Enablers and challenges of spatial omics, a melting pot of technologies

被引:12
作者
Alexandrov, Theodore [1 ,2 ,3 ]
Saez-Rodriguez, Julio [2 ,4 ,5 ]
Saka, Sinem K. [6 ]
机构
[1] European Mol Biol Lab, Struct & Computat Biol Unit, Heidelberg, Germany
[2] European Mol Biol Lab, Mol Med Partnership Unit, Heidelberg, Germany
[3] BioInnovat Inst, Copenhagen, Denmark
[4] Heidelberg Univ, Fac Med, Heidelberg, Germany
[5] Heidelberg Univ, Heidelberg Univ Hosp, Inst Computat Biomed, Heidelberg, Germany
[6] European Mol Biol Lab, Genome Biol Unit, Heidelberg, Germany
基金
欧洲研究理事会;
关键词
genomics; metabolomics; proteomics; spatial omics; transcriptomics; IMAGING MASS-SPECTROMETRY; HYBRIDIZATION CHAIN-REACTION; GENOME-WIDE EXPRESSION; IN-SITU; GENE-EXPRESSION; TISSUE-SECTIONS; SINGLE CELLS; RNA-ANALYSIS; DESIGN; RESOLUTION;
D O I
10.15252/msb.202110571
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved information for any omics data type on spatial scales ranging from subcellular to organismal. From a technology development perspective, spatial omics is a highly interdisciplinary field that integrates imaging and omics, spatial and molecular analyses, sequencing and mass spectrometry, and image analysis and bioinformatics. The emergence of this field has not only opened a window into spatial biology, but also created multiple novel opportunities, questions, and challenges for method developers. Here, we provide the perspective of technology developers on what makes the spatial omics field unique. After providing a brief overview of the state of the art, we discuss technological enablers and challenges and present our vision about the future applications and impact of this melting pot. This Review discusses the spatial omics field from the point of view of technology developers. It provides an overview of the state of the art, discusses technological enablers and challenges and presents a vision about the future applications and impact of spatial omics technologies.image
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页数:16
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共 235 条
  • [1] High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin
    Achim, Kaia
    Pettit, Jean-Baptiste
    Saraiva, Luis R.
    Gavriouchkina, Daria
    Larsson, Tomas
    Arendt, Detlev
    Marioni, John C.
    [J]. NATURE BIOTECHNOLOGY, 2015, 33 (05) : 503 - U215
  • [2] DNA-barcoded labeling probes for highly multiplexed Exchange-PAINT imaging
    Agasti, Sarit S.
    Wang, Yu
    Schueder, Florian
    Sukumar, Aishwarya
    Jungmann, Ralf
    Yin, Peng
    [J]. CHEMICAL SCIENCE, 2017, 8 (04) : 3080 - 3091
  • [3] Alexandrov T., 2019, BIORXIV, DOI DOI 10.1101/539478
  • [4] Spatial Metabolomics and Imaging Mass Spectrometry in the Age of Artificial Intelligence
    Alexandrov, Theodore
    [J]. ANNUAL REVIEW OF BIOMEDICAL DATA SCIENCE, VOL 3, 2020, 2020, 3 : 61 - 87
  • [5] Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems
    Alon, Shahar
    Goodwin, Daniel R.
    Sinha, Anubhav
    Wassie, Asmamaw T.
    Chen, Fei
    Daugharthy, Evan R.
    Bando, Yosuke
    Kajita, Atsushi
    Xue, Andrew G.
    Marrett, Karl
    Prior, Robert
    Cui, Yi
    Payne, Andrew C.
    Yao, Chun-Chen
    Suk, Ho-Jun
    Wang, Ru
    Yu, Chih-Chieh
    Tillberg, Paul
    Reginato, Paul
    Pak, Nikita
    Liu, Songlei
    Punthambaker, Sukanya
    Iyer, Eswar P. R.
    Kohman, Richie E.
    Miller, Jeremy A.
    Lein, Ed S.
    Lako, Ana
    Cullen, Nicole
    Rodig, Scott
    Helvie, Karla
    Abravanel, Daniel L.
    Wagle, Nikhil
    Johnson, Bruce E.
    Klughammer, Johanna
    Slyper, Michal
    Waldman, Julia
    Jane-Valbuena, Judit
    Rozenblatt-Rosen, Orit
    Regev, Aviv
    Church, George M.
    Marblestone, Adam H.
    Boyden, Edward S.
    [J]. SCIENCE, 2021, 371 (6528) : 481 - +
  • [6] Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography
    Andersson, Alma
    Bergenstrahle, Joseph
    Asp, Michaela
    Bergenstrahle, Ludvig
    Jurek, Aleksandra
    Fernandez Navarro, Jose
    Lundeberg, Joakim
    [J]. COMMUNICATIONS BIOLOGY, 2020, 3 (01)
  • [7] Multiplexed ion beam imaging of human breast tumors
    Angelo, Michael
    Bendall, Sean C.
    Finck, Rachel
    Hale, Matthew B.
    Hitzman, Chuck
    Borowsky, Alexander D.
    Levenson, Richard M.
    Lowe, John B.
    Liu, Scot D.
    Zhao, Shuchun
    Natkunam, Yasodha
    Nolan, Garry P.
    [J]. NATURE MEDICINE, 2014, 20 (04) : 436 - +
  • [8] LungMAP: The Molecular Atlas of Lung Development Program
    Ardini-Poleske, Maryanne E.
    Clark, Robert F.
    Ansong, Charles
    Carson, James P.
    Corley, Richard A.
    Deutsch, Gail H.
    Hagood, James S.
    Kaminski, Naftali
    Mariani, Thomas J.
    Potter, Steven S.
    Pryhuber, Gloria S.
    Warburton, David
    Whitsett, Jeffrey A.
    Palmer, Scott M.
    Ambalavanan, Namasivayam
    [J]. AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY, 2017, 313 (05) : L733 - L740
  • [9] Computational principles and challenges in single-cell data integration
    Argelaguet, Ricard
    Cuomo, Anna S. E.
    Stegle, Oliver
    Marioni, John C.
    [J]. NATURE BIOTECHNOLOGY, 2021, 39 (10) : 1202 - 1215
  • [10] Deciphering cell-cell interactions and communication from gene expression
    Armingol, Erick
    Officer, Adam
    Harismendy, Olivier
    Lewis, Nathan E.
    [J]. NATURE REVIEWS GENETICS, 2021, 22 (02) : 71 - 88