METI: deep profiling of tumor ecosystems by integrating cell morphology and spatial transcriptomics
文献类型：期刊论文
| 作者 | Jiang, Jiahui3,4; Liu, Yunhe3; Qin, Jiangjiang7,8; Chen, Jianfeng9; Wu, Jingjing10; Pizzi, Melissa P.10; Lazcano, Rossana11; Yamashita, Kohei10; Xu, Zhiyuan7; Pei, Guangsheng3 |
| 刊名 | NATURE COMMUNICATIONS
 |
| 出版日期 | 2024-08-25 |
| 卷号 | 15 |
| DOI | 10.1038/s41467-024-51708-9 |
| 通讯作者 | Hu, Jian(jian.hu@emory.edu) ; Wang, Linghua(lwang22@mdanderson.org) |
| 英文摘要 | Recent advances in spatial transcriptomics (ST) techniques provide valuable insights into cellular interactions within the tumor microenvironment (TME). However, most analytical tools lack consideration of histological features and rely on matched single-cell RNA sequencing data, limiting their effectiveness in TME studies. To address this, we introduce the Morphology-Enhanced Spatial Transcriptome Analysis Integrator (METI), an end-to-end framework that maps cancer cells and TME components, stratifies cell types and states, and analyzes cell co-localization. By integrating spatial transcriptomics, cell morphology, and curated gene signatures, METI enhances our understanding of the molecular landscape and cellular interactions within the tissue. We evaluate the performance of METI on ST data generated from various tumor tissues, including gastric, lung, and bladder cancers, as well as premalignant tissues. We also conduct a quantitative comparison of METI with existing clustering and cell deconvolution tools, demonstrating METI's robust and consistent performance. Integrating tissue histology with spatial transcriptomics (ST) can significantly enhance the analysis of tumor heterogeneity and the tumor microenvironment (TME). Here, the authors present METI, a computational framework to analyze cancer cells and the complex TME by integrating ST with histology imaging. |
| WOS关键词 | SINGLE-CELL ; INTESTINAL METAPLASIA ; CANCER ; POPULATIONS ; FIBROBLASTS ; EXPRESSION ; ATLAS ; RNA |
| 资助项目 | Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)[R01CA266280] ; Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)[U01CA264583] ; Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)[U24CA274274] ; National Institutes of Health/NCI ; University of Texas MD Anderson Cancer Center (MDACC) Institutional Research Grant (IRG) Program ; Break Through Cancer Foundation[RP220101] ; Cancer Prevention and Research Institute of Texas award[T32CA217789] ; NCI ; MDACC postdoctoral fellowship[CA016672] ; NCI P30 Core Grant ; Sheikh Khlaifa bin Zayed Foundation ; MDACC Moon Shots Program in Pancreas Cancer ; Stupid Strong Foundation |
| WOS研究方向 | Science & Technology - Other Topics |
| 语种 | 英语 |
| WOS记录号 | WOS:001298588700002 |
| 出版者 | NATURE PORTFOLIO |
| 资助机构 | Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.) ; National Institutes of Health/NCI ; University of Texas MD Anderson Cancer Center (MDACC) Institutional Research Grant (IRG) Program ; Break Through Cancer Foundation ; Cancer Prevention and Research Institute of Texas award ; NCI ; MDACC postdoctoral fellowship ; NCI P30 Core Grant ; Sheikh Khlaifa bin Zayed Foundation ; MDACC Moon Shots Program in Pancreas Cancer ; Stupid Strong Foundation |
| 源URL | [http://ir.hfcas.ac.cn:8080/handle/334002/134887]  |
| 专题 | 中国科学院合肥物质科学研究院 |
| 通讯作者 | Hu, Jian; Wang, Linghua |
| 作者单位 | 1.Univ Texas MD Anderson Canc Ctr, Dept Gynecol Oncol & Reprod Med, Houston, TX USA 2.Emory Sch Med, Dept Human Genet, Atlanta, GA 30307 USA 3.Univ Texas MD Anderson Canc Ctr, Dept Genom Med, Houston, TX 77030 USA 4.Univ Texas Hlth Sci Ctr Houston, Sch Publ Hlth, Houston, TX USA 5.Univ Texas MD Anderson Canc Ctr UTHealth, Grad Sch Biomed Sci GSBS, Houston, TX 77030 USA 6.Univ Texas MD Anderson Canc Ctr, Dept Pathol, Houston, TX USA 7.Univ Chinese Acad Sci, Zhejiang Canc Hosp, Canc Hosp, Dept Gastr Surg, Hangzhou, Peoples R China 8.Chinese Acad Sci, Inst Basic Med & Canc, Hangzhou, Zhejiang, Peoples R China 9.Univ Texas MD Anderson Canc Ctr, Dept Genitourinary Med Oncol, Houston, TX USA 10.Univ Texas MD Anderson Canc Ctr, Dept Gastrointestinal Med Oncol, Houston, TX USA |
| 推荐引用方式 GB/T 7714 | Jiang, Jiahui,Liu, Yunhe,Qin, Jiangjiang,et al. METI: deep profiling of tumor ecosystems by integrating cell morphology and spatial transcriptomics[J]. NATURE COMMUNICATIONS,2024,15. |
| APA | Jiang, Jiahui.,Liu, Yunhe.,Qin, Jiangjiang.,Chen, Jianfeng.,Wu, Jingjing.,...&Wang, Linghua.(2024).METI: deep profiling of tumor ecosystems by integrating cell morphology and spatial transcriptomics.NATURE COMMUNICATIONS,15. |
| MLA | Jiang, Jiahui,et al."METI: deep profiling of tumor ecosystems by integrating cell morphology and spatial transcriptomics".NATURE COMMUNICATIONS 15(2024). |
入库方式： OAI收割
来源：合肥物质科学研究院
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