Academic Journal
Should we build single-cell lineage trees from gene expression data?
| Τίτλος: | Should we build single-cell lineage trees from gene expression data? |
|---|---|
| Συγγραφείς: | Mulberry N; Department of Biosystems Science & Engineering, ETH Zürich, Basel 4058, Switzerland.; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland., Stadler T; Department of Biosystems Science & Engineering, ETH Zürich, Basel 4058, Switzerland.; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland. |
| Πηγή: | Genetics [Genetics] 2026 Sep 02; Vol. 234 (1). |
| Τύπος έκδοσης: | Journal Article; Research Support, Non-U.S. Gov't |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Publisher: Oxford University Press Country of Publication: United States NLM ID: 0374636 Publication Model: Print Cited Medium: Internet ISSN: 1943-2631 (Electronic) Linking ISSN: 00166731 NLM ISO Abbreviation: Genetics Subsets: MEDLINE |
| Imprint Name(s): | Publication: 2021- : [Oxford] : Oxford University Press Original Publication: Austin, Tex. [etc.] |
| Ιατρικοί όροι (MeSH): | Cell Lineage*/genetics , Single-Cell Analysis*/methods , Phylogeny* , Models, Genetic* , Transcriptome* , Gene Expression Profiling*, Single-Cell Gene Expression Analysis ; Animals |
| Περίληψη: | Gene expression data have been proposed as a natural single-cell lineage marker. Here, we critically examine the feasibility of reconstructing lineage trees from single-cell transcriptomic data using both modeling and empirical data. We first introduce a notion of neutrality for transcriptomic data, and then, under a model for neutral gene expression, establish theoretical bounds for accurate lineage tree reconstruction. Our findings indicate that reconstruction guarantees for even small trees or sub-trees require thousands of independent, neutral traits-a condition that is likely rarely met in practice due to the dominance of non-neutral developmental signals. Furthermore, errors introduced by measurement sampling have the potential to destroy any existing lineage signal. We conclude that gene expression data have limited potential as a natural lineage recorder and should not be used for phylogenetic lineage tree inference without further, rigorous validation. (© The Author(s) 2026. Published by Oxford University Press on behalf of The Genetics Society of America.) |
| Competing Interests: | Conflicts of interest: We declare no conflicts of interest. |
| References: | PeerJ. 2024 Jan 5;12:e16505. (PMID: 38192598) Nat Commun. 2023 Dec 16;14(1):8388. (PMID: 38104156) Theor Popul Biol. 2026 Apr;168:32-43. (PMID: 41554460) Nat Rev Genet. 2025 Mar;26(3):203-222. (PMID: 39587306) Nat Commun. 2024 Mar 29;15(1):2744. (PMID: 38553478) Nat Rev Genet. 2021 Apr;22(4):235-250. (PMID: 33244170) Bioinformatics. 2020 Dec 22;36(20):5007-5013. (PMID: 32619004) Genome Biol. 2016 Apr 27;17:75. (PMID: 27122128) Cell. 2023 Nov 9;186(23):5183-5199.e22. (PMID: 37852258) Proc Natl Acad Sci U S A. 2023 Mar 21;120(12):e2203352120. (PMID: 36927151) Cell Stem Cell. 2018 Aug 02;23(2):166-179. (PMID: 29754780) Science. 2019 Sep 20;365(6459):. (PMID: 31488706) Mol Biol Evol. 2026 Apr 01;43(4):. (PMID: 41883176) Nat Rev Genet. 2022 Jun;23(6):325-341. (PMID: 34983971) Evolution. 2003 Apr;57(4):717-45. (PMID: 12778543) Science. 2010 Oct 29;330(6004):612-6. (PMID: 21030644) Nature. 2022 Aug;608(7921):98-107. (PMID: 35794474) Nat Commun. 2020 Jun 16;11(1):3055. (PMID: 32546686) Nature. 2019 Feb;566(7745):490-495. (PMID: 30787436) Bioinformatics. 2019 Feb 1;35(3):526-528. (PMID: 30016406) Genome Biol. 2019 Dec 23;20(1):296. (PMID: 31870423) Cell. 2020 Aug 20;182(4):947-959.e17. (PMID: 32735851) Nat Commun. 2019 Mar 14;10(1):1208. (PMID: 30872573) Nat Biotechnol. 2021 Aug;39(8):1008-1016. (PMID: 33927416) Nat Methods. 2025 Mar;22(3):488-498. (PMID: 39820752) PLoS Comput Biol. 2025 Feb 13;21(2):e1012789. (PMID: 39937844) Science. 2011 Apr 22;332(6028):472-4. (PMID: 21415320) Nat Commun. 2026 Jun 10;17(1):. (PMID: 42270637) Nat Commun. 2021 Aug 16;12(1):4940. (PMID: 34400634) Imeta. 2022 Sep 28;1(4):e56. (PMID: 38867905) Science. 2021 Jan 15;371(6526):. (PMID: 33446527) Mol Ther Methods Clin Dev. 2018 Aug 02;10:189-196. (PMID: 30094294) |
| Grant Information: | 101001077 European Research Council (ERC) |
| Contributed Indexing: | Keywords: gene expression; lineage trees; phylogeny; single-cell RNA sequencing |
| Molecular Sequence: | GEO GSE315827 |
| Entry Date(s): | Date Created: 20260718 Date Completed: 20260902 Latest Revision: 20260918 |
| Update Code: | 20260919 |
| PubMed Central ID: | PMC13535251 |
| DOI: | 10.1093/genetics/iyag187 |
| PMID: | 42470686 |
| Βάση Δεδομένων: | MEDLINE |
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