Idiosyncratic and generic single nuclei and spatial transcriptional patterns in papillary and anaplastic thyroid cancers

Idiosyncratic and generic single nuclei and spatial transcriptional patterns in papillary and anaplastic thyroid cancers | bioRxiv Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search New Results Idiosyncratic and generic single nuclei and spatial transcriptional patterns in papillary and anaplastic thyroid cancers View ORCID Profile Adrien Tourneur , View ORCID Profile Joel Rodrigues Vitória , Manuel Saiselet , Ligia Craciun , Denis Larsimont , Anne Lefort , Frederick Libert , Carine Maenhaut , View ORCID Profile Sabine Costagliola , View ORCID Profile Maxime Tarabichi , View ORCID Profile Mirian Romitti , View ORCID Profile Vincent Detours doi: https://doi.org/10.1101/2024.02.15.580495 Adrien Tourneur 1 IRIBHM Jacques E. Dumont, Université Libre de Bruxelles (ULB) , 808 route de Lennik, 1070 Brussels, Belgium Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Adrien Tourneur Joel Rodrigues Vitória 1 IRIBHM Jacques E. Dumont, Université Libre de Bruxelles (ULB) , 808 route de Lennik, 1070 Brussels, Belgium Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Joel Rodrigues Vitória Manuel Saiselet 1 IRIBHM Jacques E. Dumont, Université Libre de Bruxelles (ULB) , 808 route de Lennik, 1070 Brussels, Belgium Find this author on Google Scholar Find this author on PubMed Search for this author on this site Ligia Craciun 2 Department of Pathology, Institut Jules Bordet , Rue Meylemeersch 90, 1070 Bruxelles, Belgium Find this author on Google Scholar Find this author on PubMed Search for this author on this site Denis Larsimont 2 Department of Pathology, Institut Jules Bordet , Rue Meylemeersch 90, 1070 Bruxelles, Belgium Find this author on Google Scholar Find this author on PubMed Search for this author on this site Anne Lefort 1 IRIBHM Jacques E. Dumont, Université Libre de Bruxelles (ULB) , 808 route de Lennik, 1070 Brussels, Belgium Find this author on Google Scholar Find this author on PubMed Search for this author on this site Frederick Libert 1 IRIBHM Jacques E. Dumont, Université Libre de Bruxelles (ULB) , 808 route de Lennik, 1070 Brussels, Belgium Find this author on Google Scholar Find this author on PubMed Search for this author on this site Carine Maenhaut 1 IRIBHM Jacques E. Dumont, Université Libre de Bruxelles (ULB) , 808 route de Lennik, 1070 Brussels, Belgium Find this author on Google Scholar Find this author on PubMed Search for this author on this site Sabine Costagliola 1 IRIBHM Jacques E. Dumont, Université Libre de Bruxelles (ULB) , 808 route de Lennik, 1070 Brussels, Belgium Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Sabine Costagliola Maxime Tarabichi 1 IRIBHM Jacques E. Dumont, Université Libre de Bruxelles (ULB) , 808 route de Lennik, 1070 Brussels, Belgium 3 Interuniversity Institute of Bioinformatics in Brussels ULB-VUB (IB2) , La Plaine Campus, Blv du Triomphe, 1050 Brussels, Belgium Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Maxime Tarabichi Mirian Romitti 1 IRIBHM Jacques E. Dumont, Université Libre de Bruxelles (ULB) , 808 route de Lennik, 1070 Brussels, Belgium Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Mirian Romitti Vincent Detours 1 IRIBHM Jacques E. Dumont, Université Libre de Bruxelles (ULB) , 808 route de Lennik, 1070 Brussels, Belgium 3 Interuniversity Institute of Bioinformatics in Brussels ULB-VUB (IB2) , La Plaine Campus, Blv du Triomphe, 1050 Brussels, Belgium Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Vincent Detours For correspondence: Vincent.Detours{at}ulb.be Abstract Full Text Info/History Metrics Supplementary material Preview PDF Abstract Sixty percent of papillary thyroid cancers (PTCs) are driven by BRAF V600E , a mutation associated with high inter- and intra-tumoral heterogeneity. PTCs may become highly aggressive anaplastic thyroid cancers (ATC). While single cell transcriptomics may resolve this heterogeneity, it is potentially confounded by technical effects whose correction may dampen inter-tumor variations. Here we profiled ATCs and BRAF V600E PTCs with single nuclei RNA-seq and spatial transcriptomics, and an experimental design disentangling biological and technical variations. It reveals that much transcriptional variation in cancer cells and several immune cell types is idiosyncratic, i.e. tumor-specific, a phenomenon obscured by batch integration in a number of single cell studies. Idiosyncrasies are associated in some cases with genomic aberrations and global tissue states like hypoxia. Beyond idiosyncrasies, differentiation markers SLC5A5 ( NIS ), TPO , TG and TSHR are lost in a sequence mirrored by their gain during human thyroid organoids maturation, suggesting a new classification of cancer cell states. PTC cells retain TSHR expression and show features of partial EMT with a massive expression of FN1 , which promotes proliferation via an autocrine loop. In contrast, ATCs undergo full blown EMT, with expression of mesenchymal extracellular components and loss of TSHR . Finally, we show that the microenvironment of cancer cells is driven by inflammation. These findings may help future stratifications of BRAF V600E PTCs. Competing Interest Statement The authors have declared no competing interest. Footnotes The authors have declared that no conflict of interest exists. Adding SCENIC results, UMI per celltype plot and replicating results of suppl fig 1 with dataset of Lu et al. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Back to top Previous Next Posted April 17, 2026. Download PDF Supplementary Material Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. 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Share Idiosyncratic and generic single nuclei and spatial transcriptional patterns in papillary and anaplastic thyroid cancers Adrien Tourneur , Joel Rodrigues Vitória , Manuel Saiselet , Ligia Craciun , Denis Larsimont , Anne Lefort , Frederick Libert , Carine Maenhaut , Sabine Costagliola , Maxime Tarabichi , Mirian Romitti , Vincent Detours bioRxiv 2024.02.15.580495; doi: https://doi.org/10.1101/2024.02.15.580495 Share This Article: Copy Citation Tools Idiosyncratic and generic single nuclei and spatial transcriptional patterns in papillary and anaplastic thyroid cancers Adrien Tourneur , Joel Rodrigues Vitória , Manuel Saiselet , Ligia Craciun , Denis Larsimont , Anne Lefort , Frederick Libert , Carine Maenhaut , Sabine Costagliola , Maxime Tarabichi , Mirian Romitti , Vincent Detours bioRxiv 2024.02.15.580495; doi: https://doi.org/10.1101/2024.02.15.580495 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Area Cancer Biology Subject Areas All Articles Animal Behavior and Cognition (8164) Biochemistry (19027) Bioengineering (15171) Bioinformatics (45807) Biophysics (22958) Cancer Biology (20248) Cell Biology (27495) Clinical Trials (138) Developmental Biology (14233) Ecology (21529) Epidemiology (2067) Evolutionary Biology (25940) Genetics (16436) Genomics (23979) Immunology (19175) Microbiology (43486) Molecular Biology (18481) Neuroscience (95839) Paleontology (717) Pathology (3064) Pharmacology and Toxicology (5253) Physiology (8339) Plant Biology (16378) Scientific Communication and Education (2123) Synthetic Biology (4675) Systems Biology (10450) Zoology (2436)

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