Literature DB >> 35859028

The emerging landscape of spatial profiling technologies.

Jeffrey R Moffitt1,2, Emma Lundberg3,4,5,6, Holger Heyn7,8.   

Abstract

Improved scale, multiplexing and resolution are establishing spatial nucleic acid and protein profiling methods as a major pillar for cellular atlas building of complex samples, from tissues to full organisms. Emerging methods yield omics measurements at resolutions covering the nano- to microscale, enabling the charting of cellular heterogeneity, complex tissue architectures and dynamic changes during development and disease. We present an overview of the developing landscape of in situ spatial genome, transcriptome and proteome technologies, exemplify their impact on cell biology and translational research, and discuss current challenges for their community-wide adoption. Among many transformative applications, we envision that spatial methods will map entire organs and enable next-generation pathology.
© 2022. Springer Nature Limited.

Entities:  

Year:  2022        PMID： 35859028     DOI： 10.1038/s41576-022-00515-3

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN： 1471-0056            Impact factor:   59.581


  186 in total

1.  Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas.

Authors:  Reuben Moncada; Dalia Barkley; Florian Wagner; Marta Chiodin; Joseph C Devlin; Maayan Baron; Cristina H Hajdu; Diane M Simeone; Itai Yanai
Journal:  Nat Biotechnol       Date:  2020-01-13       Impact factor: 54.908

2.  Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma.

Authors:  Kim Thrane; Hanna Eriksson; Jonas Maaskola; Johan Hansson; Joakim Lundeberg
Journal:  Cancer Res       Date:  2018-08-28       Impact factor: 12.701

3.  Spatiotemporal Immune Landscape of Colorectal Cancer Liver Metastasis at Single-Cell Level.

Authors:  Yingcheng Wu; Shuaixi Yang; Jiaqiang Ma; Zechuan Chen; Guohe Song; Dongning Rao; Yifei Cheng; Siyuan Huang; Yifei Liu; Shan Jiang; Jinxia Liu; Xiaowu Huang; Xiaoying Wang; Shuangjian Qiu; Jianmin Xu; Ruibin Xi; Fan Bai; Jian Zhou; Jia Fan; Xiaoming Zhang; Qiang Gao
Journal:  Cancer Discov       Date:  2021-08-20       Impact factor: 39.397

Review 4.  Single-cell atlases: shared and tissue-specific cell types across human organs.

Authors:  Rasa Elmentaite; Cecilia Domínguez Conde; Lu Yang; Sarah A Teichmann
Journal:  Nat Rev Genet       Date:  2022-02-25       Impact factor: 59.581

5.  Cells of the human intestinal tract mapped across space and time.

Authors:  Rasa Elmentaite; Natsuhiko Kumasaka; Kenny Roberts; Aaron Fleming; Emma Dann; Hamish W King; Vitalii Kleshchevnikov; Monika Dabrowska; Sophie Pritchard; Liam Bolt; Sara F Vieira; Lira Mamanova; Ni Huang; Francesca Perrone; Issac Goh Kai'En; Steven N Lisgo; Matilda Katan; Steven Leonard; Thomas R W Oliver; C Elizabeth Hook; Komal Nayak; Lia S Campos; Cecilia Domínguez Conde; Emily Stephenson; Justin Engelbert; Rachel A Botting; Krzysztof Polanski; Stijn van Dongen; Minal Patel; Michael D Morgan; John C Marioni; Omer Ali Bayraktar; Kerstin B Meyer; Xiaoling He; Roger A Barker; Holm H Uhlig; Krishnaa T Mahbubani; Kourosh Saeb-Parsy; Matthias Zilbauer; Menna R Clatworthy; Muzlifah Haniffa; Kylie R James; Sarah A Teichmann
Journal:  Nature       Date:  2021-09-08       Impact factor: 69.504

6.  A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.

Authors:  Michaela Asp; Stefania Giacomello; Ludvig Larsson; Chenglin Wu; Daniel Fürth; Xiaoyan Qian; Eva Wärdell; Joaquin Custodio; Johan Reimegård; Fredrik Salmén; Cecilia Österholm; Patrik L Ståhl; Erik Sundström; Elisabet Åkesson; Olaf Bergmann; Magda Bienko; Agneta Månsson-Broberg; Mats Nilsson; Christer Sylvén; Joakim Lundeberg
Journal:  Cell       Date:  2019-12-12       Impact factor: 41.582

7.  Spatiotemporal analysis of human intestinal development at single-cell resolution.

Authors:  David Fawkner-Corbett; Agne Antanaviciute; Kaushal Parikh; Marta Jagielowicz; Ana Sousa Gerós; Tarun Gupta; Neil Ashley; Doran Khamis; Darren Fowler; Edward Morrissey; Chris Cunningham; Paul R V Johnson; Hashem Koohy; Alison Simmons
Journal:  Cell       Date:  2021-01-05       Impact factor: 41.582

8.  Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma.

Authors:  Andrew L Ji; Adam J Rubin; Kim Thrane; Sizun Jiang; David L Reynolds; Robin M Meyers; Margaret G Guo; Benson M George; Annelie Mollbrink; Joseph Bergenstråhle; Ludvig Larsson; Yunhao Bai; Bokai Zhu; Aparna Bhaduri; Jordan M Meyers; Xavier Rovira-Clavé; S Tyler Hollmig; Sumaira Z Aasi; Garry P Nolan; Joakim Lundeberg; Paul A Khavari
Journal:  Cell       Date:  2020-06-23       Impact factor: 41.582

9.  A single-cell tumor immune atlas for precision oncology.

Authors:  Paula Nieto; Marc Elosua-Bayes; Juan L Trincado; Domenica Marchese; Ramon Massoni-Badosa; Maria Salvany; Ana Henriques; Juan Nieto; Sergio Aguilar-Fernández; Elisabetta Mereu; Catia Moutinho; Sara Ruiz; Patricia Lorden; Vanessa T Chin; Dominik Kaczorowski; Chia-Ling Chan; Richard Gallagher; Angela Chou; Ester Planas-Rigol; Carlota Rubio-Perez; Ivo Gut; Josep M Piulats; Joan Seoane; Joseph E Powell; Eduard Batlle; Holger Heyn
Journal:  Genome Res       Date:  2021-09-21       Impact factor: 9.043

10.  Cells of the adult human heart.

Authors:  Monika Litviňuková; Carlos Talavera-López; Henrike Maatz; Daniel Reichart; Catherine L Worth; Eric L Lindberg; Masatoshi Kanda; Krzysztof Polanski; Matthias Heinig; Michael Lee; Emily R Nadelmann; Kenny Roberts; Liz Tuck; Eirini S Fasouli; Daniel M DeLaughter; Barbara McDonough; Hiroko Wakimoto; Joshua M Gorham; Sara Samari; Krishnaa T Mahbubani; Kourosh Saeb-Parsy; Giannino Patone; Joseph J Boyle; Hongbo Zhang; Hao Zhang; Anissa Viveiros; Gavin Y Oudit; Omer Ali Bayraktar; J G Seidman; Christine E Seidman; Michela Noseda; Norbert Hubner; Sarah A Teichmann
Journal:  Nature       Date:  2020-09-24       Impact factor: 49.962
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  1 in total

1.  Identification of spatially variable genes with graph cuts.

Authors:  Ke Zhang; Wanwan Feng; Peng Wang
Journal:  Nat Commun       Date:  2022-09-19       Impact factor: 17.694
  1 in total

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