Spatially resolved transcriptomics and beyond

被引:369
作者
Crosetto, Nicola
Bienko, Magda
van Oudenaarden, Alexander
机构
[1] Royal Netherlands Acad Arts & Sci, Hubrecht Inst, KNAW, NL-3584 CT Utrecht, Netherlands
[2] Univ Med Ctr Utrecht, NL-3584 CT Utrecht, Netherlands
基金
欧洲研究理事会;
关键词
CELL RNA-SEQ; IN-SITU; GENOME-WIDE; INTRATUMOR HETEROGENEITY; OLIGONUCLEOTIDE PROBES; TUMOR HETEROGENEITY; IMAGE-ANALYSIS; SINGLE; RESOLUTION; EXPRESSION;
D O I
10.1038/nrg3832
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Considerable progress in sequencing technologies makes it now possible to study the genomic and transcriptomic landscape of single cells. However, to better understand the complexity of multicellular organisms, we must devise ways to perform high-throughput measurements while preserving spatial information about the tissue context or subcellular localization of analysed nucleic acids. In this Innovation article, we summarize pioneering technologies that enable spatially resolved transcriptomics and discuss how these methods have the potential to extend beyond transcriptomics to encompass spatially resolved genomics, proteomics and possibly other omic disciplines.
引用
收藏
页码:57 / 66
页数:10
相关论文
共 96 条
[1]  
AGARD DA, 1989, METHOD CELL BIOL, V30, P353
[2]   Genetic and Phenotypic Diversity in Breast Tumor Metastases [J].
Almendro, Vanessa ;
Kim, Hee Jung ;
Cheng, Yu-Kang ;
Goenen, Mithat ;
Itzkovitz, Shalev ;
Argani, Pedram ;
van Oudenaarden, Alexander ;
Sukumar, Saraswati ;
Michor, Franziska ;
Polyak, Kornelia .
CANCER RESEARCH, 2014, 74 (05) :1338-1348
[3]   Inference of Tumor Evolution during Chemotherapy by Computational Modeling and In Situ Analysis of Genetic and Phenotypic Cellular Diversity [J].
Almendro, Vanessa ;
Cheng, Yu-Kang ;
Randles, Amanda ;
Itzkovitz, Shalev ;
Marusyk, Andriy ;
Ametller, Elisabet ;
Gonzalez-Farre, Xavier ;
Munoz, Montse ;
Russnes, Hege G. ;
Helland, Aslaug ;
Rye, Inga H. ;
Borresen-Dale, Anne-Lise ;
Maruyama, Reo ;
van Oudenaarden, Alexander ;
Dowsett, Mitchell ;
Jones, Robin L. ;
Reis-Filho, Jorge ;
Gascon, Pere ;
Goenen, Mithat ;
Michor, Franziska ;
Polyak, Kornelia .
CELL REPORTS, 2014, 6 (03) :514-527
[4]   Multiplexed ion beam imaging of human breast tumors [J].
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. .
NATURE MEDICINE, 2014, 20 (04) :436-+
[5]   Image-based transcriptomics in thousands of single human cells at single-molecule resolution [J].
Battich, Nico ;
Stoeger, Thomas ;
Pelkmans, Lucas .
NATURE METHODS, 2013, 10 (11) :1127-1133
[6]   Tumour heterogeneity in the clinic [J].
Bedard, Philippe L. ;
Hansen, Aaron R. ;
Ratain, Mark J. ;
Siu, Lillian L. .
NATURE, 2013, 501 (7467) :355-364
[7]   Can some patients avoid adjuvant chemotherapy for early-stage breast cancer? [J].
Bedard, Philippe L. ;
Cardoso, Fatima .
NATURE REVIEWS CLINICAL ONCOLOGY, 2011, 8 (05) :272-279
[8]   Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes [J].
Beliveau, Brian J. ;
Joyce, Eric F. ;
Apostolopoulos, Nicholas ;
Yilmaz, Feyza ;
Fonseka, Chamith Y. ;
McCole, Ruth B. ;
Chang, Yiming ;
Li, Jin Billy ;
Senaratne, Tharanga Niroshini ;
Williams, Benjamin R. ;
Rouillard, Jean-Marie ;
Wu, Chao-ting .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2012, 109 (52) :21301-21306
[9]   Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum [J].
Bendall, Sean C. ;
Simonds, Erin F. ;
Qiu, Peng ;
Amir, El-ad D. ;
Krutzik, Peter O. ;
Finck, Rachel ;
Bruggner, Robert V. ;
Melamed, Rachel ;
Trejo, Angelica ;
Ornatsky, Olga I. ;
Balderas, Robert S. ;
Plevritis, Sylvia K. ;
Sachs, Karen ;
Pe'er, Dana ;
Tanner, Scott D. ;
Nolan, Garry P. .
SCIENCE, 2011, 332 (6030) :687-696
[10]   Localization of ASH1 mRNA particles in living yeast [J].
Bertrand, E ;
Chartrand, P ;
Schaefer, M ;
Shenoy, SM ;
Singer, RH ;
Long, RM .
MOLECULAR CELL, 1998, 2 (04) :437-445