|Table of Contents|

Spatial biology and cancer research

Journal Of Modern Oncology[ISSN:1672-4992/CN:61-1415/R]

Issue:
2024 20
Page:
3987-3990
Research Field:
Publishing date:

Info

Title:
Spatial biology and cancer research
Author(s):
YUE Hongyun1ZHANG Baihong2
1Department of Ophthalmology,940th Hospital of Joint Logistics Support Force of People's Liberation Army,Gansu Lanzhou 730050,China;2Department of Oncology,940th Hospital of Joint Logistics Support Force of People's Liberation Army,Gansu Lanzhou 730050,China.
Keywords:
cancerspatial biologyspatial omicscancer research
PACS:
R730.5
DOI:
10.3969/j.issn.1672-4992.2024.20.032
Abstract:
Spatial biology maps tissue architecture and interrogates cell to cell interactions.Spatial biology can define the identity of cancer cells and subcellular fraction,map tumor clones evolution,reveal the interactions between tumor cells and microenvironment,and predict therapeutic responses using spatial omics and deep learning within their spatial context.Spatial biology will further improve precision treatment of human cancers.

References:

[1] EISENSTEIN M.How to make spatial maps of gene activity-down to the cellular level[J].Nature,2022,606(7916):1036-1038.
[2] MOFFITT JR,LUNDBERG E,HEYN H.The emerging landscape of spatial profiling technologies[J].Nat Rev Genet,2022,23(12):741-759.
[3] LEWIS SM,ASSELIN-LABAT M,NGUYEN Q,et al.Spatial omics and multiplexed imaging to explore cancer biology[J].Nat Methods,2021,18(9):997-1012.
[4] MOSES L,PACHTER L.Museum of spatial transcriptomics[J].Nat Methods,2022,19(5):534-546.
[5] PALLA G,FISCHER DS,REGEV A,et al.Spatial components of molecular tissue biology[J].Nat Biotechnol,2022,40(3):308-318.
[6] BOUWMAN BAM,CROSETTO N,BIENKO M.The era of 3D and spatial genomics[J].Trends Genet,2022,38(10):1062-1075.
[7] FINN EH,MISTELI T.Molecular basis and biological function of variability in spatial genome organization[J].Science,2019,365(6457):eaaw9498.
[8] RAO A,BARKLEY D,FRANCA GS,et al.Exploring tissue architecture using spatial transcriptomics[J].Nature,2021,596(7871):211-220.
[9] BURGESS DJ.Spatial transcriptomics coming of age[J].Nat Rev Genet,2019,20(6):317.
[10] SCHUEDER F,BEWERSDORF J.Omics goes spatial epigenomics[J].Cell,2022,185(23):4253-4255.
[11] DENG YX,BARTOSOVIC M,KUKANJA P,et al.Spatial-CUT & Tag:Spatially resolved chromatin modification profiling at the cellular level[J].Science,2022,375(6581):681-686.
[12] KOCH L.Spatial epigenomics in single cells[J].Nat Rev Genet,2023,24(1):1.
[13] STRACK R.Spatial proteomics with subcellular resolution[J].Nat Methods,2022,19(7):780.
[14] MUND A,COSCIA F,KRISTON A,et al.Deep visual proteomics defines single-cell identity and heterogeneity[J].Nat Biotechnol,2022,40(8):1231-1240.
[15] TIMP W,TIMP G.Beyond mass spectrometry,the next step in proteomics[J].Sci Adv,2020,6(2):eaax8978.
[16] LOW V,LI Z,BLENIS J.Metabolite activation of tumorigenic signaling pathways in the tumor microenvironment[J].Sci Signal,2022,15(759):eabj4220.
[17] SCHMIDT DR,PATEL R,KIRSCH DG,et al.Metabolomics in cancer research and emerging applications in clinical oncology[J].CA Cancer J Clin,2021,71(4):333-358.
[18] CARMONA-FONTAINE C,DEFORET M,AKKARI L,et al.Metabolic origins of spatial organization in the tumor microenvironment[J].Proc Natl Acad Sci U S A,2017,114(11):2934-2939.
[19] RAVI VM,WILL P,KUECKEIHAUS J,et al.Spatially resolved multi-omics deciphers bidirectional tumor-host interdependence in glioblastoma[J].Cancer Cell,2022,40(6):639-655.e13.
[20] DHAINAUT M,ROSE SA,AKTURK G,et al.Spatial CRISPR genomics identifies regulators of the tumor microenvironment[J].Cell,2022,185(7):1223-1239.
[21] WU R,GUO WB,QIU XY,et al.Comprehensive analysis of spatial architecture in primary liver cancer[J].Sci Adv,2021,7(51):eabg3750.
[22] JI AL,RUBIN AJ,THRANE K,et al.Multimodal analysis of composition and spatial architecture in human squamous cell carcinoma[J].Cell,2020,182(2):497-514.
[23] SERRANO A,BERTHELET J,NAIK SH,et al.Mastering the use of cellular barcoding to explore cancer heterogeneity[J].Nat Rev Cancer,2022,22(11):609-624.
[24] NOBLE R,BURRI D,SUEUR CL,et al.Spatial structure governs the mode of tumour evolutino[J].Nat Ecol Evol,2022,6(2):207-217.
[25] LOMAKIN A,SVEDLUND J,STRELL C,et al.Spatial genomics maps the structure,nature and evolution of cancer clones[J].Nature,2022,611(7936):594-602.
[26] ERICKSON A,HE MX,BERGLUND E,et al.Spatially resolved clonal copy number alterations in benign and malignant tissue[J].Nature,2022,608(7922):360-367.
[27] SCHURCH CM,BHATE SS,BARLOW GL,et al.Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front[J].Cell,2020,182(5):1341-1359.
[28] WANG X,BARRERA C,BERA K,et al.Spatial interplay patterns of cancer nuclei and tumor-infiltrating lymphocytes (TILs) predict clinical benefit for immune checkpoint inhibitors[J].Sci Adv,2022,8(22):eabn3966.
[29] GAGLIA G,KABRAJ S,RAMMOS D,et al.Temporal and spatial topography of cell proliferation in cancer[J].Nat Cell Biol,2022,24(3):316-326.
[30] PELKA K,HOFREE M,CHEN JH,et al.Spatially organized multicellular immune hubs in human colorectal cancer[J].Cell,2021,184(18):4734-4752.
[31] USHIJIMA T,CLARK SJ,TAN P.Mapping genomic and epigenomic evolution in cancer ecosystems[J].Science,2021,373(6562):1474-1479.
[32] BRESSAN D,BATTISTONI G,HANNON GJ.The dawn of spatial omics[J].Science,2023,381(6657):eabq4964.
[33] BAKER EAG,SCHAPIRO D,DUMITRASCU B,et al.In silico tissue generation and power analysis for spatial omics[J].Nat Methods,2023,20(3):424-431.
[34] MANI DR,KRUG K,ZHANG B,et al.Cancer proteogenomics:current impact and future prospects[J].Nat Rev Cancer,2022,22(5):298-313.
[35] AKHOUNDOVA D,RUBIN MA.Clinical application of advanced multi-omics tumor profiling:Shaping precision oncology of the future[J].Cancer Cell,2022,40(9):920-938.

Memo

Memo:
甘肃省自然科学基金项目(编号:22JR5RA007);联勤保障部队第九四〇医院项目(编号:20yjky019)
Last Update: 1900-01-01