Modeling intercellular communication in tissues using spatial graphs of cells

被引：79
|
作者：
Fischer, David S. [1 ,2 ]
Schaar, Anna C. [1 ,3 ]
Theis, Fabian J. [1 ,2 ,3 ]
机构：
[1] Helmholtz Zentrum Munchen, Inst Computat Biol, Neuherberg, Germany
[2] Tech Univ Munich, TUM Sch Life Sci Weihenstephan, Freising Weihenstephan, Germany
[3] Tech Univ Munich, Dept Math, Garching, Germany
来源：
NATURE BIOTECHNOLOGY | 2023年 / 41卷 / 03期
基金：
英国惠康基金;
关键词：
Cell-be - Cell/B.E - Cell/BE - Expression modeling - Genes expression - Graph neural networks - Intercellular communications - Receptor ligands - Spatial graphs - Spatial proximity;
D O I：
10.1038/s41587-022-01467-z
中图分类号：
Q81 [生物工程学（生物技术）]; Q93 [微生物学];
学科分类号：
071005 ; 0836 ; 090102 ; 100705 ;
摘要：
How cells in a tissue communicate is modeled with a graph neural network. Models of intercellular communication in tissues are based on molecular profiles of dissociated cells, are limited to receptor-ligand signaling and ignore spatial proximity in situ. We present node-centric expression modeling, a method based on graph neural networks that estimates the effects of niche composition on gene expression in an unbiased manner from spatial molecular profiling data. We recover signatures of molecular processes known to underlie cell communication.
引用
收藏
页码：332 / +
页数：23
相关论文
共 50 条
  • [41] INTERCELLULAR COMMUNICATION BETWEEN EPITHELIAL AND FIBER CELLS OF THE EYE LENS
    BASSNETT, S
    KUSZAK, JR
    REINISCH, L
    BROWN, HG
    BEEBE, DC
    JOURNAL OF CELL SCIENCE, 1994, 107 : 799 - 811
  • [42] Cells in the 'hood: Influences on intercellular communication in cat striate cortex
    Snider, RK
    Kabara, JF
    Roig, BR
    Bonds, AB
    INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE, 1997, 38 (04) : 64 - 64
  • [43] Ouabain Promotes Gap Junctional Intercellular Communication in Cancer Cells
    Serrano-Rubi, Mauricio
    Jimenez, Lidia
    Martinez-Rendon, Jacqueline
    Cereijido, Marcelino
    Ponce, Arturo
    INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2021, 22 (01) : 1 - 18
  • [44] The role of stem cells and gap junctional intercellular communication in carcinogenesis
    Trosko, JE
    JOURNAL OF BIOCHEMISTRY AND MOLECULAR BIOLOGY, 2003, 36 (01): : 43 - 48
  • [45] INTERCELLULAR COMMUNICATION BETWEEN NORMAL AND TUMOR CELLS IN GLIOMA MICROENVIRONMENT
    Hossain, Anwar
    Hasan, Irtiza
    Adachi, Satoshi
    Ledbetter, Daniel
    McDonald, Malcolm
    Gumin, Joy
    Daou, Marc
    Phillips, Lynette
    Parker-Kerrigan, Brittany
    Lang, Frederick
    NEURO-ONCOLOGY, 2019, 21 : 255 - 256
  • [46] Intercellular communication in cultured human vascular smooth muscle cells
    Wang, HZ
    Day, N
    Valcic, M
    Hsieh, K
    Serels, S
    Brink, PR
    Christ, GJ
    AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY, 2001, 281 (01): : C75 - C88
  • [47] Roles of gap junctional intercellular communication in osteoblastic cells differentiation
    Ma, Xing
    Ma, Xiangdong
    Wang, Detang
    BONE, 2010, 47 : S421 - S421
  • [48] INTERCELLULAR COMMUNICATION IN CULTURED RABBIT GASTRIC EPITHELIAL-CELLS
    UEDA, F
    KYOI, T
    MIMURA, K
    KIMURA, K
    YAMAMOTO, M
    JAPANESE JOURNAL OF PHARMACOLOGY, 1991, 57 (03): : 321 - 328
  • [49] MODULATION OF INTERCELLULAR COMMUNICATION BETWEEN TRANSFORMED-CELLS BY COCULTIVATION WITH NONTRANSFORMED CELLS
    BOREIKO, CJ
    ABERNETHY, DJ
    STEDMAN, DB
    PROCEEDINGS OF THE AMERICAN ASSOCIATION FOR CANCER RESEARCH, 1988, 29 : 112 - 112
  • [50] Differential gap junctional intercellular communication between melanoma cells and cells in their microenvironment
    Haass, N
    Brandner, J
    Brafford, P
    Wladykowski, E
    Kazianis, S
    Moll, I
    Herlyn, M
    JOURNAL OF INVESTIGATIVE DERMATOLOGY, 2005, 125 (03) : A53 - A53
12345