Estimation of cell lineages in tumors from spatial transcriptomics data.
Estimation of cell lineages in tumors from spatial transcriptomics data.
复制标题
DOI：
10.1038/s41467-023-36062-6
复制
发表时间：
2023-02-02
影响因子：
16.6
通讯作者：
Jiang, Peng
中科院分区：
文献类型：
--
作者：
Ru, Beibei;Huang, Jinlin;Zhang, Yu;Aldape, Kenneth;Jiang, Peng
Spatial transcriptomics (ST) technology through in situ capturing has enabled topographical gene expression profiling of tumor tissues. However, each capturing spot may contain diverse immune and malignant cells, with different cell densities across tissue regions. Cell type deconvolution in tumor ST data remains challenging for existing methods designed to decompose general ST or bulk tumor data. We develop the Spatial Cellular Estimator for Tumors (SpaCET) to infer cell identities from tumor ST data. SpaCET first estimates cancer cell abundance by integrating a gene pattern dictionary of copy number alterations and expression changes in common malignancies. A constrained regression model then calibrates local cell densities and determines immune and stromal cell lineage fractions. SpaCET provides higher accuracy than existing methods based on simulation and real ST data with matched double-blind histopathology annotations as ground truth. Further, coupling cell fractions with ligand-receptor coexpression analysis, SpaCET reveals how intercellular interactions at the tumor-immune interface promote cancer progression. Cell type deconvolution in tumor spatial transcriptomics (ST) data remains challenging. Here, the authors develop Spatial Cellular Estimator for Tumors (SpaCET) to infer cell types and intercellular interactions from ST data in cancer across different platforms, with improved performance over similar methods.
登录
查看更多内容
影响因子：
48
作者：
Biancalani T;Scalia G;Buffoni L;Avasthi R;Lu Z;Sanger A;Tokcan N;Vanderburg CR;Segerstolpe Å;Zhang M;Avraham-Davidi I;Vickovic S;Nitzan M;Ma S;Subramanian A;Lipinski M;Buenrostro J;Brown NB;Fanelli D;Zhuang X;Macosko EZ;Regev A
通讯作者：
Regev A
DOI：
10.1126/science.1245075
发表时间：
2015-05-15
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Ginzberg MB;Kafri R;Kirschner M
通讯作者：
Kirschner M
影响因子：
5.9
作者：
Andersson A;Bergenstråhle J;Asp M;Bergenstråhle L;Jurek A;Fernández Navarro J;Lundeberg J
通讯作者：
Lundeberg J
影响因子：
2.8
作者：
Cui, Juncheng;Dean, Dylan;Duan, Zhenfeng
通讯作者：
Duan, Zhenfeng
DOI：
10.1093/bioinformatics/btu474
发表时间：
2014-09-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Gobbi A;Iorio F;Dawson KJ;Wedge DC;Tamborero D;Alexandrov LB;Lopez-Bigas N;Garnett MJ;Jurman G;Saez-Rodriguez J
通讯作者：
Saez-Rodriguez J