Hallmarks of transcriptional intratumour heterogeneity across a thousand tumours.
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
Jun 2023
Jun 2023
Historique:
received:
05
05
2022
accepted:
25
04
2023
medline:
16
6
2023
pubmed:
1
6
2023
entrez:
31
5
2023
Statut:
ppublish
Résumé
Each tumour contains diverse cellular states that underlie intratumour heterogeneity (ITH), a central challenge of cancer therapeutics
Identifiants
pubmed: 37258682
doi: 10.1038/s41586-023-06130-4
pii: 10.1038/s41586-023-06130-4
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
598-606Commentaires et corrections
Type : CommentIn
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer Nature Limited.
Références
Marusyk, A., Almendro, V. & Polyak, K. Intra-tumour heterogeneity: a looking glass for cancer? Nat. Rev. Cancer 12, 323–334 (2012).
doi: 10.1038/nrc3261
pubmed: 22513401
Suva, M. L. & Tirosh, I. Single-cell RNA sequencing in cancer: lessons learned and emerging challenges. Mol. Cell 75, 7–12 (2019).
doi: 10.1016/j.molcel.2019.05.003
pubmed: 31299208
Tirosh, I. et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science 352, 189–196 (2016).
doi: 10.1126/science.aad0501
pubmed: 27124452
pmcid: 4944528
Rambow, F. et al. Toward minimal residual disease-directed therapy in melanoma. Cell 174, 843–855 (2018).
doi: 10.1016/j.cell.2018.06.025
pubmed: 30017245
Neftel, C. et al. An integrative model of cellular states, plasticity, and genetics for glioblastoma. Cell 178, 835–849 (2019).
doi: 10.1016/j.cell.2019.06.024
pubmed: 31327527
pmcid: 6703186
Puram, S. et al. Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer. Cell 171, 1611–1624 (2017).
doi: 10.1016/j.cell.2017.10.044
pubmed: 29198524
pmcid: 5878932
Kinker, G. S. et al. Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity. Nat. Genet. 52, 1208–1218 (2020).
doi: 10.1038/s41588-020-00726-6
pubmed: 33128048
pmcid: 8135089
Baron, M. et al. The stress-like cancer cell state is a consistent component of tumorigenesis. Cell Syst. 11, 536–546 (2020).
doi: 10.1016/j.cels.2020.08.018
pubmed: 32910905
pmcid: 8027961
Barkley, D. et al. Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment. Nat. Genet. 54, 1192–1201 (2022).
doi: 10.1038/s41588-022-01141-9
pubmed: 35931863
pmcid: 9886402
Aibar, S. et al. SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–1086 (2017).
doi: 10.1038/nmeth.4463
pubmed: 28991892
pmcid: 5937676
Meister, N. et al. Interferon-gamma mediated up-regulation of caspase-8 sensitizes medulloblastoma cells to radio- and chemotherapy. Eur. J. Cancer 43, 1833–1841 (2007).
doi: 10.1016/j.ejca.2007.05.028
pubmed: 17627812
Vander Heiden, M. G., Cantley, L. C. & Thompson, C. B. Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science 324, 1029–1033 (2009).
doi: 10.1126/science.1160809
Denisenko, E. et al. Spatial transcriptomics reveals ovarian cancer subclones with distinct tumour microenvironments. Preprint at https://doi.org/10.1101/2022.08.29.505206 (2022).
Ji, A. L. et al. Multimodal analysis of composition and spatial architecture in human squamous cell carcinoma. Cell 182, 1661–1662 (2020).
doi: 10.1016/j.cell.2020.08.043
pubmed: 32946785
pmcid: 7505493
Ravi, V. M. et al. Spatially resolved multi-omics deciphers bidirectional tumor-host interdependence in glioblastoma. Cancer Cell 40, 639–655 e613 (2022).
doi: 10.1016/j.ccell.2022.05.009
pubmed: 35700707
Moffitt, R. A. et al. Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma. Nat. Genet. 47, 1168–1178 (2015).
doi: 10.1038/ng.3398
pubmed: 26343385
pmcid: 4912058
Raghavan, S. et al. Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer. Cell 184, 6119–6137 (2021).
doi: 10.1016/j.cell.2021.11.017
pubmed: 34890551
pmcid: 8822455
Shim, H. S. et al. Unique genetic and survival characteristics of invasive mucinous adenocarcinoma of the lung. J. Thorac. Oncol. 10, 1156–1162 (2015).
doi: 10.1097/JTO.0000000000000579
pubmed: 26200269
Asada, R. et al. The endoplasmic reticulum stress transducer OASIS is involved in the terminal differentiation of goblet cells in the large intestine. J. Biol. Chem. 287, 8144–8153 (2012).
doi: 10.1074/jbc.M111.332593
pubmed: 22262831
pmcid: 3318704
Chen, G. et al. Foxa3 induces goblet cell metaplasia and inhibits innate antiviral immunity. Am. J. Respir. Crit. Care Med. 189, 301–313 (2014).
doi: 10.1164/rccm.201306-1181OC
pubmed: 24392884
pmcid: 3977731
Chen, B. et al. Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps. Cell 184, 6262–6280 (2021).
doi: 10.1016/j.cell.2021.11.031
pubmed: 34910928
pmcid: 8941949
Guilliams, M. et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell 185, 379–396 (2022).
doi: 10.1016/j.cell.2021.12.018
pubmed: 35021063
pmcid: 8809252
Deprez, M. et al. A single-cell atlas of the human healthy airways. Am. J. Respir. Crit. Care Med. 202, 1636–1645 (2020).
doi: 10.1164/rccm.201911-2199OC
pubmed: 32726565
Burclaff, J. et al. A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics. Cell Mol. Gastroenterol. Hepatol. 13, 1554–1589 (2022).
doi: 10.1016/j.jcmgh.2022.02.007
pubmed: 35176508
pmcid: 9043569
The Tabula Sapiens Consortium. The Tabula Sapiens: a multiple-organ, single-cell transcriptomic atlas of humans. Science 376, eabl4896 (2022).
Toulmin, S. A. et al. Type II alveolar cell MHCII improves respiratory viral disease outcomes while exhibiting limited antigen presentation. Nat. Commun. 12, 3993 (2021).
doi: 10.1038/s41467-021-23619-6
pubmed: 34183650
pmcid: 8239023
Lugano, R., Ramachandran, M. & Dimberg, A. Tumor angiogenesis: causes, consequences, challenges and opportunities. Cell. Mol. Life Sci. 77, 1745–1770 (2020).
doi: 10.1007/s00018-019-03351-7
pubmed: 31690961
Schurch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 182, 1341–1359 (2020).
doi: 10.1016/j.cell.2020.07.005
pubmed: 32763154
pmcid: 7479520
Zhang, W. et al. Identification of cell types in multiplexed in situ images by combining protein expression and spatial information using CELESTA. Nat. Methods 19, 759–769 (2022).
doi: 10.1038/s41592-022-01498-z
pubmed: 35654951
pmcid: 9728133
Blise, K. E., Sivagnanam, S., Banik, G. L., Coussens, L. M. & Goecks, J. Single-cell spatial architectures associated with clinical outcome in head and neck squamous cell carcinoma. NPJ Precis. Oncol. 6, 10 (2022).
doi: 10.1038/s41698-022-00253-z
pubmed: 35217711
pmcid: 8881577
Borzi, C. et al. c-Myc shuttled by tumour-derived extracellular vesicles promotes lung bronchial cell proliferation through miR-19b and miR-92a. Cell Death Dis. 10, 759 (2019).
doi: 10.1038/s41419-019-2003-5
pubmed: 31591389
pmcid: 6779734
Hua, Y. et al. Cancer immunotherapies transition endothelial cells into HEVs that generate TCF1
doi: 10.1016/j.ccell.2022.11.002
pubmed: 36423635
Lee, H.-O. et al. Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer. Nat. Genet., https://doi.org/10.1038/s41588-020-0636-z (2020).
Steele, N. G. et al. Multimodal mapping of the tumor and peripheral blood immune landscape in human pancreatic cancer. Nat. Cancer 1, 1097–1112 (2020).
Luca, B. A. et al. Atlas of clinically distinct cell states and ecosystems across human solid tumors. Cell, https://doi.org/10.1016/j.cell.2021.09.014 (2021).
Tirosh, I. et al. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature 539, 309–313 (2016).
Lawrence, M. S. et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505, 495–501 (2014).
doi: 10.1038/nature12912
pubmed: 24390350
pmcid: 4048962
Liu, J. et al. An integrated TCGA pan-cancer clinical data resource to drive high-quality survival outcome analytics. Cell 173, 400–416 (2018).
doi: 10.1016/j.cell.2018.02.052
pubmed: 29625055
pmcid: 6066282
Bankhead, P. et al. QuPath: open source software for digital pathology image analysis. Sci. Rep. 7, 16878 (2017).
doi: 10.1038/s41598-017-17204-5
pubmed: 29203879
pmcid: 5715110
Ramilowski, J. A. et al. A draft network of ligand-receptor-mediated multicellular signalling in human. Nat. Commun. 6, 7866 (2015).
doi: 10.1038/ncomms8866
pubmed: 26198319
Chan-Seng-Yue, M. et al. Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution. Nat. Genet. 52, 231–240 (2020).
Tyler, M. & Gavish, A. tiroshlab/3ca: First release (v1.0.0). Zenodo, https://doi.org/10.5281/zenodo.7688626 (2023).