دورية أكاديمية
أعرض في EDS

Unveiling the Dynamics behind Glioblastoma Multiforme Single-Cell Data Heterogeneity.

التفاصيل البيبلوغرافية
العنوان: Unveiling the Dynamics behind Glioblastoma Multiforme Single-Cell Data Heterogeneity.
المؤلفون: Junior MGV; Graduate Program in Computational and Systems Biology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil., Côrtes AMA; Department of Applied Mathematics, Institute of Mathematics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, Brazil.; Systems Engineering and Computer Science Program, Coordination of Postgraduate Programs in Engineering (COPPE), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-972, Brazil., Carneiro FRG; Center of Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-361, Brazil.; Laboratório Interdisciplinar de Pesquisas Médicas, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil.; Program of Immunology and Tumor Biology, Brazilian National Cancer Institute (INCA), Rio de Janeiro 20231-050, Brazil., Carels N; Laboratory of Biological System Modeling, Center of Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-361, Brazil., Silva FABD; Scientific Computing Program, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21041-222, Brazil.
المصدر: International journal of molecular sciences [Int J Mol Sci] 2024 Apr 30; Vol. 25 (9). Date of Electronic Publication: 2024 Apr 30.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Basel, Switzerland : MDPI, [2000-
مواضيع طبية MeSH: Glioblastoma*/genetics , Glioblastoma*/pathology , Glioblastoma*/metabolism , Single-Cell Analysis*/methods , Brain Neoplasms*/genetics , Brain Neoplasms*/pathology , Brain Neoplasms*/metabolism, Humans ; Gene Expression Regulation, Neoplastic ; Genetic Heterogeneity ; Gene Expression Profiling/methods ; Genomic Instability ; Sequence Analysis, RNA/methods ; Cluster Analysis
مستخلص: Glioblastoma Multiforme is a brain tumor distinguished by its aggressiveness. We suggested that this aggressiveness leads single-cell RNA-sequence data (scRNA-seq) to span a representative portion of the cancer attractors domain. This conjecture allowed us to interpret the scRNA-seq heterogeneity as reflecting a representative trajectory within the attractor's domain. We considered factors such as genomic instability to characterize the cancer dynamics through stochastic fixed points. The fixed points were derived from centroids obtained through various clustering methods to verify our method sensitivity. This methodological foundation is based upon sample and time average equivalence, assigning an interpretative value to the data cluster centroids and supporting parameters estimation. We used stochastic simulations to reproduce the dynamics, and our results showed an alignment between experimental and simulated dataset centroids. We also computed the Waddington landscape, which provided a visual framework for validating the centroids and standard deviations as characterizations of cancer attractors. Additionally, we examined the stability and transitions between attractors and revealed a potential interplay between subtypes. These transitions might be related to cancer recurrence and progression, connecting the molecular mechanisms of cancer heterogeneity with statistical properties of gene expression dynamics. Our work advances the modeling of gene expression dynamics and paves the way for personalized therapeutic interventions.
References: Biomed Pharmacother. 2023 Jan;157:114036. (PMID: 36436493)
PLoS Comput Biol. 2013;9(8):e1003165. (PMID: 23935477)
Cancer Cell. 2010 Jan 19;17(1):98-110. (PMID: 20129251)
Patterns (N Y). 2021 Apr 09;2(4):100226. (PMID: 33982021)
Genome Biol. 2019 Dec 23;20(1):296. (PMID: 31870423)
Cell Rep. 2017 Oct 31;21(5):1399-1410. (PMID: 29091775)
Curr Oncol. 2015 Aug;22(4):e273-81. (PMID: 26300678)
Cell Syst. 2022 Jan 19;13(1):12-28.e3. (PMID: 34536382)
Cancer Discov. 2022 Jan;12(1):31-46. (PMID: 35022204)
Oncotarget. 2012 Jul;3(7):709-22. (PMID: 22869205)
J R Soc Interface. 2014 Nov 6;11(100):20140774. (PMID: 25232051)
Asia Pac J Clin Oncol. 2018 Feb;14(1):40-51. (PMID: 28840962)
Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2467-E2476. (PMID: 29463712)
F1000Res. 2015 Oct 14;4:1070. (PMID: 26674615)
Nature. 2014 Oct 2;514(7520):54-8. (PMID: 25079331)
Philos Trans R Soc Lond B Biol Sci. 2011 Aug 12;366(1575):2247-59. (PMID: 21727130)
Cell. 2005 Aug 26;122(4):565-78. (PMID: 16122424)
Cell. 2017 Feb 9;168(4):613-628. (PMID: 28187284)
Cancer Res. 2015 Jul 1;75(13):2607-18. (PMID: 25972342)
Nature. 2013 Sep 19;501(7467):338-45. (PMID: 24048066)
Nat Biotechnol. 2019 May;37(5):547-554. (PMID: 30936559)
Proc Natl Acad Sci U S A. 2011 May 17;108(20):8257-62. (PMID: 21536909)
Science. 2013 Mar 29;339(6127):1546-58. (PMID: 23539594)
Nature. 2007 May 24;447(7143):425-32. (PMID: 17522676)
PLoS Comput Biol. 2019 Sep 12;15(9):e1007279. (PMID: 31513575)
N Engl J Med. 2008 Mar 13;358(11):1148-59. (PMID: 18337604)
Nat Rev Clin Oncol. 2017 Oct;14(10):587. (PMID: 28762385)
Cancer Cell. 2017 Jul 10;32(1):42-56.e6. (PMID: 28697342)
J R Soc Interface. 2013 Oct 16;10(89):20130787. (PMID: 24132204)
Science. 2014 Jun 20;344(6190):1396-401. (PMID: 24925914)
Sci Adv. 2020 May 27;6(22):eaaz4125. (PMID: 32832595)
Cell. 2018 May 3;173(4):879-893.e13. (PMID: 29681456)
Cancer Metastasis Rev. 2013 Dec;32(3-4):403-21. (PMID: 23615877)
Trends Cancer. 2022 Sep;8(9):711-725. (PMID: 35599231)
Biophys J. 2010 Jul 7;99(1):29-39. (PMID: 20655830)
Cell Syst. 2022 Jan 19;13(1):83-102.e6. (PMID: 34626539)
Nat Rev Drug Discov. 2023 Jan;22(1):38-58. (PMID: 36202931)
Cell. 2019 Aug 8;178(4):835-849.e21. (PMID: 31327527)
Curr Biol. 2012 Jun 5;22(11):R458-66. (PMID: 22677291)
BMC Syst Biol. 2014 Apr 04;8:43. (PMID: 24708864)
Trends Cancer. 2020 Jun;6(6):454-461. (PMID: 32460001)
J Chem Phys. 2007 May 14;126(18):184511. (PMID: 17508815)
Cell. 2013 Mar 28;153(1):38-55. (PMID: 23540689)
Proc Natl Acad Sci U S A. 2016 Mar 8;113(10):2672-7. (PMID: 26929366)
Nat Rev Genet. 2017 Mar;18(3):164-179. (PMID: 27990019)
Quant Biol. 2014 Mar;2(1):1-29. (PMID: 25632368)
Cancer Cell. 2006 Mar;9(3):157-73. (PMID: 16530701)
Science. 2016 Apr 8;352(6282):189-96. (PMID: 27124452)
Sci Rep. 2016 Feb 08;6:20679. (PMID: 26854017)
Semin Cell Dev Biol. 2009 Sep;20(7):869-76. (PMID: 19595782)
Nature. 2001 Mar 8;410(6825):268-76. (PMID: 11258382)
Nature. 2012 Jan 18;481(7381):306-13. (PMID: 22258609)
Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):1907-11. (PMID: 25691697)
Science. 2004 Oct 22;306(5696):704-8. (PMID: 15499023)
Sci Rep. 2019 Jun 27;9(1):9332. (PMID: 31249353)
Nat Biotechnol. 2015 May;33(5):495-502. (PMID: 25867923)
معلومات مُعتمدة: 88887.597339/2021-00 Coordenação de Aperfeicoamento de Pessoal de Nível Superior
فهرسة مساهمة: Keywords: Glioblastoma Multiforme; cancer attractors; epigenetic landscape; gene regulatory network dynamics; heterogeneity; parameter sets estimation; single-cell RNA sequencing
تواريخ الأحداث: Date Created: 20240511 Date Completed: 20240511 Latest Revision: 20240513
رمز التحديث: 20240513
مُعرف محوري في PubMed: PMC11084314
DOI: 10.3390/ijms25094894
PMID: 38732140
قاعدة البيانات: MEDLINE
الوصف
تدمد:1422-0067
DOI:10.3390/ijms25094894