{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T17:49:54Z","timestamp":1768585794617,"version":"3.49.0"},"reference-count":42,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2026,1,14]],"date-time":"2026-01-14T00:00:00Z","timestamp":1768348800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100018536","name":"NuCana plc","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100018536","id-type":"DOI","asserted-by":"crossref"}]},{"name":"University of St Andrews Sanctuary Scholarship"},{"name":"European Union\u2019s Horizon 2020 research and innovation programme","award":["101017453"],"award-info":[{"award-number":["101017453"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cancers"],"abstract":"<jats:p>Background: Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney cancer and is marked by pronounced intra-tumoural heterogeneity that complicates therapeutic response. Patient-derived organoids offer a physiologically relevant model to capture this diversity and evaluate treatment effects. When integrated with spatial transcriptomics, they might enable the mapping of spatially resolved transcriptional and isoform-level changes within the tumour microenvironment. Methods: We established a robust workflow for generating patient-derived ccRCC organoids, that are not passaged and retain original cellular components. These retain key features of the original tumours, including cancer cell, stromal, and immune components. Results: Spatial transcriptomic profiling revealed multiple transcriptionally distinct regions within and across organoids, reflecting the intrinsic heterogeneity of ccRCC. Isoform-level analysis identified spatially variable expression of glutaminase (GLS) isoforms, with heterogeneous distributions of both the GAC and KGA variants. Treatment with NUC-7738, a phosphoramidate derivative of 3\u2032-deoxyadenosine, induced marked transcriptional remodelling of organoids, including alterations in ribosomal and mitochondrial gene expression. Conclusions: This study demonstrates that combining long-read spatial transcriptomics with patient-derived organoid models provides a powerful and scalable approach for dissecting gene and isoform-level heterogeneity in ccRCC and for elucidating spatially resolved transcriptional responses to novel therapeutics.<\/jats:p>","DOI":"10.3390\/cancers18020254","type":"journal-article","created":{"date-parts":[[2026,1,14]],"date-time":"2026-01-14T15:12:04Z","timestamp":1768403524000},"page":"254","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Long-Read Spatial Transcriptomics of Patient-Derived Clear Cell Renal Cell Carcinoma Organoids Identifies Heterogeneity and Transcriptional Remodelling Following NUC-7738 Treatment"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-3476-6258","authenticated-orcid":false,"given":"Hazem","family":"Abdullah","sequence":"first","affiliation":[{"name":"School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-2325-5412","authenticated-orcid":false,"given":"Ying","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kathryn","family":"Kirkwood","sequence":"additional","affiliation":[{"name":"Pathology, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7296-025X","authenticated-orcid":false,"given":"Alexander","family":"Laird","sequence":"additional","affiliation":[{"name":"Edinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0841-609X","authenticated-orcid":false,"given":"Peter","family":"Mullen","sequence":"additional","affiliation":[{"name":"School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9041-9988","authenticated-orcid":false,"given":"David J.","family":"Harrison","sequence":"additional","affiliation":[{"name":"School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, UK"},{"name":"NuCana plc, 3, Lochside Way, Edinburgh EH12 9DT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2724-0325","authenticated-orcid":false,"given":"Mustafa","family":"Elshani","sequence":"additional","affiliation":[{"name":"School of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, UK"},{"name":"NuCana plc, 3, Lochside Way, Edinburgh EH12 9DT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,14]]},"reference":[{"key":"ref_1","first-page":"229","article-title":"Global cancer statistics 2022: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries","volume":"74","author":"Bray","year":"2024","journal-title":"CA Cancer J. 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