Zobrazit v EDS

Spatial transcriptomics in breast cancer: providing insight into tumor heterogeneity and promoting individualized therapy.

Uloženo v:
Podrobná bibliografie
Název: Spatial transcriptomics in breast cancer: providing insight into tumor heterogeneity and promoting individualized therapy.
Autoři: An J; West China School of Pharmacy, Sichuan University, Chengdu, China.; State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China.; Cardiovascular Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China., Lu Y; West China School of Pharmacy, Sichuan University, Chengdu, China., Chen Y; West China School of Pharmacy, Sichuan University, Chengdu, China., Chen Y; West China School of Pharmacy, Sichuan University, Chengdu, China., Zhou Z; Department of Clinical Medicine, Zhengzhou University, Zhengzhou, China., Chen J; School of Chinese Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China., Peng C; State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China., Huang R; Cardiovascular Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China., Peng F; West China School of Pharmacy, Sichuan University, Chengdu, China.; Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, Sichuan University, Chengdu, China.
Zdroj: Frontiers in immunology [Front Immunol] 2024 Dec 19; Vol. 15, pp. 1499301. Date of Electronic Publication: 2024 Dec 19 (Print Publication: 2024).
Způsob vydávání: Journal Article; Review
Jazyk: English
Informace o časopise: Publisher: Frontiers Research Foundation] Country of Publication: Switzerland NLM ID: 101560960 Publication Model: eCollection Cited Medium: Internet ISSN: 1664-3224 (Electronic) Linking ISSN: 16643224 NLM ISO Abbreviation: Front Immunol Subsets: MEDLINE
Imprint Name(s): Original Publication: [Lausanne : Frontiers Research Foundation]
Výrazy ze slovníku MeSH: Breast Neoplasms*/genetics , Precision Medicine*/methods , Tumor Microenvironment*/genetics , Gene Expression Profiling*/methods , Transcriptome*, Biomarkers, Tumor/genetics ; Single-Cell Analysis/methods ; Humans ; Female ; Gene Expression Regulation, Neoplastic ; Genetic Heterogeneity
Abstrakt: A comprehensive understanding of tumor heterogeneity, tumor microenvironment and the mechanisms of drug resistance is fundamental to advancing breast cancer research. While single-cell RNA sequencing has resolved the issue of "temporal dynamic expression" of genes at the single-cell level, the lack of spatial information still prevents us from gaining a comprehensive understanding of breast cancer. The introduction and application of spatial transcriptomics addresses this limitation. As the annual technical method of 2020, spatial transcriptomics preserves the spatial location of tissues and resolves RNA-seq data to help localize and differentiate the active expression of functional genes within a specific tissue region, enabling the study of spatial location attributes of gene locations and cellular tissue environments. In the context of breast cancer, spatial transcriptomics can assist in the identification of novel breast cancer subtypes and spatially discriminative features that show promise for individualized precise treatment. This article summarized the key technical approaches, recent advances in spatial transcriptomics and its applications in breast cancer, and discusses the limitations of current spatial transcriptomics methods and the prospects for future development, with a view to advancing the application of this technology in clinical practice.
(Copyright © 2024 An, Lu, Chen, Chen, Zhou, Chen, Peng, Huang and Peng.)
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
References: Sci Rep. 2020 Feb 26;10(1):3490. (PMID: 32103057)
Cell. 2023 Apr 13;186(8):1708-1728. (PMID: 36931265)
Nat Genet. 2024 Oct;56(10):2259-2270. (PMID: 39256584)
Front Oncol. 2024 Jan 18;14:1273841. (PMID: 38304870)
Cell. 2020 Dec 10;183(6):1665-1681.e18. (PMID: 33188776)
Tumour Biol. 2016 Nov;37(11):14463-14477. (PMID: 27644253)
J Natl Cancer Inst. 2014 Aug 12;106(8):. (PMID: 25118203)
Nat Commun. 2016 Jul 08;7:12139. (PMID: 27387371)
Cell. 2015 Nov 5;163(4):799-810. (PMID: 26544934)
Nat Commun. 2022 Apr 1;13(1):1742. (PMID: 35365629)
Cell. 2011 Sep 16;146(6):1044, 1044.e1-2. (PMID: 21925324)
Drug Resist Updat. 2024 May;74:101068. (PMID: 38402670)
Cell. 2022 May 12;185(10):1694-1708.e19. (PMID: 35447074)
Science. 2016 Jul 1;353(6294):78-82. (PMID: 27365449)
Signal Transduct Target Ther. 2020 Aug 25;5(1):166. (PMID: 32843638)
Nat Rev Genet. 2021 Oct;22(10):627-644. (PMID: 34145435)
Science. 2015 Apr 24;348(6233):aaa6090. (PMID: 25858977)
Science. 2019 Mar 29;363(6434):1463-1467. (PMID: 30923225)
Nature. 2022 Nov;611(7937):733-743. (PMID: 36289335)
Science. 1998 Apr 24;280(5363):585-90. (PMID: 9554849)
Curr Opin Biotechnol. 2017 Aug;46:126-133. (PMID: 28346891)
Genome Med. 2024 Jan 12;16(1):12. (PMID: 38217035)
Clin Cancer Res. 2024 Aug 1;30(15):3298-3315. (PMID: 38772416)
Oncoimmunology. 2022 Jun 8;11(1):2085432. (PMID: 35712121)
Nat Rev Genet. 2022 Dec;23(12):741-759. (PMID: 35859028)
Science. 2017 Dec 22;358(6370):1622-1626. (PMID: 29217582)
Sci Rep. 2016 Nov 16;6:37137. (PMID: 27849009)
Nat Protoc. 2024 Sep;19(9):2685-2711. (PMID: 38806741)
Front Immunol. 2023 Jul 26;14:1188351. (PMID: 37564657)
Nat Genet. 2022 Aug;54(8):1192-1201. (PMID: 35931863)
Nature. 2023 Aug;620(7972):181-191. (PMID: 37380767)
Cell. 2024 Jul 25;187(15):3953-3972.e26. (PMID: 38917789)
Adv Sci (Weinh). 2023 Feb;10(6):e2205395. (PMID: 36594618)
Trends Biotechnol. 2021 Jan;39(1):43-58. (PMID: 32505359)
Ann Oncol. 2024 Jul;35(7):588-606. (PMID: 38834388)
Mol Cancer. 2023 Oct 13;22(1):170. (PMID: 37833788)
Nucleic Acids Res. 2021 Sep 7;49(15):9002. (PMID: 34331448)
Nat Commun. 2017 Nov 1;8(1):1245. (PMID: 29093438)
Science. 2023 Jun 30;380(6652):eadd3067. (PMID: 37384709)
Nat Commun. 2021 Aug 12;12(1):4884. (PMID: 34385460)
Genomics. 2023 Sep;115(5):110671. (PMID: 37353093)
EBioMedicine. 2019 Oct;48:212-223. (PMID: 31526717)
Nat Methods. 2014 Apr;11(4):360-1. (PMID: 24681720)
Breast Cancer Res. 2020 Jan 13;22(1):6. (PMID: 31931856)
Nucleic Acids Res. 2022 Aug 12;50(14):e80. (PMID: 35536287)
Pharmacol Res. 2023 Dec;198:107008. (PMID: 37995895)
Nature. 2021 Aug;596(7871):211-220. (PMID: 34381231)
Adv Sci (Weinh). 2023 Jun;10(16):e2206939. (PMID: 37026425)
Cancer Cell Int. 2024 Apr 17;24(1):140. (PMID: 38632642)
Sci Adv. 2023 Jun 16;9(24):eadf5464. (PMID: 37327339)
Nat Rev Genet. 2020 Jan;21(1):65. (PMID: 31659302)
Acta Biochim Biophys Sin (Shanghai). 2022 Sep 25;54(9):1336-1348. (PMID: 36148946)
Cell. 2021 Sep 2;184(18):4734-4752.e20. (PMID: 34450029)
Cell. 2020 Aug 20;182(4):976-991.e19. (PMID: 32702314)
Cell. 2019 Jun 27;178(1):229-241.e16. (PMID: 31230717)
PLoS One. 2013 Aug 12;8(8):e71820. (PMID: 23951250)
Gut. 2021 Oct;70(10):1823-1832. (PMID: 33229445)
Cell. 2019 Jul 11;178(2):473-490.e26. (PMID: 31230715)
Genome Biol. 2019 Dec 23;20(1):296. (PMID: 31870423)
Cell. 2024 May 9;187(10):2485-2501.e26. (PMID: 38653236)
PLoS Comput Biol. 2018 Jun 25;14(6):e1006245. (PMID: 29939984)
Nat Protoc. 2017 Mar;12(3):566-580. (PMID: 28207000)
Science. 2018 Jul 27;361(6400):. (PMID: 29930089)
Nature. 1970 Mar 7;225(5236):946-8. (PMID: 5416464)
Nat Commun. 2021 Sep 27;12(1):5668. (PMID: 34580291)
Nat Methods. 2023 Aug;20(8):1179-1182. (PMID: 37349575)
Sci Rep. 2019 Dec 12;9(1):18975. (PMID: 31831833)
Trends Genet. 1998 Jul;14(7):272-6. (PMID: 9676529)
Nat Methods. 2018 Jul;15(7):547-553. (PMID: 29786092)
Nat Commun. 2024 May 23;15(1):4388. (PMID: 38782901)
Nature. 2024 Mar;627(8005):854-864. (PMID: 38480880)
Nat Biotechnol. 2023 Jun;41(6):788-793. (PMID: 36593397)
Cancers (Basel). 2021 Sep 04;13(17):. (PMID: 34503266)
Comput Biol Med. 2023 May;158:106836. (PMID: 37031511)
Cancer Cell. 2024 Jun 10;42(6):1067-1085.e11. (PMID: 38759655)
Int J Mol Sci. 2023 Jan 11;24(2):. (PMID: 36674951)
Clin Transl Med. 2024 Jan;14(1):e1548. (PMID: 38282415)
Science. 2021 Jul 2;373(6550):111-117. (PMID: 34210887)
Genome Biol. 2022 Apr 14;23(1):97. (PMID: 35422018)
Drug Discov Today. 2024 Mar;29(3):103889. (PMID: 38244672)
Cancer Immunol Immunother. 2023 Mar;72(3):679-695. (PMID: 36040519)
Cell Rep Med. 2024 Jun 18;5(6):101582. (PMID: 38781959)
Theranostics. 2023 Feb 21;13(4):1381-1400. (PMID: 36923542)
Nat Rev Genet. 2019 Nov;20(11):631-656. (PMID: 31341269)
Lab Invest. 2023 Dec;103(12):100258. (PMID: 37813278)
Nat Commun. 2023 Dec 1;14(1):7930. (PMID: 38040768)
Science. 2022 Jun 3;376(6597):eabo0510. (PMID: 35549310)
Nat Commun. 2023 Dec 19;14(1):8353. (PMID: 38114474)
Nat Biotechnol. 2018 Jun;36(5):411-420. (PMID: 29608179)
Nat Methods. 2013 Sep;10(9):857-60. (PMID: 23852452)
J Transl Med. 2021 Nov 27;19(1):480. (PMID: 34838031)
Nat Rev Genet. 2009 Jan;10(1):57-63. (PMID: 19015660)
Cell. 2023 Dec 21;186(26):5677-5689. (PMID: 38065099)
Mil Med Res. 2023 Aug 17;10(1):38. (PMID: 37592342)
Cancer Res. 2023 Jan 4;83(1):34-48. (PMID: 36283023)
Int J Cancer. 2023 Nov 1;153(9):1568-1578. (PMID: 37306359)
J Clin Invest. 2024 Mar 26;134(10):. (PMID: 38530357)
Front Immunol. 2023 Sep 12;14:1263537. (PMID: 37767092)
J Clin Invest. 2011 Oct;121(10):3786-8. (PMID: 21965334)
Nat Commun. 2022 Oct 10;13(1):5983. (PMID: 36216799)
Nucleic Acids Res. 2023 May 8;51(8):e47. (PMID: 36928528)
Nat Biotechnol. 2023 Mar;41(3):367-377. (PMID: 36203012)
Nat Methods. 2020 Jan;17(1):101-106. (PMID: 31740815)
NPJ Breast Cancer. 2022 Jul 12;8(1):81. (PMID: 35821504)
Science. 2017 Oct 6;358(6359):64-69. (PMID: 28983044)
Nat Comput Sci. 2024 Feb;4(2):94-95. (PMID: 38365998)
Nat Biotechnol. 2024 Feb;42(2):293-304. (PMID: 37231261)
Trends Immunol. 2023 Dec;44(12):971-985. (PMID: 37995659)
Nat Rev Nephrol. 2024 Oct;20(10):659-671. (PMID: 38719971)
Int Immunopharmacol. 2023 Dec;125(Pt B):111196. (PMID: 37972471)
Nat Protoc. 2015 Mar;10(3):442-58. (PMID: 25675209)
Cell Death Dis. 2021 Nov 20;12(12):1095. (PMID: 34799559)
Nat Biotechnol. 2020 Mar;38(3):333-342. (PMID: 31932730)
Nat Med. 2022 Jun;28(6):1232-1239. (PMID: 35469069)
Nat Genet. 2021 Sep;53(9):1334-1347. (PMID: 34493872)
Proc Natl Acad Sci U S A. 1969 Jun;63(2):378-83. (PMID: 4895535)
Cancer Cell. 2022 Jun 13;40(6):639-655.e13. (PMID: 35700707)
Cell Rep Med. 2024 May 21;5(5):101536. (PMID: 38697103)
Sci Rep. 2023 Aug 21;13(1):13604. (PMID: 37604916)
Nucleic Acids Res. 2022 Dec 9;50(22):e131. (PMID: 36250636)
Nat Commun. 2023 May 10;14(1):2692. (PMID: 37164975)
Cancer Res. 2021 Oct 1;81(19):5115-5126. (PMID: 34341074)
Nat Commun. 2024 Apr 1;15(1):2806. (PMID: 38561380)
Nat Biomed Eng. 2020 Aug;4(8):827-834. (PMID: 32572199)
J Immunother Cancer. 2024 Jun 19;12(6):. (PMID: 38901879)
Nat Commun. 2022 Nov 8;13(1):6753. (PMID: 36347854)
Science. 2021 Jan 29;371(6528):. (PMID: 33509999)
Genome Biol. 2024 Aug 5;25(1):206. (PMID: 39103939)
Ann Oncol. 2012 Dec;23(12):2997-3006. (PMID: 23166150)
Cancer Cell. 2024 Jan 8;42(1):70-84.e8. (PMID: 38194915)
Cancer Immunol Res. 2024 Jan 3;12(1):120-134. (PMID: 37856875)
Nat Methods. 2014 Feb;11(2):190-6. (PMID: 24412976)
Nature. 2023 Oct;622(7983):552-561. (PMID: 37758947)
Cancer Res. 2024 Jul 2;84(13):2202-2217. (PMID: 38657117)
Int J Mol Sci. 2022 Nov 23;23(23):. (PMID: 36498893)
Front Oncol. 2022 Mar 04;12:828438. (PMID: 35311116)
Nat Commun. 2024 Mar 2;15(1):1929. (PMID: 38431724)
Cell Res. 2024 Jan;34(1):58-75. (PMID: 38168642)
Breast Cancer Res. 2021 Jul 15;23(1):73. (PMID: 34266469)
Adv Sci (Weinh). 2021 Nov;8(22):e2101176. (PMID: 34605222)
Nucleic Acids Res. 2018 Feb 28;46(4):e22. (PMID: 29190363)
J Am Coll Cardiol. 2023 Jun 13;81(23):2213-2227. (PMID: 37286250)
Nature. 2019 Apr;568(7751):235-239. (PMID: 30911168)
Nat Methods. 2021 Jan;18(1):9-14. (PMID: 33408395)
Acta Biomater. 2020 Apr 1;106:1-21. (PMID: 32045679)
Nat Rev Clin Oncol. 2024 Sep;21(9):660-674. (PMID: 39043872)
Nat Methods. 2024 Mar 20;:. (PMID: 38509327)
Theranostics. 2024 May 11;14(7):2946-2968. (PMID: 38773973)
EMBO Mol Med. 2024 Apr;16(4):823-853. (PMID: 38480932)
Cell. 2014 Oct 23;159(3):662-75. (PMID: 25417113)
J Mol Diagn. 2012 Jan;14(1):22-9. (PMID: 22166544)
Nat Methods. 2021 Sep;18(9):997-1012. (PMID: 34341583)
Genome Res. 2021 Oct;31(10):1706-1718. (PMID: 34599004)
Genomics Proteomics Bioinformatics. 2023 Feb;21(1):24-47. (PMID: 36252814)
BMB Rep. 2013 Feb;46(2):65-72. (PMID: 23433107)
Nat Rev Clin Oncol. 2015 Jul;12(7):381-94. (PMID: 25895611)
Nat Rev Cancer. 2012 Apr 19;12(5):323-34. (PMID: 22513401)
Cell. 2021 Jun 24;184(13):3559-3572.e22. (PMID: 34115981)
Nucleic Acids Res. 2024 Jan 11;52(1):e2. (PMID: 37953397)
J Hematol Oncol. 2022 Mar 3;15(1):19. (PMID: 35241110)
Nat Methods. 2019 Oct;16(10):987-990. (PMID: 31501547)
Nat Rev Cancer. 2023 Aug;23(8):544-564. (PMID: 37349410)
Signal Transduct Target Ther. 2022 Apr 1;7(1):111. (PMID: 35365599)
Nat Methods. 2009 May;6(5):377-82. (PMID: 19349980)
Cell. 2022 May 12;185(10):1777-1792.e21. (PMID: 35512705)
Nat Cell Biol. 2020 Jan;22(1):38-48. (PMID: 31871321)
Nat Biotechnol. 2024 Mar 21;:. (PMID: 38514799)
Nat Biotechnol. 2015 May;33(5):495-502. (PMID: 25867923)
Contributed Indexing: Keywords: breast cancer; heterogeneity; individualized precise treatment; spatial transcriptomics; tumor microenvironment
Substance Nomenclature: 0 (Biomarkers, Tumor)
Entry Date(s): Date Created: 20250103 Date Completed: 20250103 Latest Revision: 20250106
Update Code: 20260130
PubMed Central ID: PMC11693744
DOI: 10.3389/fimmu.2024.1499301
PMID: 39749323
Databáze: MEDLINE
Popis
Abstrakt:A comprehensive understanding of tumor heterogeneity, tumor microenvironment and the mechanisms of drug resistance is fundamental to advancing breast cancer research. While single-cell RNA sequencing has resolved the issue of "temporal dynamic expression" of genes at the single-cell level, the lack of spatial information still prevents us from gaining a comprehensive understanding of breast cancer. The introduction and application of spatial transcriptomics addresses this limitation. As the annual technical method of 2020, spatial transcriptomics preserves the spatial location of tissues and resolves RNA-seq data to help localize and differentiate the active expression of functional genes within a specific tissue region, enabling the study of spatial location attributes of gene locations and cellular tissue environments. In the context of breast cancer, spatial transcriptomics can assist in the identification of novel breast cancer subtypes and spatially discriminative features that show promise for individualized precise treatment. This article summarized the key technical approaches, recent advances in spatial transcriptomics and its applications in breast cancer, and discusses the limitations of current spatial transcriptomics methods and the prospects for future development, with a view to advancing the application of this technology in clinical practice.<br /> (Copyright © 2024 An, Lu, Chen, Chen, Zhou, Chen, Peng, Huang and Peng.)
ISSN:1664-3224
DOI:10.3389/fimmu.2024.1499301