name":"Annick","orcid_id":"0000-0002-1977-4263","ugent_id":["801001668457","974031488132"]},"affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics","path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE09"}],"ugent_id":"WE09"},{"ugent_id":"VIB","path":[{"ugent_id":"ResearchCenter"},{"ugent_id":"VIB"}],"name":"VIB"}],"date_created":"2026-01-26 11:17:32","external":0,"language":["eng"],"publication_status":"published","keyword":["DAMAGE RESPONSE","TRANSCRIPTION FACTORS","PHOSPHORYLATION","PROTEIN","KINASE","ATR","DYNAMICS","FAMILY","P53"],"type":"journalArticle","article_number":"gkaf1522","status":"public","issue":"2","year":"2026","issn":["0305-1048","1362-4962"],"file":[{"_id":"01KFX0SF60M4BTG0Q0VBTB6K5P","publication_version":"acceptedVersion","size":"1699158","thumbnail_url":"https://biblio.ugent.be/publication/01KFX0BWVWEK66706ZB0AFAD9K/file/01KFX0SF60M4BTG0Q0VBTB6K5P/thumbnail.png","access":"private","sha256":"d5823b94bc13c89bae52f8ab832b351b60769e413695237fe5e8ab374e798ef8","kind":"fullText"},{"url":"https://biblio.ugent.be/publication/01KFX0BWVWEK66706ZB0AFAD9K/file/01KFX0X48KDH202XGAK9TG0DHN.pdf","size":"6359554","content_type":"application/pdf","publication_version":"publishedVersion","_id":"01KFX0X48KDH202XGAK9TG0DHN","kind":"fullText","sha256":"5bfb95242e0fb99f37381f676c1f015d9145736db00e44011c4166524eafb4d6","access":"open","name":"Mignon et al. (2026)Nucleic Acids Research 54, gkaf1522.pdf","thumbnail_url":"https://biblio.ugent.be/publication/01KFX0BWVWEK66706ZB0AFAD9K/file/01KFX0X48KDH202XGAK9TG0DHN/thumbnail.png"}],"pubmed_id":"41556342","wos_id":"001664623800001","copyright_statement":"Creative Commons Attribution-NonCommercial 4.0 International Public License (CC BY-NC 4.0)","volume":"54","wos_type":"Article"},{"handle":"http://hdl.handle.net/1854/LU-01KN45M60AVNEPZ9T3A2SY7656","_id":"01KN45M60AVNEPZ9T3A2SY7656","author":[{"affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI04"}],"ugent_id":"DI04"}],"name":"Pablo Vangeenderhuysen","first_name":"Pablo","orcid_id":"0000-0002-5492-6904","ugent_id":["000150711829","802003552862","973330059510"],"name_last_first":"Vangeenderhuysen, Pablo","_id":"D23B2954-4E99-11E5-BF8D-A886B5D1D7B1","last_name":"Vangeenderhuysen","biblio_id":"D23B2954-4E99-11E5-BF8D-A886B5D1D7B1"},{"ugent_id":["802001595987","976349364766"],"orcid_id":"0000-0001-9875-385X","first_name":"Matthijs","name":"Matthijs Vynck","affiliation":[{"ugent_id":"DI04","path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI04"}]}],"biblio_id":"07F697D4-F0EE-11E1-A9DE-61C894A0A6B4","last_name":"Vynck","_id":"07F697D4-F0EE-11E1-A9DE-61C894A0A6B4","name_last_first":"Vynck, Matthijs"},{"name_last_first":"Engelen, Liesa","first_name":"Liesa","name":"Liesa Engelen","last_name":"Engelen"},{"last_name":"Covaci","name_last_first":"Covaci, Adrian","first_name":"Adrian","name":"Adrian Covaci"},{"last_name":"Nawrot","name_last_first":"Nawrot, Tim","first_name":"Tim","name":"Tim Nawrot"},{"name":"Trancizeo Lipenga","first_name":"Trancizeo","affiliation":[{"ugent_id":"FW03","path":[{"ugent_id":"UGent"},{"ugent_id":"FW"},{"ugent_id":"FW03"}]}],"ugent_id":["000200570940","802003603483","973780296326"],"_id":"d40cd0d4-2ddf-11eb-a93c-e35591999b61","name_last_first":"Lipenga, Trancizeo","biblio_id":"d40cd0d4-2ddf-11eb-a93c-e35591999b61","last_name":"Lipenga"},{"ugent_id":["802003693615"],"orcid_id":"0000-0001-5019-1405","first_name":"Roger","name":"Roger Peró Gascón","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"FW"},{"ugent_id":"FW03"}],"ugent_id":"FW03"}],"biblio_id":"af4d77b1-aac8-11eb-8deb-f53b156d7cda","last_name":"Peró Gascón","_id":"af4d77b1-aac8-11eb-8deb-f53b156d7cda","name_last_first":"Peró Gascón, Roger"},{"affiliation":[{"ugent_id":"FW03","path":[{"ugent_id":"UGent"},{"ugent_id":"FW"},{"ugent_id":"FW03"}]},{"path":[{"ugent_id":"UGent"},{"ugent_id":"FW58"}],"ugent_id":"FW58"}],"name":"Sarah De Saeger","first_name":"Sarah","orcid_id":"0000-0002-2160-7253","ugent_id":["801000957125","974809966884"],"name_last_first":"De Saeger, Sarah","_id":"F4CD454A-F0ED-11E1-A9DE-61C894A0A6B4","last_name":"De Saeger","biblio_id":"F4CD454A-F0ED-11E1-A9DE-61C894A0A6B4"},{"first_name":"Marthe","name":"Marthe De Boevre","affiliation":[{"ugent_id":"CA05","path":[{"ugent_id":"UGent"},{"ugent_id":"CA"},{"ugent_id":"CA05"}]},{"path":[{"ugent_id":"UGent"},{"ugent_id":"FW"},{"ugent_id":"FW03"}],"ugent_id":"FW03"}],"ugent_id":["802000610328","973148559372"],"orcid_id":"0000-0002-6151-5126","_id":"0BAC47AC-F0EE-11E1-A9DE-61C894A0A6B4","name_last_first":"De Boevre, Marthe","biblio_id":"0BAC47AC-F0EE-11E1-A9DE-61C894A0A6B4","last_name":"De Boevre"},{"last_name":"Mccormack","first_name":"Valerie","name":"Valerie Mccormack","name_last_first":"Mccormack, Valerie"},{"_id":"F77AFAE4-F0ED-11E1-A9DE-61C894A0A6B4","name_last_first":"Vanhaecke, Lynn","biblio_id":"F77AFAE4-F0ED-11E1-A9DE-61C894A0A6B4","last_name":"Vanhaecke","first_name":"Lynn","name":"Lynn Vanhaecke","affiliation":[{"ugent_id":"DI04","path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI04"}]}],"ugent_id":["801001950969","976961995245"],"orcid_id":"0000-0003-0400-2188"},{"_id":"01FC9C02-F0EE-11E1-A9DE-61C894A0A6B4","name_last_first":"Hemeryck, Lieselot","biblio_id":"01FC9C02-F0EE-11E1-A9DE-61C894A0A6B4","last_name":"Hemeryck","first_name":"Lieselot","name":"Lieselot Hemeryck","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI04"}],"ugent_id":"DI04"}],"ugent_id":["802001258309","971264450772"],"orcid_id":"0000-0002-2451-3375"}],"article_type":"original","abstract":["DNA adductomics is the study of the whole of DNA adducts in a biological sample and is a valuable asset to exposomics research. To date, a clear view on how to analyze larger sample series is lacking in DNA adductomics, and the preprocessing of untargeted DNA adductomics data is seldom applied. This work aimed to optimize a DNA adductomics data preprocessing workflow (in true untargeted mode). Building upon the xcms R package, we optimized parameters for peak detection, retention time alignment, and peak grouping to reliably detect and integrate putative DNA adduct LC-MS peaks. Next, to ensure reliable downstream data analysis, six sample- and feature-based normalization methods were tested and quantitatively evaluated in two data sets (placental tissue, n = 375, and blood samples, n = 51). As a result, a successful and reproducible procedure for optimization of xcms parameters for DNA adductomics is proposed. Furthermore, evaluation of normalization methods demonstrated the importance and limitations of objective (RSD* and D-ratio) and subjective, i.e., visual (PCA score plot) evaluation. This work supports reproducible and transparent untargeted DNA adductomics data preprocessing to be implemented in large-scale exposomics studies."],"biblio_id":"01KN45M60AVNEPZ9T3A2SY7656","subject":["Chemistry"],"abstract_full":[{"lang":"eng","text":"DNA adductomics is the study of the whole of DNA adducts in a biological sample and is a valuable asset to exposomics research. To date, a clear view on how to analyze larger sample series is lacking in DNA adductomics, and the preprocessing of untargeted DNA adductomics data is seldom applied. This work aimed to optimize a DNA adductomics data preprocessing workflow (in true untargeted mode). Building upon the xcms R package, we optimized parameters for peak detection, retention time alignment, and peak grouping to reliably detect and integrate putative DNA adduct LC-MS peaks. Next, to ensure reliable downstream data analysis, six sample- and feature-based normalization methods were tested and quantitatively evaluated in two data sets (placental tissue, n = 375, and blood samples, n = 51). As a result, a successful and reproducible procedure for optimization of xcms parameters for DNA adductomics is proposed. Furthermore, evaluation of normalization methods demonstrated the importance and limitations of objective (RSD* and D-ratio) and subjective, i.e., visual (PCA score plot) evaluation. This work supports reproducible and transparent untargeted DNA adductomics data preprocessing to be implemented in large-scale exposomics studies."}],"jcr":{},"classification":"A1","publication_status_sort":2,"parent":{"short_title":"Anal. Chem.","title":"ANALYTICAL CHEMISTRY"},"cite":{"fwo":"  <div class=\"csl-entry\">Vangeenderhuysen, Pablo, Matthijs Vynck, Liesa Engelen, Adrian Covaci, Tim Nawrot, Trancizeo Lipenga, Roger Peró Gascón, Sarah De Saeger, Marthe De Boevre, Valerie Mccormack, Lynn Vanhaecke, and Lieselot Hemeryck. 2026. “Challenges and Good Practices in Preprocessing and Normalization of Untargeted DNA Adductomics Data in Exposomics Research.” <i>ANALYTICAL CHEMISTRY</i> 98 (12): 8947–8955. doi:10.1021/acs.analchem.5c06549.</div>\n","apa":"  <div class=\"csl-entry\">Vangeenderhuysen, P., Vynck, M., Engelen, L., Covaci, A., Nawrot, T., Lipenga, T., … Hemeryck, L. (2026). Challenges and good practices in preprocessing and normalization of untargeted DNA adductomics data in exposomics research. <i>ANALYTICAL CHEMISTRY</i>, <i>98</i>(12), 8947–8955. https://doi.org/10.1021/acs.analchem.5c06549</div>\n","ieee":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">[1]</div><div class=\"csl-right-inline\">P. Vangeenderhuysen <i>et al.</i>, “Challenges and good practices in preprocessing and normalization of untargeted DNA adductomics data in exposomics research,” <i>ANALYTICAL CHEMISTRY</i>, vol. 98, no. 12, pp. 8947–8955, 2026.</div>\n  </div>\n","vancouver":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">1. </div><div class=\"csl-right-inline\">Vangeenderhuysen P, Vynck M, Engelen L, Covaci A, Nawrot T, Lipenga T, et al. Challenges and good practices in preprocessing and normalization of untargeted DNA adductomics data in exposomics research. ANALYTICAL CHEMISTRY. 2026;98(12):8947–55.</div>\n   </div>\n","bof":"  <div class=\"csl-entry\">Vangeenderhuysen, Pablo, Matthijs Vynck, Liesa Engelen, Adrian Covaci, Tim Nawrot, Trancizeo Lipenga, Roger Peró Gascón, Sarah De Saeger, Marthe De Boevre, Valerie Mccormack, Lynn Vanhaecke, and Lieselot Hemeryck. 2026. “Challenges and Good Practices in Preprocessing and Normalization of Untargeted DNA Adductomics Data in Exposomics Research.” <i>ANALYTICAL CHEMISTRY</i> 98 (12): 8947–8955. doi:10.1021/acs.analchem.5c06549.</div>\n","mla":"  <div class=\"csl-entry\">Vangeenderhuysen, Pablo, et al. “Challenges and Good Practices in Preprocessing and Normalization of Untargeted DNA Adductomics Data in Exposomics Research.” <i>ANALYTICAL CHEMISTRY</i>, vol. 98, no. 12, 2026, pp. 8947–55, doi:10.1021/acs.analchem.5c06549.</div>\n","chicago-author-date":"  <div class=\"csl-entry\">Vangeenderhuysen, Pablo, Matthijs Vynck, Liesa Engelen, Adrian Covaci, Tim Nawrot, Trancizeo Lipenga, Roger Peró Gascón, et al. 2026. “Challenges and Good Practices in Preprocessing and Normalization of Untargeted DNA Adductomics Data in Exposomics Research.” <i>ANALYTICAL CHEMISTRY</i> 98 (12): 8947–55. https://doi.org/10.1021/acs.analchem.5c06549.</div>\n"},"created_by":{"biblio_id":"07F697D4-F0EE-11E1-A9DE-61C894A0A6B4","last_name":"Vynck","_id":"07F697D4-F0EE-11E1-A9DE-61C894A0A6B4","name_last_first":"Vynck, Matthijs","ugent_id":["802001595987","976349364766"],"orcid_id":"0000-0001-9875-385X","name":"Matthijs Vynck","first_name":"Matthijs","affiliation":[{"ugent_id":"DI04","path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI04"}]}]},"affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI04"}],"name":"Department of Translational Physiology, Infectiology and Public Health","ugent_id":"DI04"},{"ugent_id":"FW03","name":"Department of Bio-analysis","path":[{"ugent_id":"UGent"},{"ugent_id":"FW"},{"ugent_id":"FW03"}]}],"date_created":"2026-04-01 09:22:37","language":["eng"],"external":0,"publication_status":"published","page":{"last":"8955","first":"8947"},"date_updated":"2026-04-02 10:37:41","doi":["10.1021/acs.analchem.5c06549"],"title":"Challenges and good practices in preprocessing and normalization of untargeted DNA adductomics data in exposomics research","status":"public","year":"2026","issue":"12","keyword":["MASS-SPECTROMETRY","EXPOSURE","IDENTIFICATION","ALIGNMENT","HEALTH","RISK"],"type":"journalArticle","file":[{"publication_version":"publishedVersion","_id":"01KN46BBDCGMSNV50FADNDNMCF","url":"https://biblio.ugent.be/publication/01KN45M60AVNEPZ9T3A2SY7656/file/01KN46BBDCGMSNV50FADNDNMCF.pdf","content_type":"application/pdf","size":"3408556","name":"challenges-and-good-practices-in-preprocessing-and-normalization-of-untargeted-dna-adductomics-data-in-exposomics.pdf","thumbnail_url":"https://biblio.ugent.be/publication/01KN45M60AVNEPZ9T3A2SY7656/file/01KN46BBDCGMSNV50FADNDNMCF/thumbnail.png","sha256":"18adadda2a144293c7284c6d7cbf83b448406afb00f44fdde0e62e837195989c","kind":"fullText","access":"restricted"}],"wos_id":"001715675700001","pubmed_id":"41834712","copyright_statement":"No license (in copyright)","issn":["0003-2700","1520-6882"],"volume":"98","wos_type":"Article"},{"project":[{"publication_count":56,"end_date":"2029-09-30","start_date":"2024-10-01","_id":"1800725N","iweto_id":"1800725N","abstract":"<p>Lipomatous tumors constitute a clinically, biologically and pathologically diverse group. Despite <br />significant advances in recent years in classifying and understanding the pathogenesis in lipomatous <br />tumors, the molecular events responsible for tumorigenesis in well-differentiated and dedifferentiated <br />liposarcoma, and the recently described ‘liposarcoma mimic’ atypical spindle cell/pleomorphic <br />lipomatous tumor (ASPLT) are still poorly understood. Using state-of-the-art (Next-Generation <br />Sequencing and genome-wide methylation sequencing) molecular testing and CRISPR/Cas9 genome <br />editing techniques in our novel Xenopus tropicalis liposarcoma model, our first aim is to in-depth <br />characterize the (epi)genetic and genomic landscape in (well-differentiated and dedifferentiated) <br />liposarcomas and ASPLTs to unveil the underlying complex process of tumor initiation, progression <br />and dedifferentiation in lipomatous tumors. A better fundamental understanding of this liposarcoma <br />disease process will present opportunities to identify new molecular (diagnostic, prognostic and/or <br />theragnostic) biomarkers (targets), which is the second aim of this project. In parallel, we will <br />explore our preclinical Xenopus tropicalis liposarcoma model as a screening platform for future <br />targeted molecular therapies. The results of this project will be valuable for increasing the diagnostic <br />accuracy and therapeutic management in lipomatous tumors.</p>","title":"Unraveling the (epi)genetic and genomic mechanisms responsible for tumorigenesis in liposarcomas and atypical spindle cell/pleomorphic lipomatous tumors to identify novel biomarkers and pave the way for new treatment modalities","gismo_id":"a0b57b00-fa51-49d7-9bbf-00e9a593d20d"}],"parent":{"short_title":"Radiother. Oncol.","title":"RADIOTHERAPY AND ONCOLOGY"},"publication_status_sort":2,"cite":{"apa":"  <div class=\"csl-entry\">Vermassen, T., Hamerlinck, H., Creytens, D., Dhanyns, A., Padalko, E., Rottey, S., … Huvenne, W. (2026). DNA-methylation as diagnostic and prognostic biomarker for oropharyngeal cancer : a proof-of-concept study. <i>RADIOTHERAPY AND ONCOLOGY</i>, <i>216</i>(Supplement 1), S26–S27. https://doi.org/10.1016/s0167-8140(26)00189-1</div>\n","fwo":"  <div class=\"csl-entry\">Vermassen, Tijl, Hannelore Hamerlinck, David Creytens, Anouk Dhanyns, Elizaveta Padalko, Sylvie Rottey, Jens Debacker, Michael Saerens, and Wouter Huvenne. 2026. “DNA-Methylation as Diagnostic and Prognostic Biomarker for Oropharyngeal Cancer : A Proof-of-Concept Study.” In <i>RADIOTHERAPY AND ONCOLOGY</i>, 216:S26–S27. doi:10.1016/s0167-8140(26)00189-1.</div>\n","vancouver":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">1. </div><div class=\"csl-right-inline\">Vermassen T, Hamerlinck H, Creytens D, Dhanyns A, Padalko E, Rottey S, et al. DNA-methylation as diagnostic and prognostic biomarker for oropharyngeal cancer : a proof-of-concept study. In: RADIOTHERAPY AND ONCOLOGY. 2026. p. S26–7.</div>\n   </div>\n","mla":"  <div class=\"csl-entry\">Vermassen, Tijl, et al. “DNA-Methylation as Diagnostic and Prognostic Biomarker for Oropharyngeal Cancer : A Proof-of-Concept Study.” <i>RADIOTHERAPY AND ONCOLOGY</i>, vol. 216, no. Supplement 1, 2026, pp. S26–27, doi:10.1016/s0167-8140(26)00189-1.</div>\n","ieee":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">[1]</div><div class=\"csl-right-inline\">T. Vermassen <i>et al.</i>, “DNA-methylation as diagnostic and prognostic biomarker for oropharyngeal cancer : a proof-of-concept study,” in <i>RADIOTHERAPY AND ONCOLOGY</i>, Sevilla, Spain, 2026, vol. 216, no. Supplement 1, pp. S26–S27.</div>\n  </div>\n","bof":"  <div class=\"csl-entry\">Vermassen, Tijl, Hannelore Hamerlinck, David Creytens, Anouk Dhanyns, Elizaveta Padalko, Sylvie Rottey, Jens Debacker, Michael Saerens, and Wouter Huvenne. 2026. “DNA-Methylation as Diagnostic and Prognostic Biomarker for Oropharyngeal Cancer : A Proof-of-Concept Study.” In <i>RADIOTHERAPY AND ONCOLOGY</i>, 216:S26–S27. doi:10.1016/s0167-8140(26)00189-1.</div>\n","chicago-author-date":"  <div class=\"csl-entry\">Vermassen, Tijl, Hannelore Hamerlinck, David Creytens, Anouk Dhanyns, Elizaveta Padalko, Sylvie Rottey, Jens Debacker, Michael Saerens, and Wouter Huvenne. 2026. “DNA-Methylation as Diagnostic and Prognostic Biomarker for Oropharyngeal Cancer : A Proof-of-Concept Study.” In <i>RADIOTHERAPY AND ONCOLOGY</i>, 216:S26–27. https://doi.org/10.1016/s0167-8140(26)00189-1.</div>\n"},"abstract":["Purpose/Objective\nUp to 70% of oropharyngeal cancers (OPSCC) are caused by the human papillomavirus (HPV). Nowadays, HPV+ OPSCC is the most prevalent HPV-related malignancy worldwide, surpassing HPV+ cervical cancer1. HPV+ OPSCC carries a distinct pathogenesis versus HPV– OPSCC, translating into a different tumor microenvironment and gene expression patterns2-3. DNA-methylation alterations are considered a cancer hallmark with DNA-methylation leading to tumor suppressor gene repression, uncontrolled carcinogenesis and unfavorable prognosis4-6. This study assessed the feasibility of applying DNA-methylation markers to distinguish between healthy tonsils, HPV– OPSCC and HPV+ OPSCC.\nMaterial/Methods\nThirty patients were included: ten adult non-cancer-related tonsillectomy patients, ten HPV+ OPSCC patients and ten HPV– OPSCC patients. DNA was isolated from tissue and bisulfite-converted. DNA-methylation of several targets (FAM19A4, hsa-miR124-2, ASCL1, ZNF582 and LHX8) was assessed by calculating ∆∆Cq values, using ACTB as the reference gene and a calibrator for normalization. Difference in ΔΔCq was compared between groups.\nResults\nIncreased DNA-methylation was observed in cancerous versus healthy tissue. Moreover, all targets showed a difference in DNA-methylation between HPV+ OPSCC and healthy tissue, except for ASCL1 (AnoGYN kit). In addition, ZNF582 DNA-methylation was different for both HPV– and HPV+ OPSCC versus healthy tonsils. All data are illustrated in Table 1. A preliminary analysis into the prognostic properties in this small cohort showed that LHX8 DNA-methylation was more frequent in patients without recurrent disease (n=11, median ∆∆Cq=4.20) versus patients with disease recurrence (n=6, median ∆∆Cq=6.41; P=0.0477)."],"author":[{"biblio_id":"0D167612-F0EE-11E1-A9DE-61C894A0A6B4","last_name":"Vermassen","_id":"0D167612-F0EE-11E1-A9DE-61C894A0A6B4","name_last_first":"Vermassen, Tijl","ugent_id":["802001050767"],"orcid_id":"0000-0002-1335-9966","first_name":"Tijl","name":"Tijl Vermassen","affiliation":[{"ugent_id":"GE33","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE33"}]}]},{"last_name":"Hamerlinck","biblio_id":"11A5C78C-F0EE-11E1-A9DE-61C894A0A6B4","name_last_first":"Hamerlinck, Hannelore","_id":"11A5C78C-F0EE-11E1-A9DE-61C894A0A6B4","orcid_id":"0000-0003-3675-2397","ugent_id":["000080278109","802003343405"],"affiliation":[{"ugent_id":"GE32","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE32"}]},{"ugent_id":"UZGent","path":[{"ugent_id":"UZGent"}]}],"first_name":"Hannelore","name":"Hannelore Hamerlinck"},{"last_name":"Creytens","biblio_id":"9E10BFB8-1EEF-11E2-A298-0C6810BDE39D","name_last_first":"Creytens, David","_id":"9E10BFB8-1EEF-11E2-A298-0C6810BDE39D","orcid_id":"0000-0002-6064-1673","ugent_id":["802001346013"],"affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE32"}],"ugent_id":"GE32"},{"ugent_id":"UZGent","path":[{"ugent_id":"UZGent"}]}],"first_name":"David","name":"David Creytens"},{"first_name":"Anouk","name":"Anouk Dhanyns","ugent_id":["974057977115"],"_id":"b0745d23-fa26-11eb-a093-f59591323c5a","name_last_first":"Dhanyns, Anouk","biblio_id":"b0745d23-fa26-11eb-a093-f59591323c5a","last_name":"Dhanyns"},{"orcid_id":"0000-0002-8101-6957","ugent_id":["802001876681"],"affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE32"}],"ugent_id":"GE32"},{"path":[{"ugent_id":"UZGent"}],"ugent_id":"UZGent"}],"name":"Elizaveta Padalko","first_name":"Elizaveta","last_name":"Padalko","biblio_id":"B129260A-49B6-11E4-AA90-F166B5D1D7B1","name_last_first":"Padalko, Elizaveta","_id":"B129260A-49B6-11E4-AA90-F166B5D1D7B1"},{"affiliation":[{"ugent_id":"GE33","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE33"}]},{"ugent_id":"UZGent","path":[{"ugent_id":"UZGent"}]}],"name":"Sylvie Rottey","first_name":"Sylvie","orcid_id":"0000-0003-2060-3725","ugent_id":["802000456441","919015706627"],"name_last_first":"Rottey, Sylvie","_id":"FB6E9C32-F0ED-11E1-A9DE-61C894A0A6B4","last_name":"Rottey","biblio_id":"FB6E9C32-F0ED-11E1-A9DE-61C894A0A6B4"},{"_id":"301CD584-F0EE-11E1-A9DE-61C894A0A6B4","name_last_first":"Debacker, Jens","biblio_id":"301CD584-F0EE-11E1-A9DE-61C894A0A6B4","last_name":"Debacker","first_name":"Jens","name":"Jens Debacker","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE34"}],"ugent_id":"GE34"}],"ugent_id":["802002063813"],"orcid_id":"0000-0002-8293-2885"},{"name":"Michael Saerens","first_name":"Michael","affiliation":[{"ugent_id":"GE33","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE33"}]},{"ugent_id":"UZGent","path":[{"ugent_id":"UZGent"}]}],"ugent_id":["002001200330","802004715145","910004403997"],"orcid_id":"0000-0001-5523-6537","_id":"0D1D536A-F0EE-11E1-A9DE-61C894A0A6B4","name_last_first":"Saerens, Michael","biblio_id":"0D1D536A-F0EE-11E1-A9DE-61C894A0A6B4","last_name":"Saerens"},{"affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE34"}],"ugent_id":"GE34"},{"path":[{"ugent_id":"UZGent"}],"ugent_id":"UZGent"}],"name":"Wouter Huvenne","first_name":"Wouter","orcid_id":"0000-0002-0567-8983","ugent_id":["802000102187"],"name_last_first":"Huvenne, Wouter","_id":"F898A516-F0ED-11E1-A9DE-61C894A0A6B4","last_name":"Huvenne","biblio_id":"F898A516-F0ED-11E1-A9DE-61C894A0A6B4"}],"biblio_id":"01M1EZMEXQMHGQZPZHQWSRF4BH","handle":"http://hdl.handle.net/1854/LU-01M1EZMEXQMHGQZPZHQWSRF4BH","_id":"01M1EZMEXQMHGQZPZHQWSRF4BH","subject":["Medicine and Health Sciences"],"jcr":{},"abstract_full":[{"lang":"eng","text":"Purpose/Objective\nUp to 70% of oropharyngeal cancers (OPSCC) are caused by the human papillomavirus (HPV). Nowadays, HPV+ OPSCC is the most prevalent HPV-related malignancy worldwide, surpassing HPV+ cervical cancer1. HPV+ OPSCC carries a distinct pathogenesis versus HPV– OPSCC, translating into a different tumor microenvironment and gene expression patterns2-3. DNA-methylation alterations are considered a cancer hallmark with DNA-methylation leading to tumor suppressor gene repression, uncontrolled carcinogenesis and unfavorable prognosis4-6. This study assessed the feasibility of applying DNA-methylation markers to distinguish between healthy tonsils, HPV– OPSCC and HPV+ OPSCC.\nMaterial/Methods\nThirty patients were included: ten adult non-cancer-related tonsillectomy patients, ten HPV+ OPSCC patients and ten HPV– OPSCC patients. DNA was isolated from tissue and bisulfite-converted. DNA-methylation of several targets (FAM19A4, hsa-miR124-2, ASCL1, ZNF582 and LHX8) was assessed by calculating ∆∆Cq values, using ACTB as the reference gene and a calibrator for normalization. Difference in ΔΔCq was compared between groups.\nResults\nIncreased DNA-methylation was observed in cancerous versus healthy tissue. Moreover, all targets showed a difference in DNA-methylation between HPV+ OPSCC and healthy tissue, except for ASCL1 (AnoGYN kit). In addition, ZNF582 DNA-methylation was different for both HPV– and HPV+ OPSCC versus healthy tonsils. All data are illustrated in Table 1. A preliminary analysis into the prognostic properties in this small cohort showed that LHX8 DNA-methylation was more frequent in patients without recurrent disease (n=11, median ∆∆Cq=4.20) versus patients with disease recurrence (n=6, median ∆∆Cq=6.41; P=0.0477)."}],"classification":"C3","series_title":"Radiotherapy and Oncology","wos_id":"001752705100026","copyright_statement":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Public License (CC BY-NC-ND 4.0)","file":[{"thumbnail_url":"https://biblio.ugent.be/publication/01M1EZMEXQMHGQZPZHQWSRF4BH/file/01M1F02NZHDE9EE97XZHBPT63T/thumbnail.png","name":"DNA methylation oropharyngeal cancer.pdf","sha256":"1977cc932529a9c68c2bc3ba3dbec0ce4e7a0e82e5e564bc5b4a7cee440e5843","kind":"fullText","access":"restricted","publication_version":"publishedVersion","_id":"01M1F02NZHDE9EE97XZHBPT63T","url":"https://biblio.ugent.be/publication/01M1EZMEXQMHGQZPZHQWSRF4BH/file/01M1F02NZHDE9EE97XZHBPT63T.pdf","content_type":"application/pdf","size":"145597"},{"access":"restricted","change":{"on":"2027-04-10","to":"open"},"sha256":"b34d511c3c09440b4ee3bc54a9578a0aa96444a32603bbbe14ec9b9d55e9e080","kind":"fullText","name":"ICHNO 2026_abstract DNAmeth_TV_20251001_HHA.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","size":"30976","url":"https://biblio.ugent.be/publication/01M1EZMEXQMHGQZPZHQWSRF4BH/file/01M1F0ADENBBBQ1NTN0YTHN77C.docx","_id":"01M1F0ADENBBBQ1NTN0YTHN77C","publication_version":"acceptedVersion"}],"issn":["0167-8140","1879-0887"],"wos_type":"Meeting Abstract","volume":"216","conference_type":"meetingAbstract","publication_status":"published","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE32"}],"name":"Department of Diagnostic Sciences","ugent_id":"GE32"},{"path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE33"}],"name":"Department of Basic and Applied Medical Sciences","ugent_id":"GE33"},{"ugent_id":"GE34","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE34"}],"name":"Department of Head and Skin"},{"path":[{"ugent_id":"UZGent"}],"name":"Ghent University Hospital","ugent_id":"UZGent"}],"created_by":{"name_last_first":"Creytens, David","_id":"9E10BFB8-1EEF-11E2-A298-0C6810BDE39D","last_name":"Creytens","biblio_id":"9E10BFB8-1EEF-11E2-A298-0C6810BDE39D","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE32"}],"ugent_id":"GE32"},{"path":[{"ugent_id":"UZGent"}],"ugent_id":"UZGent"}],"first_name":"David","name":"David Creytens","orcid_id":"0000-0002-6064-1673","ugent_id":["802001346013"]},"external":0,"date_created":"2026-09-01 17:17:55","language":["eng"],"conference":{"end_date":"2026-03-21","start_date":"2026-03-19","organizer":"European SocieTy for Radiotherapy and Oncology (ESTRO), the European Head and Neck Society (EHNS) and the European Society for Medical Oncology (ESMO)","location":"Sevilla, Spain","name":"10th International Congress on Innovative Approaches in Head and Neck Oncology (ICHNO)"},"date_updated":"2026-09-07 13:27:39","title":"DNA-methylation as diagnostic and prognostic biomarker for oropharyngeal cancer : a proof-of-concept study","doi":["10.1016/s0167-8140(26)00189-1"],"page":{"first":"S26","last":"S27"},"issue":"Supplement 1","year":"2026","status":"public","type":"conference","article_number":"364"},{"issn":["2079-6374"],"file":[{"kind":"fullText","sha256":"3803238a5454be852973c16d44171cd83ec74a470f991d00094b9d7df7afe296","access":"open","thumbnail_url":"https://biblio.ugent.be/publication/01KJ5NTYVJQTBSB1Y4Z0N5YN05/file/01KK9KJPDF69ADNV38AYWS621J/thumbnail.png","name":"publisher_version.pdf","url":"https://biblio.ugent.be/publication/01KJ5NTYVJQTBSB1Y4Z0N5YN05/file/01KK9KJPDF69ADNV38AYWS621J.pdf","size":"1822214","content_type":"application/pdf","publication_version":"publishedVersion","_id":"01KK9KJPDF69ADNV38AYWS621J"}],"copyright_statement":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","wos_id":"001700552600001","volume":"16","wos_type":"Article","page":{"count":"15"},"title":"Rapid forensic DNA profiling via real-time recombinase polymerase amplification of InDel markers","doi":["10.3390/bios16020106"],"date_updated":"2026-03-31 05:30:24","external":0,"language":["eng"],"date_created":"2026-02-23 16:38:05","created_by":{"affiliation":[{"ugent_id":"FW01","path":[{"ugent_id":"UGent"},{"ugent_id":"FW"},{"ugent_id":"FW01"}]}],"name":"Sonja Skevin","first_name":"Sonja","orcid_id":"0000-0001-5542-0799","ugent_id":["000211563666","802003541243","919079758454","977455322895"],"name_last_first":"Skevin, Sonja","_id":"8ac66c99-0431-11eb-a74c-f0272e2c9e46","last_name":"Skevin","biblio_id":"8ac66c99-0431-11eb-a74c-f0272e2c9e46"},"affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"FW"},{"ugent_id":"FW01"}],"name":"Department of Pharmaceutics","ugent_id":"FW01"}],"publication_status":"published","article_number":"106","keyword":["recombinase polymerase amplification","InDel genotyping","forensic genetics","DNA probes","lab-on-a-chip","ASSAY"],"type":"journalArticle","status":"public","issue":"2","year":"2026","cite":{"apa":"  <div class=\"csl-entry\">De Keyzer, L., Skevin, S., Deserranno, K., Deforce, D., &#38; Van Nieuwerburgh, F. (2026). Rapid forensic DNA profiling via real-time recombinase polymerase amplification of InDel markers. <i>BIOSENSORS-BASEL</i>, <i>16</i>(2). https://doi.org/10.3390/bios16020106</div>\n","fwo":"  <div class=\"csl-entry\">De Keyzer, Liesl, Sonja Skevin, Koen Deserranno, Dieter Deforce, and Filip Van Nieuwerburgh. 2026. “Rapid Forensic DNA Profiling via Real-Time Recombinase Polymerase Amplification of InDel Markers.” <i>BIOSENSORS-BASEL</i> 16 (2). doi:10.3390/bios16020106.</div>\n","vancouver":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">1. </div><div class=\"csl-right-inline\">De Keyzer L, Skevin S, Deserranno K, Deforce D, Van Nieuwerburgh F. Rapid forensic DNA profiling via real-time recombinase polymerase amplification of InDel markers. BIOSENSORS-BASEL. 2026;16(2).</div>\n   </div>\n","ieee":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">[1]</div><div class=\"csl-right-inline\">L. De Keyzer, S. Skevin, K. Deserranno, D. Deforce, and F. Van Nieuwerburgh, “Rapid forensic DNA profiling via real-time recombinase polymerase amplification of InDel markers,” <i>BIOSENSORS-BASEL</i>, vol. 16, no. 2, 2026.</div>\n  </div>\n","mla":"  <div class=\"csl-entry\">De Keyzer, Liesl, et al. “Rapid Forensic DNA Profiling via Real-Time Recombinase Polymerase Amplification of InDel Markers.” <i>BIOSENSORS-BASEL</i>, vol. 16, no. 2, 2026, doi:10.3390/bios16020106.</div>\n","bof":"  <div class=\"csl-entry\">De Keyzer, Liesl, Sonja Skevin, Koen Deserranno, Dieter Deforce, and Filip Van Nieuwerburgh. 2026. “Rapid Forensic DNA Profiling via Real-Time Recombinase Polymerase Amplification of InDel Markers.” <i>BIOSENSORS-BASEL</i> 16 (2). doi:10.3390/bios16020106.</div>\n","chicago-author-date":"  <div class=\"csl-entry\">De Keyzer, Liesl, Sonja Skevin, Koen Deserranno, Dieter Deforce, and Filip Van Nieuwerburgh. 2026. “Rapid Forensic DNA Profiling via Real-Time Recombinase Polymerase Amplification of InDel Markers.” <i>BIOSENSORS-BASEL</i> 16 (2). https://doi.org/10.3390/bios16020106.</div>\n"},"publication_status_sort":2,"parent":{"title":"BIOSENSORS-BASEL","short_title":"Biosensors-Basel"},"project":[{"iweto_id":"1S02625N","start_date":"2024-11-01","_id":"1S02625N","end_date":"2028-10-31","gismo_id":"22e1895a-914d-11ef-8809-7d0ab6a46a95","title":"Isothermal STR Analysis Using Recombinase Polymerase Amplification with Probe-Based Genotyping for Microfluidic Chip Integration","abstract":"<p>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.</p>"}],"_id":"01KJ5NTYVJQTBSB1Y4Z0N5YN05","handle":"http://hdl.handle.net/1854/LU-01KJ5NTYVJQTBSB1Y4Z0N5YN05","biblio_id":"01KJ5NTYVJQTBSB1Y4Z0N5YN05","author":[{"name_last_first":"De Keyzer, Liesl","credit_role":["first_author"],"_id":"98E8AFC4-C45F-11E9-9607-F1515707D3EF","last_name":"De Keyzer","biblio_id":"98E8AFC4-C45F-11E9-9607-F1515707D3EF","affiliation":[{"ugent_id":"FW01","path":[{"ugent_id":"UGent"},{"ugent_id":"FW"},{"ugent_id":"FW01"}]}],"first_name":"Liesl","name":"Liesl De Keyzer","orcid_id":"0009-0009-9809-6840","ugent_id":["000190007236","802004693321","974171065977"]},{"credit_role":["writing_review_editing"],"name_last_first":"Skevin, Sonja","_id":"8ac66c99-0431-11eb-a74c-f0272e2c9e46","last_name":"Skevin","biblio_id":"8ac66c99-0431-11eb-a74c-f0272e2c9e46","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"FW"},{"ugent_id":"FW01"}],"ugent_id":"FW01"}],"name":"Sonja Skevin","first_name":"Sonja","orcid_id":"0000-0001-5542-0799","ugent_id":["000211563666","802003541243","919079758454","977455322895"]},{"_id":"EA4B363A-5E7C-11E6-BCAC-C275B5D1D7B1","name_last_first":"Deserranno, Koen","credit_role":["writing_review_editing"],"biblio_id":"EA4B363A-5E7C-11E6-BCAC-C275B5D1D7B1","last_name":"Deserranno","first_name":"Koen","name":"Koen Deserranno","affiliation":[{"ugent_id":"FW01","path":[{"ugent_id":"UGent"},{"ugent_id":"FW"},{"ugent_id":"FW01"}]}],"ugent_id":["802003765454","979434486849"],"orcid_id":"0000-0003-0364-1957"},{"credit_role":["supervision"],"name_last_first":"Deforce, Dieter","_id":"F4D02620-F0ED-11E1-A9DE-61C894A0A6B4","last_name":"Deforce","biblio_id":"F4D02620-F0ED-11E1-A9DE-61C894A0A6B4","affiliation":[{"ugent_id":"FW01","path":[{"ugent_id":"UGent"},{"ugent_id":"FW"},{"ugent_id":"FW01"}]}],"name":"Dieter Deforce","first_name":"Dieter","orcid_id":"0000-0002-0635-661X","ugent_id":["801000962680","977347599547"]},{"biblio_id":"F5BC58D8-F0ED-11E1-A9DE-61C894A0A6B4","last_name":"Van Nieuwerburgh","_id":"F5BC58D8-F0ED-11E1-A9DE-61C894A0A6B4","credit_role":["supervision"],"name_last_first":"Van Nieuwerburgh, Filip","ugent_id":["801001335829","971455938573"],"orcid_id":"0000-0001-8815-5485","name":"Filip Van Nieuwerburgh","first_name":"Filip","affiliation":[{"ugent_id":"FW01","path":[{"ugent_id":"UGent"},{"ugent_id":"FW"},{"ugent_id":"FW01"}]}]}],"abstract":["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."],"article_type":"original","classification":"A1","abstract_full":[{"lang":"eng","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."}],"jcr":{},"subject":["Biology and Life Sciences"]},{"affiliation":[{"name":"Ghent University","path":[{"ugent_id":"UGent"}],"ugent_id":"UGent"},{"path":[{"ugent_id":"UGent"},{"ugent_id":"LA"},{"ugent_id":"LA25"}],"name":"Department of Biotechnology","ugent_id":"LA25"},{"ugent_id":"FW01","name":"Department of Pharmaceutics","path":[{"ugent_id":"UGent"},{"ugent_id":"FW"},{"ugent_id":"FW01"}]}],"created_by":{"orcid_id":"0000-0003-3214-2604","ugent_id":["972664614551"],"affiliation":[{"path":[{"ugent_id":"UGent"}],"name":"Ghent University","ugent_id":"UGent"}],"first_name":"Jasper","name":"Jasper Matthys","last_name":"Matthys","biblio_id":"1C52730E-76D9-11E6-A3D8-516FB5D1D7B1","name_last_first":"Matthys, Jasper","_id":"1C52730E-76D9-11E6-A3D8-516FB5D1D7B1"},"external":0,"date_created":"2026-10-11 09:25:57","language":["eng"],"publication_status":"published","handle":"http://hdl.handle.net/1854/LU-01M4N4H0D8960KAGAYT9RVFYQE","publisher":{"name":"Wiley"},"_id":"01M4N4H0D8960KAGAYT9RVFYQE","abstract":["<jats:title>Summary</jats:title>\n                  <jats:p>\n                    <jats:list list-type=\"bullet\">\n                      <jats:list-item>\n                        <jats:p>Cytosine methylation drives transcriptional reprogramming during plant innate and acquired immunity. Beyond RNA adenosine methylation, DNA adenine methylation (6mA) has recently emerged as a candidate regulator of gene expression, though its role in plant immunity is unknown.</jats:p>\n                      </jats:list-item>\n                      <jats:list-item>\n                        <jats:p>\n                          Using the bacterial elicitor Flg22, we examined genome‐wide DNA methylation responses of\n                          <jats:italic>Arabidopsis thaliana</jats:italic>\n                          and\n                          <jats:italic>Oryza sativa</jats:italic>\n                          to identify shared epigenetic responses across divergent genomes. High‐resolution Oxford Nanopore sequencing enabled simultaneous detection of 5‐methylcytosine (5mC) and 6mA DNA modifications.\n                        </jats:p>\n                      </jats:list-item>\n                      <jats:list-item>\n                        <jats:p>\n                          In both species, early immune activation was marked by non‐CG 5mC hypomethylation at short euchromatic transposable elements. By 72 hpt, both species showed elevated 5mC levels at (peri)centromeric regions, targeted to pericentromeric non‐CG sites in Arabidopsis and accompanied by lasting chromosomal arm hypomethylation in rice. Despite species‐specific global 6mA responses, both species exhibited a conserved bimodal 6mA distribution flanking transcription start and termination sites of genes, intensified at defence‐related genes following Flg22 elicitation. In Arabidopsis, these 6mA signatures correlated with Flg22‐primed gene activation, while mutation of 6mA demethylase ALKBH1D increased susceptibility to\n                          <jats:italic>Pseudomonas syringae</jats:italic>\n                          and\n                          <jats:italic>Meloidogyne incognita</jats:italic>\n                          .\n                        </jats:p>\n                      </jats:list-item>\n                      <jats:list-item>\n                        <jats:p>Together, our findings reveal conserved 5mC dynamics during immune activation and highlight a role for 6mA in modulating defence‐related transcriptional reprogramming.</jats:p>\n                      </jats:list-item>\n                    </jats:list>\n                  </jats:p>"],"article_type":"original","date_updated":"2026-10-11 10:18:04","author":[{"affiliation":[{"path":[{"ugent_id":"UGent"}],"name":"Ghent University","ugent_id":"UGent"}],"first_name":"Jasper","name":"Jasper Matthys","orcid_id":"0000-0003-3214-2604","ugent_id":["972664614551"],"name_last_first":"Matthys, Jasper","credit_role":["first_author"],"_id":"1C52730E-76D9-11E6-A3D8-516FB5D1D7B1","last_name":"Matthys","biblio_id":"1C52730E-76D9-11E6-A3D8-516FB5D1D7B1"},{"affiliation":[{"ugent_id":"LA25","path":[{"ugent_id":"UGent"},{"ugent_id":"LA"},{"ugent_id":"LA25"}]}],"first_name":"Ibe","name":"Ibe Naessens","orcid_id":"0000-0003-1122-5208","ugent_id":["000171105976","802004138397"],"name_last_first":"Naessens, Ibe","_id":"C79CD562-9B2A-11E7-B6A4-767EAD28A064","last_name":"Naessens","biblio_id":"C79CD562-9B2A-11E7-B6A4-767EAD28A064"},{"last_name":"Van Nieuwerburgh","biblio_id":"F5BC58D8-F0ED-11E1-A9DE-61C894A0A6B4","name_last_first":"Van Nieuwerburgh, Filip","credit_role":["methodology"],"_id":"F5BC58D8-F0ED-11E1-A9DE-61C894A0A6B4","orcid_id":"0000-0001-8815-5485","ugent_id":["801001335829"],"affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"FW"},{"ugent_id":"FW01"}],"ugent_id":"FW01"}],"first_name":"Filip","name":"Filip Van Nieuwerburgh"},{"name":"Jurriaan Ton","first_name":"Jurriaan","credit_role":["conceptualization","writing_review_editing"],"name_last_first":"Ton, Jurriaan","last_name":"Ton"},{"ugent_id":["801001607429","919021522583"],"orcid_id":"0000-0002-5267-5013","name":"Tina Kyndt","first_name":"Tina","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"LA"},{"ugent_id":"LA25"}],"ugent_id":"LA25"}],"biblio_id":"F6622844-F0ED-11E1-A9DE-61C894A0A6B4","last_name":"Kyndt","_id":"F6622844-F0ED-11E1-A9DE-61C894A0A6B4","credit_role":["last_author"],"name_last_first":"Kyndt, Tina"}],"biblio_id":"01M4N4H0D8960KAGAYT9RVFYQE","doi":["10.1111/nph.71600"],"title":"Distinct targeting of 5mC and 6mA DNA methylation during the onset of Flg22‐induced immunity between Arabidopsis and rice","subject":["Biology and Life Sciences"],"status":"public","year":"2026","jcr":{},"keyword":["Epigenetics","DNA methylation","DNA adenine methylation","Arabidopsis","Rice","Plant immunity","Priming","Oxford Nanopore sequencing"],"abstract_full":[{"text":"<jats:title>Summary</jats:title>\n                  <jats:p>\n                    <jats:list list-type=\"bullet\">\n                      <jats:list-item>\n                        <jats:p>Cytosine methylation drives transcriptional reprogramming during plant innate and acquired immunity. Beyond RNA adenosine methylation, DNA adenine methylation (6mA) has recently emerged as a candidate regulator of gene expression, though its role in plant immunity is unknown.</jats:p>\n                      </jats:list-item>\n                      <jats:list-item>\n                        <jats:p>\n                          Using the bacterial elicitor Flg22, we examined genome‐wide DNA methylation responses of\n                          <jats:italic>Arabidopsis thaliana</jats:italic>\n                          and\n                          <jats:italic>Oryza sativa</jats:italic>\n                          to identify shared epigenetic responses across divergent genomes. High‐resolution Oxford Nanopore sequencing enabled simultaneous detection of 5‐methylcytosine (5mC) and 6mA DNA modifications.\n                        </jats:p>\n                      </jats:list-item>\n                      <jats:list-item>\n                        <jats:p>\n                          In both species, early immune activation was marked by non‐CG 5mC hypomethylation at short euchromatic transposable elements. By 72 hpt, both species showed elevated 5mC levels at (peri)centromeric regions, targeted to pericentromeric non‐CG sites in Arabidopsis and accompanied by lasting chromosomal arm hypomethylation in rice. Despite species‐specific global 6mA responses, both species exhibited a conserved bimodal 6mA distribution flanking transcription start and termination sites of genes, intensified at defence‐related genes following Flg22 elicitation. In Arabidopsis, these 6mA signatures correlated with Flg22‐primed gene activation, while mutation of 6mA demethylase ALKBH1D increased susceptibility to\n                          <jats:italic>Pseudomonas syringae</jats:italic>\n                          and\n                          <jats:italic>Meloidogyne incognita</jats:italic>\n                          .\n                        </jats:p>\n                      </jats:list-item>\n                      <jats:list-item>\n                        <jats:p>Together, our findings reveal conserved 5mC dynamics during immune activation and highlight a role for 6mA in modulating defence‐related transcriptional reprogramming.</jats:p>\n                      </jats:list-item>\n                    </jats:list>\n                  </jats:p>","lang":"und"}],"type":"journalArticle","article_number":"nph.71600","classification":"U","project":[{"iweto_id":"3F016421","start_date":"2021-11-01","_id":"3F016421","end_date":"2025-10-31","gismo_id":"19d35cad-2a82-11ec-95aa-05ef7abe0c3c","title":"Epigenetic shock: Early alterations in DNA methylation and histone modifications as part of the plant immune response","abstract":"<p>This proposal aims to deliver fundamental insights into the role of early DNA hypomethylation and histone modification changes - a phenomenon that we call the ‘epigenetic shock’ - in plant immunity. By focusing on two model plants, Arabidopsis and rice, this proposal will allow to assess the evolutionary conservation of the epigenetic shock, increasing the potential broad impact of the project results. Rice is one of the most important staple crops in the world, it feeds more than 50% of the human population on a daily basis. The Kyndt research group focusses on rice immunity and epigenetics, an increasingly important subject to sustainably deal with pathogens/pests. Preliminary results from the group, together with recent Arabidopsis research (a.o. from the co-promoter of this application) indicate a role for DNA hypomethylation in pattern triggered immunity and induced resistance, and of unilateral histone modifications in plant immunity. This proposal will expand the fragmented data, check the conservation of this response over different stimuli and assess the causes and consequences of the epigenetic shock, which remain largely elusive today. The project includes ELISA assays to assess the epigenetic changes over time, stimuli and species; mRNA-seq and mutant analyses to identify the mediators; and ATAC-Me sequencing to check the consequences. In the long term, our research aims at providing answers to the growing problems with diseases in agriculture.</p>","publication_count":2}],"parent":{"title":"New Phytologist","short_title":"New Phytologist"},"publication_status_sort":2,"issn":["0028-646X","1469-8137"],"cite":{"chicago-author-date":"  <div class=\"csl-entry\">Matthys, Jasper, Ibe Naessens, Filip Van Nieuwerburgh, Jurriaan Ton, and Tina Kyndt. 2026. “Distinct Targeting of 5mC and 6mA DNA Methylation during the Onset of Flg22‐induced Immunity between Arabidopsis and Rice.” <i>New Phytologist</i>. https://doi.org/10.1111/nph.71600.</div>\n","mla":"  <div class=\"csl-entry\">Matthys, Jasper, et al. “Distinct Targeting of 5mC and 6mA DNA Methylation during the Onset of Flg22‐induced Immunity between Arabidopsis and Rice.” <i>New Phytologist</i>, Wiley, 2026, doi:10.1111/nph.71600.</div>\n","bof":"  <div class=\"csl-entry\">Matthys, Jasper, Ibe Naessens, Filip Van Nieuwerburgh, Jurriaan Ton, and Tina Kyndt. 2026. “Distinct Targeting of 5mC and 6mA DNA Methylation during the Onset of Flg22‐induced Immunity between Arabidopsis and Rice.” <i>New Phytologist</i>. doi:10.1111/nph.71600.</div>\n","apa":"  <div class=\"csl-entry\">Matthys, J., Naessens, I., Van Nieuwerburgh, F., Ton, J., &#38; Kyndt, T. (2026). Distinct targeting of 5mC and 6mA DNA methylation during the onset of Flg22‐induced immunity between Arabidopsis and rice. <i>New Phytologist</i>. https://doi.org/10.1111/nph.71600</div>\n","fwo":"  <div class=\"csl-entry\">Matthys, Jasper, Ibe Naessens, Filip Van Nieuwerburgh, Jurriaan Ton, and Tina Kyndt. 2026. “Distinct Targeting of 5mC and 6mA DNA Methylation during the Onset of Flg22‐induced Immunity between Arabidopsis and Rice.” <i>New Phytologist</i>. doi:10.1111/nph.71600.</div>\n","vancouver":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">1. </div><div class=\"csl-right-inline\">Matthys J, Naessens I, Van Nieuwerburgh F, Ton J, Kyndt T. Distinct targeting of 5mC and 6mA DNA methylation during the onset of Flg22‐induced immunity between Arabidopsis and rice. New Phytologist. 2026;</div>\n   </div>\n","ieee":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">[1]</div><div class=\"csl-right-inline\">J. Matthys, I. Naessens, F. Van Nieuwerburgh, J. Ton, and T. Kyndt, “Distinct targeting of 5mC and 6mA DNA methylation during the onset of Flg22‐induced immunity between Arabidopsis and rice,” <i>New Phytologist</i>, 2026.</div>\n  </div>\n"}},{"project":[{"abstract":"<p>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.</p>","title":"Development of a fast, minimally-invasive and affordable test for accurate diagnosis of Cancer of Unknown Primary (CUP) using DNA methylation profiling.","gismo_id":"d3c074b7-0fb3-11eb-89fc-81e15036b2fa","end_date":"2022-10-31","start_date":"2020-11-01","_id":"3S010820","iweto_id":"3S010820","publication_count":7}],"publication_status_sort":2,"copyright_statement":"No license (in copyright)","file":[{"access":"restricted","sha256":"f67c9bdda41f71283920149af121703e176fada51667035dd7afee3894419b56","change":{"on":"2031-06-30","to":"open"},"kind":"fullText","name":"dissertation Jilke_final.pdf","thumbnail_url":"https://biblio.ugent.be/publication/01KWG3WD02D7FJ9BXJE7R0N71M/file/01KWYF7JT5Q9HBZVSRRH7BYV5S/thumbnail.png","content_type":"application/pdf","size":"72732137","url":"https://biblio.ugent.be/publication/01KWG3WD02D7FJ9BXJE7R0N71M/file/01KWYF7JT5Q9HBZVSRRH7BYV5S.pdf","_id":"01KWYF7JT5Q9HBZVSRRH7BYV5S","publication_version":"publishedVersion"}],"cite":{"bof":"  <div class=\"csl-entry\">De Wilde, Jilke. 2026. “Advancing Cancer Diagnostics through DNA Methylation Profiling of Liquid and FFPE Biopsies.” Ghent, Belgium: Ghent University. Faculty of Medicine and Health Sciences.</div>\n","mla":"  <div class=\"csl-entry\">De Wilde, Jilke. <i>Advancing Cancer Diagnostics through DNA Methylation Profiling of Liquid and FFPE Biopsies</i>. Ghent University. Faculty of Medicine and Health Sciences, 2026.</div>\n","chicago-author-date":"  <div class=\"csl-entry\">De Wilde, Jilke. 2026. “Advancing Cancer Diagnostics through DNA Methylation Profiling of Liquid and FFPE Biopsies.” Ghent, Belgium: Ghent University. Faculty of Medicine and Health Sciences.</div>\n","fwo":"  <div class=\"csl-entry\">De Wilde, Jilke. 2026. “Advancing Cancer Diagnostics through DNA Methylation Profiling of Liquid and FFPE Biopsies.” Ghent, Belgium: Ghent University. Faculty of Medicine and Health Sciences.</div>\n","apa":"  <div class=\"csl-entry\">De Wilde, J. (2026). <i>Advancing cancer diagnostics through DNA methylation profiling of liquid and FFPE biopsies</i>. Ghent University. Faculty of Medicine and Health Sciences, Ghent, Belgium.</div>\n","ieee":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">[1]</div><div class=\"csl-right-inline\">J. De Wilde, “Advancing cancer diagnostics through DNA methylation profiling of liquid and FFPE biopsies,” Ghent University. Faculty of Medicine and Health Sciences, Ghent, Belgium, 2026.</div>\n  </div>\n","vancouver":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">1. </div><div class=\"csl-right-inline\">De Wilde J. Advancing cancer diagnostics through DNA methylation profiling of liquid and FFPE biopsies. [Ghent, Belgium]: Ghent University. Faculty of Medicine and Health Sciences; 2026.</div>\n   </div>\n"},"promoter":[{"orcid_id":"0000-0002-7726-5096","ugent_id":["801001465060"],"affiliation":[{"ugent_id":"GE31","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE31"}]}],"first_name":"Katleen","name":"Katleen De Preter","last_name":"De Preter","biblio_id":"F60746CC-F0ED-11E1-A9DE-61C894A0A6B4","name_last_first":"De Preter, Katleen","_id":"F60746CC-F0ED-11E1-A9DE-61C894A0A6B4"},{"_id":"9E10BFB8-1EEF-11E2-A298-0C6810BDE39D","name_last_first":"Creytens, David","biblio_id":"9E10BFB8-1EEF-11E2-A298-0C6810BDE39D","last_name":"Creytens","first_name":"David","name":"David Creytens","affiliation":[{"ugent_id":"GE32","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE32"}]},{"path":[{"ugent_id":"UZGent"}],"ugent_id":"UZGent"}],"ugent_id":["802001346013"],"orcid_id":"0000-0002-6064-1673"},{"affiliation":[{"ugent_id":"GE32","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE32"}]},{"ugent_id":"UZGent","path":[{"ugent_id":"UZGent"}]}],"name":"Jo Van Dorpe","first_name":"Jo","orcid_id":"0000-0001-8175-2930","ugent_id":["802001876075"],"name_last_first":"Van Dorpe, Jo","_id":"B7E2A26E-49B6-11E4-AA90-F166B5D1D7B1","last_name":"Van Dorpe","biblio_id":"B7E2A26E-49B6-11E4-AA90-F166B5D1D7B1"}],"defense":{"location":"Gent : Ghent University and Ghent University Hospital","date":"2026-06-30"},"publication_status":"published","created_by":{"name":"David Creytens","first_name":"David","affiliation":[{"ugent_id":"GE32","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE32"}]},{"ugent_id":"UZGent","path":[{"ugent_id":"UZGent"}]}],"ugent_id":["802001346013"],"orcid_id":"0000-0002-6064-1673","_id":"9E10BFB8-1EEF-11E2-A298-0C6810BDE39D","name_last_first":"Creytens, David","biblio_id":"9E10BFB8-1EEF-11E2-A298-0C6810BDE39D","last_name":"Creytens"},"affiliation":[{"name":"Department of Diagnostic Sciences","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE32"}],"ugent_id":"GE32"},{"name":"Department of Biomolecular Medicine","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE31"}],"ugent_id":"GE31"}],"external":0,"language":["eng"],"date_created":"2026-07-02 00:32:55","author":[{"_id":"0797DE42-F0EE-11E1-A9DE-61C894A0A6B4","name_last_first":"De Wilde, Jilke","biblio_id":"0797DE42-F0EE-11E1-A9DE-61C894A0A6B4","last_name":"De Wilde","name":"Jilke De Wilde","first_name":"Jilke","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE31"}],"ugent_id":"GE31"},{"path":[{"ugent_id":"UGent"},{"ugent_id":"WE"},{"ugent_id":"WE10"}],"ugent_id":"WE10"}],"ugent_id":["000070326515","802003068670"],"orcid_id":"0000-0003-0392-7162"}],"date_updated":"2026-08-14 06:55:52","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."],"title":"Advancing cancer diagnostics through DNA methylation profiling of liquid and FFPE biopsies","biblio_id":"01KWG3WD02D7FJ9BXJE7R0N71M","publisher":{"location":"Ghent, Belgium","name":"Ghent University. Faculty of Medicine and Health Sciences"},"handle":"http://hdl.handle.net/1854/LU-01KWG3WD02D7FJ9BXJE7R0N71M","page":{"count":"217"},"_id":"01KWG3WD02D7FJ9BXJE7R0N71M","year":"2026","status":"public","subject":["Medicine and Health Sciences"],"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."}],"type":"dissertation","jcr":{},"classification":"D1"},{"cite":{"ieee":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">[1]</div><div class=\"csl-right-inline\">A. Peymen, A. Valverde, T. Van der Snickt, E. Daems, P. Mestdagh, and K. De Wael, “Locked nucleic acid probes enable enzyme-free photoelectrochemical detection of double-stranded DNA cancer biomarkers,” <i>MICROCHIMICA ACTA</i>, vol. 193, no. 4, 2026.</div>\n  </div>\n","bof":"  <div class=\"csl-entry\">Peymen, Anouk, Alejandro Valverde, Thijs Van der Snickt, Elise Daems, Pieter Mestdagh, and Karolien De Wael. 2026. “Locked Nucleic Acid Probes Enable Enzyme-Free Photoelectrochemical Detection of Double-Stranded DNA Cancer Biomarkers.” <i>MICROCHIMICA ACTA</i> 193 (4). doi:10.1007/s00604-026-07951-6.</div>\n","mla":"  <div class=\"csl-entry\">Peymen, Anouk, et al. “Locked Nucleic Acid Probes Enable Enzyme-Free Photoelectrochemical Detection of Double-Stranded DNA Cancer Biomarkers.” <i>MICROCHIMICA ACTA</i>, vol. 193, no. 4, 2026, doi:10.1007/s00604-026-07951-6.</div>\n","vancouver":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">1. </div><div class=\"csl-right-inline\">Peymen A, Valverde A, Van der Snickt T, Daems E, Mestdagh P, De Wael K. Locked nucleic acid probes enable enzyme-free photoelectrochemical detection of double-stranded DNA cancer biomarkers. MICROCHIMICA ACTA. 2026;193(4).</div>\n   </div>\n","fwo":"  <div class=\"csl-entry\">Peymen, Anouk, Alejandro Valverde, Thijs Van der Snickt, Elise Daems, Pieter Mestdagh, and Karolien De Wael. 2026. “Locked Nucleic Acid Probes Enable Enzyme-Free Photoelectrochemical Detection of Double-Stranded DNA Cancer Biomarkers.” <i>MICROCHIMICA ACTA</i> 193 (4). doi:10.1007/s00604-026-07951-6.</div>\n","apa":"  <div class=\"csl-entry\">Peymen, A., Valverde, A., Van der Snickt, T., Daems, E., Mestdagh, P., &#38; De Wael, K. (2026). Locked nucleic acid probes enable enzyme-free photoelectrochemical detection of double-stranded DNA cancer biomarkers. <i>MICROCHIMICA ACTA</i>, <i>193</i>(4). https://doi.org/10.1007/s00604-026-07951-6</div>\n","chicago-author-date":"  <div class=\"csl-entry\">Peymen, Anouk, Alejandro Valverde, Thijs Van der Snickt, Elise Daems, Pieter Mestdagh, and Karolien De Wael. 2026. “Locked Nucleic Acid Probes Enable Enzyme-Free Photoelectrochemical Detection of Double-Stranded DNA Cancer Biomarkers.” <i>MICROCHIMICA ACTA</i> 193 (4). https://doi.org/10.1007/s00604-026-07951-6.</div>\n"},"project":[{"abstract":"<p>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.</p>","gismo_id":"4633e20b-8108-11ed-9393-1d2a5b1ada47","title":"A new photoelectrochemical singlet oxygen-based detection platform for a panel of cancer biomarkers in tissue and liquid biopsies (SOCAN)","end_date":"2026-12-31","iweto_id":"01IB5223","start_date":"2023-01-01","_id":"01IB5223","publication_count":3}],"publication_status_sort":2,"parent":{"title":"MICROCHIMICA ACTA","short_title":"Microchim. Acta"},"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."}],"jcr":{},"classification":"A1","subject":["Medicine and Health Sciences","Biology and Life Sciences"],"author":[{"name_last_first":"Peymen, Anouk","credit_role":["first_author"],"_id":"4a3a6332-168c-11f1-8219-b18bd7f88a7a","last_name":"Peymen","biblio_id":"4a3a6332-168c-11f1-8219-b18bd7f88a7a","affiliation":[{"ugent_id":"GE31","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE31"}]}],"first_name":"Anouk","name":"Anouk Peymen","ugent_id":["000241878186","802005080715"]},{"first_name":"Alejandro","name":"Alejandro Valverde","name_last_first":"Valverde, Alejandro","last_name":"Valverde"},{"affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE31"}],"ugent_id":"GE31"}],"name":"Thijs Van der Snickt","first_name":"Thijs","orcid_id":"0000-0001-9865-0367","ugent_id":["000150620990","802003388063"],"name_last_first":"Van der Snickt, Thijs","_id":"1BA56604-4B75-11E5-A422-DA3AB5D1D7B1","last_name":"Van der Snickt","biblio_id":"1BA56604-4B75-11E5-A422-DA3AB5D1D7B1"},{"last_name":"Daems","name":"Elise Daems","first_name":"Elise","name_last_first":"Daems, Elise"},{"ugent_id":["802000056519"],"orcid_id":"0000-0001-7821-9684","first_name":"Pieter","name":"Pieter Mestdagh","affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE31"}],"ugent_id":"GE31"}],"biblio_id":"F86E58A6-F0ED-11E1-A9DE-61C894A0A6B4","last_name":"Mestdagh","_id":"F86E58A6-F0ED-11E1-A9DE-61C894A0A6B4","name_last_first":"Mestdagh, Pieter"},{"last_name":"De Wael","first_name":"Karolien","name":"Karolien De Wael","name_last_first":"De Wael, Karolien"}],"abstract":["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."],"article_type":"original","biblio_id":"01KKB9TY6HBRSMJ4DEE8WHB4XG","handle":"http://hdl.handle.net/1854/LU-01KKB9TY6HBRSMJ4DEE8WHB4XG","_id":"01KKB9TY6HBRSMJ4DEE8WHB4XG","wos_type":"Article","volume":"193","issn":["0026-3672","1436-5073"],"wos_id":"001714151600001","copyright_statement":"No license (in copyright)","file":[{"name":"Manuscript.docx","access":"open","sha256":"708ac102930d4fb9ae1e5d92abfb23022abc73aa36c0f5cd04bb13bc716a98b2","kind":"fullText","_id":"01KKBA56Y33974FC6WF921H19K","publication_version":"acceptedVersion","size":"1092919","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","url":"https://biblio.ugent.be/publication/01KKB9TY6HBRSMJ4DEE8WHB4XG/file/01KKBA56Y33974FC6WF921H19K.docx"},{"_id":"01KKHBM6TZ4KK35FJYG75GQ0TA","publication_version":"publishedVersion","content_type":"application/pdf","size":"3254912","url":"https://biblio.ugent.be/publication/01KKB9TY6HBRSMJ4DEE8WHB4XG/file/01KKHBM6TZ4KK35FJYG75GQ0TA.pdf","thumbnail_url":"https://biblio.ugent.be/publication/01KKB9TY6HBRSMJ4DEE8WHB4XG/file/01KKHBM6TZ4KK35FJYG75GQ0TA/thumbnail.png","name":"publisher version.pdf","access":"restricted","sha256":"df83010678f15a564cd52ec379ae69ca6895354c76b9b7db051200b346f4e733","kind":"fullText"}],"keyword":["Photoelectrochemistry","Biosensor","Locked nucleic acid (LNA)","Double-stranded DNA","KRAS G12C mutation","Singlet oxygen","Cancer diagnostics","BIOSENSOR","DESIGN"],"type":"journalArticle","article_number":"228","year":"2026","issue":"4","status":"public","date_updated":"2026-09-10 00:00:05","title":"Locked nucleic acid probes enable enzyme-free photoelectrochemical detection of double-stranded DNA cancer biomarkers","doi":["10.1007/s00604-026-07951-6"],"page":{"count":"12"},"publication_status":"published","created_by":{"name":"Thijs Van der Snickt","first_name":"Thijs","affiliation":[{"ugent_id":"GE31","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE31"}]}],"ugent_id":["000150620990","802003388063"],"orcid_id":"0000-0001-9865-0367","_id":"1BA56604-4B75-11E5-A422-DA3AB5D1D7B1","name_last_first":"Van der Snickt, Thijs","biblio_id":"1BA56604-4B75-11E5-A422-DA3AB5D1D7B1","last_name":"Van der Snickt"},"affiliation":[{"ugent_id":"GE31","name":"Department of Biomolecular Medicine","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE31"}]}],"external":0,"language":["eng"],"date_created":"2026-03-10 07:19:30"},{"file":[{"content_type":"application/pdf","size":"8418877","url":"https://biblio.ugent.be/publication/01KS7E4JP5YBZYP9MH5TGE9EBR/file/01KQJZWCZQGPTF4SPNBTKM2ZQZ.pdf","_id":"01KQJZWCZQGPTF4SPNBTKM2ZQZ","publication_version":"publishedVersion","access":"restricted","kind":"fullText","sha256":"eebadd125bfb57b4f4c0d1bb296d60a7e1c53308178a4b9f76322a44def3a22c","name":"10792.pdf","thumbnail_url":"https://biblio.ugent.be/publication/01KS7E4JP5YBZYP9MH5TGE9EBR/file/01KQJZWCZQGPTF4SPNBTKM2ZQZ/thumbnail.png"}],"publication_status_sort":2,"copyright_statement":"No license (in copyright)","project":[{"end_date":"2025-09-30","_id":"3S001922","start_date":"2021-10-01","iweto_id":"3S001922","abstract":"<p>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.</p>\n<p>Despite 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.</p>\n<p>The 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 &amp; 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.</p>\n<p>&#160;</p>","title":"PetSect: Edible insects as a novel protein source for pet food","gismo_id":"6dbb775d-8f9f-4614-9321-40bb4547de38","publication_count":8}],"isbn":["9789493542099"],"cite":{"fwo":"  <div class=\"csl-entry\">Leocadio dos Santos Neto, Elias. 2026. “Nutritional and Technological Aspects of Black Soldier Fly and Yellow Mealworm in Pet Food.” Ghent, Belgium: Ghent University. Faculty of Bioscience Engineering.</div>\n","apa":"  <div class=\"csl-entry\">Leocadio dos Santos Neto, E. (2026). <i>Nutritional and technological aspects of black soldier fly and yellow mealworm in pet food</i>. Ghent University. Faculty of Bioscience Engineering, Ghent, Belgium.</div>\n","ieee":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">[1]</div><div class=\"csl-right-inline\">E. Leocadio dos Santos Neto, “Nutritional and technological aspects of black soldier fly and yellow mealworm in pet food,” Ghent University. Faculty of Bioscience Engineering, Ghent, Belgium, 2026.</div>\n  </div>\n","vancouver":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">1. </div><div class=\"csl-right-inline\">Leocadio dos Santos Neto E. Nutritional and technological aspects of black soldier fly and yellow mealworm in pet food. [Ghent, Belgium]: Ghent University. Faculty of Bioscience Engineering; 2026.</div>\n   </div>\n","chicago-author-date":"  <div class=\"csl-entry\">Leocadio dos Santos Neto, Elias. 2026. “Nutritional and Technological Aspects of Black Soldier Fly and Yellow Mealworm in Pet Food.” Ghent, Belgium: Ghent University. Faculty of Bioscience Engineering.</div>\n","bof":"  <div class=\"csl-entry\">Leocadio dos Santos Neto, Elias. 2026. “Nutritional and Technological Aspects of Black Soldier Fly and Yellow Mealworm in Pet Food.” Ghent, Belgium: Ghent University. Faculty of Bioscience Engineering.</div>\n","mla":"  <div class=\"csl-entry\">Leocadio dos Santos Neto, Elias. <i>Nutritional and Technological Aspects of Black Soldier Fly and Yellow Mealworm in Pet Food</i>. Ghent University. Faculty of Bioscience Engineering, 2026.</div>\n"},"alternative_title":["Nutritionele en technologische aspecten van zwarte soldaten vlieg en meelworrm in huisdiervoeding"],"promoter":[{"biblio_id":"F8F4AE24-F0ED-11E1-A9DE-61C894A0A6B4","last_name":"Eeckhout","_id":"F8F4AE24-F0ED-11E1-A9DE-61C894A0A6B4","name_last_first":"Eeckhout, Mia","ugent_id":["802000193834","919014292548"],"orcid_id":"0000-0002-8537-5084","name":"Mia Eeckhout","first_name":"Mia","affiliation":[{"ugent_id":"LA23","path":[{"ugent_id":"UGent"},{"ugent_id":"LA"},{"ugent_id":"LA23"}]}]},{"last_name":"Hesta","biblio_id":"F52858F4-F0ED-11E1-A9DE-61C894A0A6B4","name_last_first":"Hesta, Myriam","_id":"F52858F4-F0ED-11E1-A9DE-61C894A0A6B4","orcid_id":"0000-0001-9423-9765","ugent_id":["801001127479"],"affiliation":[{"ugent_id":"DI11","path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI11"}]}],"first_name":"Myriam","name":"Myriam Hesta"}],"language":["eng"],"external":0,"date_created":"2026-05-22 08:51:53","created_by":{"affiliation":[{"ugent_id":"LA23","path":[{"ugent_id":"UGent"},{"ugent_id":"LA"},{"ugent_id":"LA23"}]}],"name":"Elias Leocadio dos Santos Neto","first_name":"Elias","ugent_id":["000221594880","802004251666"],"name_last_first":"Leocadio dos Santos Neto, Elias","_id":"28a331b7-7b3a-11ed-9d28-cd7f23b577ed","last_name":"Leocadio dos Santos Neto","biblio_id":"28a331b7-7b3a-11ed-9d28-cd7f23b577ed"},"affiliation":[{"ugent_id":"LA23","path":[{"ugent_id":"UGent"},{"ugent_id":"LA"},{"ugent_id":"LA23"}],"name":"Department of Food technology, Safety and Health"},{"path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI11"}],"name":"Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition","ugent_id":"DI11"}],"publication_status":"published","defense":{"location":"Gent : Campus Schoonmeersen (lokaal GSCH.C.0.125)","date":"2026-04-28"},"_id":"01KS7E4JP5YBZYP9MH5TGE9EBR","page":{"count":"224"},"publisher":{"location":"Ghent, Belgium","name":"Ghent University. Faculty of Bioscience Engineering"},"handle":"http://hdl.handle.net/1854/LU-01KS7E4JP5YBZYP9MH5TGE9EBR","source":{"db":"plato","id":"10792"},"title":"Nutritional and technological aspects of black soldier fly and yellow mealworm in pet food","biblio_id":"01KS7E4JP5YBZYP9MH5TGE9EBR","date_updated":"2026-07-15 09:19:32","author":[{"name":"Elias Leocadio dos Santos Neto","first_name":"Elias","affiliation":[{"ugent_id":"LA23","path":[{"ugent_id":"UGent"},{"ugent_id":"LA"},{"ugent_id":"LA23"}]}],"ugent_id":["000221594880","802004251666"],"_id":"28a331b7-7b3a-11ed-9d28-cd7f23b577ed","name_last_first":"Leocadio dos Santos Neto, Elias","biblio_id":"28a331b7-7b3a-11ed-9d28-cd7f23b577ed","last_name":"Leocadio dos Santos Neto"}],"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."],"status":"public","subject":["Biology and Life Sciences"],"year":"2026","classification":"D1","type":"dissertation","abstract_full":[{"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.","lang":"eng"},{"lang":"eng","text":"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."}],"jcr":{}},{"volume":"8","wos_type":"Article","file":[{"publication_version":"publishedVersion","_id":"01KQ2X2QQDNMXEMB1JSCFX2ECZ","url":"https://biblio.ugent.be/publication/01KQ2WZF3RA0B4YMGR943KZ53F/file/01KQ2X2QQDNMXEMB1JSCFX2ECZ.pdf","size":"10135107","content_type":"application/pdf","name":"Heine_etal_2026_Simplified  Portable and Cost‐Efficient Airborne eDNA Metabarcoding to Expand Tropical Biodiversity Assessments.pdf","thumbnail_url":"https://biblio.ugent.be/publication/01KQ2WZF3RA0B4YMGR943KZ53F/file/01KQ2X2QQDNMXEMB1JSCFX2ECZ/thumbnail.png","kind":"fullText","sha256":"bc414b5a40a2337a619f59d3c52731289417926cce10dd691984e6bfcdaf5cb1","access":"open"}],"copyright_statement":"Creative Commons Attribution-NonCommercial 4.0 International Public License (CC BY-NC 4.0)","issn":["2637-4943"],"status":"public","issue":"2","year":"2026","article_number":"e70289","keyword":["aerial sampling","biodiversity monitoring","conservation","environmental DNA","metabarcoding","ENVIRONMENTAL DNA","PERFORMANCE"],"type":"journalArticle","language":["eng"],"external":0,"date_created":"2026-04-25 18:03:39","created_by":{"affiliation":[{"ugent_id":"DI05","path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI05"}]}],"name":"Amadeus Plewnia","first_name":"Amadeus","orcid_id":"0000-0001-8731-6312","ugent_id":["000251533932","802005130427","979451985952"],"name_last_first":"Plewnia, Amadeus","_id":"8f73abb3-b452-11f0-a866-f9285233d40d","last_name":"Plewnia","biblio_id":"8f73abb3-b452-11f0-a866-f9285233d40d"},"affiliation":[{"name":"Department of Pathobiology, Pharmacology and Zoological Medicine","path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI05"}],"ugent_id":"DI05"}],"publication_status":"published","page":{"count":"14"},"title":"Simplified, portable and cost-efficient airborne eDNA metabarcoding to expand tropical biodiversity assessments","doi":["10.1002/edn3.70289"],"date_updated":"2026-04-27 13:07:36","publication_status_sort":2,"parent":{"title":"ENVIRONMENTAL DNA","short_title":"Environ. DNA"},"esci_id":"001745439100001","cite":{"fwo":"  <div class=\"csl-entry\">Heine, Christopher, Jesse Erens, Lukas Reese, Henrik Krehenwinkel, Claudia Lansac, Stefan Lötters, and Amadeus Plewnia. 2026. “Simplified, Portable and Cost-Efficient Airborne EDNA Metabarcoding to Expand Tropical Biodiversity Assessments.” <i>ENVIRONMENTAL DNA</i> 8 (2). doi:10.1002/edn3.70289.</div>\n","apa":"  <div class=\"csl-entry\">Heine, C., Erens, J., Reese, L., Krehenwinkel, H., Lansac, C., Lötters, S., &#38; Plewnia, A. (2026). Simplified, portable and cost-efficient airborne eDNA metabarcoding to expand tropical biodiversity assessments. <i>ENVIRONMENTAL DNA</i>, <i>8</i>(2). https://doi.org/10.1002/edn3.70289</div>\n","ieee":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">[1]</div><div class=\"csl-right-inline\">C. Heine <i>et al.</i>, “Simplified, portable and cost-efficient airborne eDNA metabarcoding to expand tropical biodiversity assessments,” <i>ENVIRONMENTAL DNA</i>, vol. 8, no. 2, 2026.</div>\n  </div>\n","vancouver":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">1. </div><div class=\"csl-right-inline\">Heine C, Erens J, Reese L, Krehenwinkel H, Lansac C, Lötters S, et al. Simplified, portable and cost-efficient airborne eDNA metabarcoding to expand tropical biodiversity assessments. ENVIRONMENTAL DNA. 2026;8(2).</div>\n   </div>\n","chicago-author-date":"  <div class=\"csl-entry\">Heine, Christopher, Jesse Erens, Lukas Reese, Henrik Krehenwinkel, Claudia Lansac, Stefan Lötters, and Amadeus Plewnia. 2026. “Simplified, Portable and Cost-Efficient Airborne EDNA Metabarcoding to Expand Tropical Biodiversity Assessments.” <i>ENVIRONMENTAL DNA</i> 8 (2). https://doi.org/10.1002/edn3.70289.</div>\n","bof":"  <div class=\"csl-entry\">Heine, Christopher, Jesse Erens, Lukas Reese, Henrik Krehenwinkel, Claudia Lansac, Stefan Lötters, and Amadeus Plewnia. 2026. “Simplified, Portable and Cost-Efficient Airborne EDNA Metabarcoding to Expand Tropical Biodiversity Assessments.” <i>ENVIRONMENTAL DNA</i> 8 (2). doi:10.1002/edn3.70289.</div>\n","mla":"  <div class=\"csl-entry\">Heine, Christopher, et al. “Simplified, Portable and Cost-Efficient Airborne EDNA Metabarcoding to Expand Tropical Biodiversity Assessments.” <i>ENVIRONMENTAL DNA</i>, vol. 8, no. 2, 2026, doi:10.1002/edn3.70289.</div>\n"},"subject":["Earth and Environmental Sciences"],"classification":"A2","abstract_full":[{"text":"Aquatic environmental DNA (eDNA) analysis has been widely established as a sensitive and non‐invasive species detection tool for global biodiversity monitoring. In contrast, the uptake of airborne eDNA has been constrained by the absence of robust, high‐throughput samplers suited to humid tropical settings. We present a simplified, portable, and cost‐efficient active air sampler that injects air into a liquid collection medium, shifting airborne eDNA from stationary, resource‐heavy set‐ups to field‐deployable, scalable workflows. Using a greenhouse vertebrate mock community to test the sensitivity of our approach, airborne eDNA sampling recovered most taxa present, with high detection rates for birds, mammals, and reptiles. An optimized collection buffer increased sequencing yield by about one fourth over sterile water. To subsequently assess its application in biodiversity research and conservation science, we tested its functionality in the Chocó‐Andean montane forests of northern South America, using a tree‐of‐life metabarcoding approach as part of ongoing biodiversity surveys to inform the establishment of a protected area network. While aquatic eDNA detected hundreds of vertebrates and thousands of arthropods and embryophytes, airborne eDNA recovered slightly lower OTU richness. Airborne sampling was particularly effective for mammals, whereas aquatic sampling recovered more actinopterid, amphibian, and avian OTUs. Overlap in species detection between methods was low, highlighting the complementarity of airborne and aquatic eDNA‐based species assessments. By integrating accessibility, portability, and scalability, our approach broadens the applicability of airborne eDNA, where combining airborne and aquatic eDNA metabarcoding can rapidly deliver broad‐scale biodiversity data to support conservation planning in megadiverse yet resource‐limited regions.","lang":"eng"}],"jcr":{},"_id":"01KQ2WZF3RA0B4YMGR943KZ53F","handle":"http://hdl.handle.net/1854/LU-01KQ2WZF3RA0B4YMGR943KZ53F","biblio_id":"01KQ2WZF3RA0B4YMGR943KZ53F","author":[{"last_name":"Heine","name_last_first":"Heine, Christopher","first_name":"Christopher","name":"Christopher Heine"},{"last_name":"Erens","name_last_first":"Erens, Jesse","first_name":"Jesse","name":"Jesse Erens"},{"name":"Lukas Reese","first_name":"Lukas","name_last_first":"Reese, Lukas","last_name":"Reese"},{"last_name":"Krehenwinkel","name":"Henrik Krehenwinkel","first_name":"Henrik","name_last_first":"Krehenwinkel, Henrik"},{"name":"Claudia Lansac","first_name":"Claudia","name_last_first":"Lansac, Claudia","last_name":"Lansac"},{"last_name":"Lötters","name_last_first":"Lötters, Stefan","first_name":"Stefan","name":"Stefan Lötters"},{"biblio_id":"8f73abb3-b452-11f0-a866-f9285233d40d","last_name":"Plewnia","_id":"8f73abb3-b452-11f0-a866-f9285233d40d","name_last_first":"Plewnia, Amadeus","ugent_id":["000251533932","802005130427","979451985952"],"orcid_id":"0000-0001-8731-6312","name":"Amadeus Plewnia","first_name":"Amadeus","affiliation":[{"ugent_id":"DI05","path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI05"}]}]}],"abstract":["Aquatic environmental DNA (eDNA) analysis has been widely established as a sensitive and non‐invasive species detection tool for global biodiversity monitoring. In contrast, the uptake of airborne eDNA has been constrained by the absence of robust, high‐throughput samplers suited to humid tropical settings. We present a simplified, portable, and cost‐efficient active air sampler that injects air into a liquid collection medium, shifting airborne eDNA from stationary, resource‐heavy set‐ups to field‐deployable, scalable workflows. Using a greenhouse vertebrate mock community to test the sensitivity of our approach, airborne eDNA sampling recovered most taxa present, with high detection rates for birds, mammals, and reptiles. An optimized collection buffer increased sequencing yield by about one fourth over sterile water. To subsequently assess its application in biodiversity research and conservation science, we tested its functionality in the Chocó‐Andean montane forests of northern South America, using a tree‐of‐life metabarcoding approach as part of ongoing biodiversity surveys to inform the establishment of a protected area network. While aquatic eDNA detected hundreds of vertebrates and thousands of arthropods and embryophytes, airborne eDNA recovered slightly lower OTU richness. Airborne sampling was particularly effective for mammals, whereas aquatic sampling recovered more actinopterid, amphibian, and avian OTUs. Overlap in species detection between methods was low, highlighting the complementarity of airborne and aquatic eDNA‐based species assessments. By integrating accessibility, portability, and scalability, our approach broadens the applicability of airborne eDNA, where combining airborne and aquatic eDNA metabarcoding can rapidly deliver broad‐scale biodiversity data to support conservation planning in megadiverse yet resource‐limited regions."],"article_type":"original"},{"cite":{"ieee":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">[1]</div><div class=\"csl-right-inline\">S. Aerts, N. Daelman, G. Sys, H. De Rooster, and W. De Spiegelaere, “Mitochondrial DNA digital PCR improves metastasis quantification in the chick chorioallantoic membrane (CAM) assay,” <i>ANALYTICAL BIOCHEMISTRY</i>, vol. 718, 2026.</div>\n  </div>\n","vancouver":"  <div class=\"csl-entry\">\n    <div class=\"csl-left-margin\">1. </div><div class=\"csl-right-inline\">Aerts S, Daelman N, Sys G, De Rooster H, De Spiegelaere W. Mitochondrial DNA digital PCR improves metastasis quantification in the chick chorioallantoic membrane (CAM) assay. ANALYTICAL BIOCHEMISTRY. 2026;718.</div>\n   </div>\n","fwo":"  <div class=\"csl-entry\">Aerts, Shari, Niene Daelman, Gwen Sys, Hilde De Rooster, and Ward De Spiegelaere. 2026. “Mitochondrial DNA Digital PCR Improves Metastasis Quantification in the Chick Chorioallantoic Membrane (CAM) Assay.” <i>ANALYTICAL BIOCHEMISTRY</i> 718. doi:10.1016/j.ab.2026.116212.</div>\n","apa":"  <div class=\"csl-entry\">Aerts, S., Daelman, N., Sys, G., De Rooster, H., &#38; De Spiegelaere, W. (2026). Mitochondrial DNA digital PCR improves metastasis quantification in the chick chorioallantoic membrane (CAM) assay. <i>ANALYTICAL BIOCHEMISTRY</i>, <i>718</i>. https://doi.org/10.1016/j.ab.2026.116212</div>\n","chicago-author-date":"  <div class=\"csl-entry\">Aerts, Shari, Niene Daelman, Gwen Sys, Hilde De Rooster, and Ward De Spiegelaere. 2026. “Mitochondrial DNA Digital PCR Improves Metastasis Quantification in the Chick Chorioallantoic Membrane (CAM) Assay.” <i>ANALYTICAL BIOCHEMISTRY</i> 718. https://doi.org/10.1016/j.ab.2026.116212.</div>\n","bof":"  <div class=\"csl-entry\">Aerts, Shari, Niene Daelman, Gwen Sys, Hilde De Rooster, and Ward De Spiegelaere. 2026. “Mitochondrial DNA Digital PCR Improves Metastasis Quantification in the Chick Chorioallantoic Membrane (CAM) Assay.” <i>ANALYTICAL BIOCHEMISTRY</i> 718. doi:10.1016/j.ab.2026.116212.</div>\n","mla":"  <div class=\"csl-entry\">Aerts, Shari, et al. “Mitochondrial DNA Digital PCR Improves Metastasis Quantification in the Chick Chorioallantoic Membrane (CAM) Assay.” <i>ANALYTICAL BIOCHEMISTRY</i>, vol. 718, 2026, doi:10.1016/j.ab.2026.116212.</div>\n"},"publication_status_sort":2,"parent":{"title":"ANALYTICAL BIOCHEMISTRY","short_title":"Anal. Biochem."},"abstract_full":[{"lang":"eng","text":"The chick chorioallantoic membrane (CAM) assay is an in vivo metastasis model, yet traditional Alu-qPCR quantification suffers from non-specific background noise in avian tissue. To improve analytical specificity, we developed a species-specific digital PCR (dPCR) assay targeting the human mitochondrial locus MT-ND4. While Alu-qPCR generated false positives in chicken-only DNA, MT-ND4 dPCR provided high species specificity and robust relative quantification of human mitochondrial DNA across various embryonic organs. As a proof of concept in five embryos, organ-dependent differences in metastatic burden were detected (p < 0.001) with high technical precision. This MT-ND4 dPCR assay avoids false-positive overestimations, providing a specific tool for quantifying human metastatic burden in the CAM model."}],"jcr":{},"classification":"A1","subject":["Medicine and Health Sciences","Biology and Life Sciences"],"author":[{"orcid_id":"0000-0002-2023-2488","ugent_id":["000211739983","802003802941"],"affiliation":[{"ugent_id":"DI11","path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI11"}]}],"first_name":"Shari","name":"Shari Aerts","last_name":"Aerts","biblio_id":"40063dcc-2303-11ec-ac25-a924b83804a4","name_last_first":"Aerts, Shari","credit_role":["first_author"],"_id":"40063dcc-2303-11ec-ac25-a924b83804a4"},{"ugent_id":["972902780166"],"first_name":"Niene","name":"Niene Daelman","affiliation":[{"ugent_id":"UGent","name":"Ghent University","path":[{"ugent_id":"UGent"}]}],"biblio_id":"c4ce6a25-cc56-11ee-88c7-8e97d15dd863","last_name":"Daelman","_id":"c4ce6a25-cc56-11ee-88c7-8e97d15dd863","name_last_first":"Daelman, Niene"},{"name":"Gwen Sys","first_name":"Gwen","affiliation":[{"ugent_id":"GE38","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE38"}]},{"ugent_id":"UZGent","path":[{"ugent_id":"UZGent"}]}],"ugent_id":["801001664013"],"orcid_id":"0000-0002-5308-7846","_id":"F68679BA-F0ED-11E1-A9DE-61C894A0A6B4","name_last_first":"Sys, Gwen","biblio_id":"F68679BA-F0ED-11E1-A9DE-61C894A0A6B4","last_name":"Sys"},{"last_name":"De Rooster","biblio_id":"F4F0E81A-F0ED-11E1-A9DE-61C894A0A6B4","name_last_first":"De Rooster, Hilde","_id":"F4F0E81A-F0ED-11E1-A9DE-61C894A0A6B4","orcid_id":"0000-0001-8087-256X","ugent_id":["801001036240"],"affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI09"}],"ugent_id":"DI09"}],"name":"Hilde De Rooster","first_name":"Hilde"},{"last_name":"De Spiegelaere","biblio_id":"F87618B6-F0ED-11E1-A9DE-61C894A0A6B4","credit_role":["last_author"],"name_last_first":"De Spiegelaere, Ward","_id":"F87618B6-F0ED-11E1-A9DE-61C894A0A6B4","orcid_id":"0000-0003-2097-8439","ugent_id":["802000063993"],"affiliation":[{"ugent_id":"DI11","path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI11"}]}],"name":"Ward De Spiegelaere","first_name":"Ward"}],"abstract":["The chick chorioallantoic membrane (CAM) assay is an in vivo metastasis model, yet traditional Alu-qPCR quantification suffers from non-specific background noise in avian tissue. To improve analytical specificity, we developed a species-specific digital PCR (dPCR) assay targeting the human mitochondrial locus MT-ND4. While Alu-qPCR generated false positives in chicken-only DNA, MT-ND4 dPCR provided high species specificity and robust relative quantification of human mitochondrial DNA across various embryonic organs. As a proof of concept in five embryos, organ-dependent differences in metastatic burden were detected (p < 0.001) with high technical precision. This MT-ND4 dPCR assay avoids false-positive overestimations, providing a specific tool for quantifying human metastatic burden in the CAM model."],"article_type":"original","biblio_id":"01M13W788MS5HTXMY78DNC09JD","handle":"http://hdl.handle.net/1854/LU-01M13W788MS5HTXMY78DNC09JD","_id":"01M13W788MS5HTXMY78DNC09JD","wos_type":"Article","volume":"718","issn":["0003-2697","1096-0309"],"wos_id":"001840580900001","copyright_statement":"No license (in copyright)","file":[{"access":"restricted","sha256":"d5f861da1bd09ba39f3abede6f800619e4065faff27931644c5d4e52ceb49b66","change":{"on":"2027-02-01","to":"open"},"kind":"fullText","name":"Authors accepted manuscript (AAM) .pdf","thumbnail_url":"https://biblio.ugent.be/publication/01M13W788MS5HTXMY78DNC09JD/file/01M13WBSJE4E8GJQDE1DS64HBS/thumbnail.png","size":"376228","content_type":"application/pdf","url":"https://biblio.ugent.be/publication/01M13W788MS5HTXMY78DNC09JD/file/01M13WBSJE4E8GJQDE1DS64HBS.pdf","_id":"01M13WBSJE4E8GJQDE1DS64HBS","publication_version":"acceptedVersion"},{"name":"Supplementary S1_v2.png","access":"restricted","sha256":"bea8b57d85f719875f3996e372397fb8a2dbc8f5468cbb1f245765409969ecb6","change":{"on":"2027-02-01","to":"open"},"kind":"dataset","_id":"01M13WK40H6RY5B36YWM91SMPN","content_type":"image/png","size":"1491710","url":"https://biblio.ugent.be/publication/01M13W788MS5HTXMY78DNC09JD/file/01M13WK40H6RY5B36YWM91SMPN.png"},{"name":"Supplementary S2_v2.png","change":{"on":"2027-02-01","to":"open"},"sha256":"266c047f80f9e39fe5527410eca5fe0951897802b05a67c50030773c73652427","kind":"dataset","access":"restricted","_id":"01M13WMJ3XEACCGKZ89AZK8ATG","url":"https://biblio.ugent.be/publication/01M13W788MS5HTXMY78DNC09JD/file/01M13WMJ3XEACCGKZ89AZK8ATG.png","content_type":"image/png","size":"3219284"},{"kind":"dataset","sha256":"910ca8c27fe140e03866a481b0e5505a6c7e83e548fb354b01be2c4a5fc4df64","change":{"to":"open","on":"2027-02-01"},"access":"restricted","name":"Graphical abstract.png","url":"https://biblio.ugent.be/publication/01M13W788MS5HTXMY78DNC09JD/file/01M13WNE0GC0NMQK3KZ5S9XRCX.png","content_type":"image/png","size":"2596171","_id":"01M13WNE0GC0NMQK3KZ5S9XRCX"},{"publication_version":"publishedVersion","_id":"01M1XWNTDKHNWDXCMPTMF5XFV4","url":"https://biblio.ugent.be/publication/01M13W788MS5HTXMY78DNC09JD/file/01M1XWNTDKHNWDXCMPTMF5XFV4.pdf","size":"2126951","content_type":"application/pdf","name":"publisher version.pdf","sha256":"520ea87ae12826e699a8529b70f126a1c87fd084e8f0e0cb413873657a2eb06c","kind":"fullText","access":"restricted"}],"type":"journalArticle","keyword":["Digital PCR","Mitochondrial DNA","Chicken chorioallantoic membrane (CAM) assay","Metastatic burden","Patient-derived xenograft (PDX)","POLYMERASE-CHAIN-REACTION","EMBRYO","MODEL"],"article_number":"116212","year":"2026","status":"public","date_updated":"2026-09-07 12:17:21","title":"Mitochondrial DNA digital PCR improves metastasis quantification in the chick chorioallantoic membrane (CAM) assay","doi":["10.1016/j.ab.2026.116212"],"page":{"count":"5"},"publication_status":"published","created_by":{"orcid_id":"0000-0002-2023-2488","ugent_id":["000211739983","802003802941"],"affiliation":[{"path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI11"}],"ugent_id":"DI11"}],"first_name":"Shari","name":"Shari Aerts","last_name":"Aerts","biblio_id":"40063dcc-2303-11ec-ac25-a924b83804a4","name_last_first":"Aerts, Shari","_id":"40063dcc-2303-11ec-ac25-a924b83804a4"},"affiliation":[{"name":"Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition","path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI11"}],"ugent_id":"DI11"},{"ugent_id":"GE38","name":"Department of Human Structure and Repair","path":[{"ugent_id":"UGent"},{"ugent_id":"GE"},{"ugent_id":"GE38"}]},{"ugent_id":"DI09","path":[{"ugent_id":"UGent"},{"ugent_id":"DI"},{"ugent_id":"DI09"}],"name":"Department of Small animals"}],"external":0,"language":["eng"],"date_created":"2026-08-28 09:46:38"}],"start":0,"size":10,"limit":10,"total":5508});