Spatial proteomics in three-dimensional intact specimens

Research output: Contribution to journal › Journal article › Research › peer-review

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Spatial proteomics in three-dimensional intact specimens. / Bhatia, Harsharan Singh; Brunner, Andreas-David; Öztürk, Furkan; Kapoor, Saketh; Rong, Zhouyi; Mai, Hongcheng; Thielert, Marvin; Ali, Mayar; Al-Maskari, Rami; Paetzold, Johannes Christian; Kofler, Florian; Todorov, Mihail Ivilinov; Molbay, Muge; Kolabas, Zeynep Ilgin; Negwer, Moritz; Hoeher, Luciano; Steinke, Hanno; Dima, Alina; Gupta, Basavdatta; Kaltenecker, Doris; Caliskan, Özüm Sehnaz; Brandt, Daniel; Krahmer, Natalie; Müller, Stephan; Lichtenthaler, Stefan Frieder; Hellal, Farida; Bechmann, Ingo; Menze, Bjoern; Theis, Fabian; Mann, Matthias; Ertürk, Ali.

In: Cell, Vol. 185, No. 26, 2022, p. 5040-5058.e19.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Bhatia, HS, Brunner, A-D, Öztürk, F, Kapoor, S, Rong, Z, Mai, H, Thielert, M, Ali, M, Al-Maskari, R, Paetzold, JC, Kofler, F, Todorov, MI, Molbay, M, Kolabas, ZI, Negwer, M, Hoeher, L, Steinke, H, Dima, A, Gupta, B, Kaltenecker, D, Caliskan, ÖS, Brandt, D, Krahmer, N, Müller, S, Lichtenthaler, SF, Hellal, F, Bechmann, I, Menze, B, Theis, F, Mann, M & Ertürk, A 2022, 'Spatial proteomics in three-dimensional intact specimens', Cell, vol. 185, no. 26, pp. 5040-5058.e19. https://doi.org/10.1016/j.cell.2022.11.021

APA

Bhatia, H. S., Brunner, A-D., Öztürk, F., Kapoor, S., Rong, Z., Mai, H., Thielert, M., Ali, M., Al-Maskari, R., Paetzold, J. C., Kofler, F., Todorov, M. I., Molbay, M., Kolabas, Z. I., Negwer, M., Hoeher, L., Steinke, H., Dima, A., Gupta, B., ... Ertürk, A. (2022). Spatial proteomics in three-dimensional intact specimens. Cell, 185(26), 5040-5058.e19. https://doi.org/10.1016/j.cell.2022.11.021

Vancouver

Bhatia HS, Brunner A-D, Öztürk F, Kapoor S, Rong Z, Mai H et al. Spatial proteomics in three-dimensional intact specimens. Cell. 2022;185(26):5040-5058.e19. https://doi.org/10.1016/j.cell.2022.11.021

Author

Bhatia, Harsharan Singh ; Brunner, Andreas-David ; Öztürk, Furkan ; Kapoor, Saketh ; Rong, Zhouyi ; Mai, Hongcheng ; Thielert, Marvin ; Ali, Mayar ; Al-Maskari, Rami ; Paetzold, Johannes Christian ; Kofler, Florian ; Todorov, Mihail Ivilinov ; Molbay, Muge ; Kolabas, Zeynep Ilgin ; Negwer, Moritz ; Hoeher, Luciano ; Steinke, Hanno ; Dima, Alina ; Gupta, Basavdatta ; Kaltenecker, Doris ; Caliskan, Özüm Sehnaz ; Brandt, Daniel ; Krahmer, Natalie ; Müller, Stephan ; Lichtenthaler, Stefan Frieder ; Hellal, Farida ; Bechmann, Ingo ; Menze, Bjoern ; Theis, Fabian ; Mann, Matthias ; Ertürk, Ali. / Spatial proteomics in three-dimensional intact specimens. In: Cell. 2022 ; Vol. 185, No. 26. pp. 5040-5058.e19.

Bibtex

@article{1c6e15a03fe24e1a85db03baa5ecce03,
title = "Spatial proteomics in three-dimensional intact specimens",
abstract = "Spatial molecular profiling of complex tissues is essential to investigate cellular function in physiological and pathological states. However, methods for molecular analysis of large biological specimens imaged in 3D are lacking. Here, we present DISCO-MS, a technology that combines whole-organ/whole-organism clearing and imaging, deep-learning-based image analysis, robotic tissue extraction, and ultra-high-sensitivity mass spectrometry. DISCO-MS yielded proteome data indistinguishable from uncleared samples in both rodent and human tissues. We used DISCO-MS to investigate microglia activation along axonal tracts after brain injury and characterized early- and late-stage individual amyloid-beta plaques in a mouse model of Alzheimer's disease. DISCO-bot robotic sample extraction enabled us to study the regional heterogeneity of immune cells in intact mouse bodies and aortic plaques in a complete human heart. DISCO-MS enables unbiased proteome analysis of preclinical and clinical tissues after unbiased imaging of entire specimens in 3D, identifying diagnostic and therapeutic opportunities for complex diseases. VIDEO ABSTRACT.",
keywords = "Mice, Humans, Animals, Proteome/analysis, Proteomics/methods, Alzheimer Disease/pathology, Amyloid beta-Peptides, Mass Spectrometry, Plaque, Amyloid",
author = "Bhatia, {Harsharan Singh} and Andreas-David Brunner and Furkan {\"O}zt{\"u}rk and Saketh Kapoor and Zhouyi Rong and Hongcheng Mai and Marvin Thielert and Mayar Ali and Rami Al-Maskari and Paetzold, {Johannes Christian} and Florian Kofler and Todorov, {Mihail Ivilinov} and Muge Molbay and Kolabas, {Zeynep Ilgin} and Moritz Negwer and Luciano Hoeher and Hanno Steinke and Alina Dima and Basavdatta Gupta and Doris Kaltenecker and Caliskan, {{\"O}z{\"u}m Sehnaz} and Daniel Brandt and Natalie Krahmer and Stephan M{\"u}ller and Lichtenthaler, {Stefan Frieder} and Farida Hellal and Ingo Bechmann and Bjoern Menze and Fabian Theis and Matthias Mann and Ali Ert{\"u}rk",
note = "Copyright {\textcopyright} 2022 Elsevier Inc. All rights reserved.",
year = "2022",
doi = "10.1016/j.cell.2022.11.021",
language = "English",
volume = "185",
pages = "5040--5058.e19",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "26",

}

RIS

TY - JOUR

T1 - Spatial proteomics in three-dimensional intact specimens

AU - Bhatia, Harsharan Singh

AU - Brunner, Andreas-David

AU - Öztürk, Furkan

AU - Kapoor, Saketh

AU - Rong, Zhouyi

AU - Mai, Hongcheng

AU - Thielert, Marvin

AU - Ali, Mayar

AU - Al-Maskari, Rami

AU - Paetzold, Johannes Christian

AU - Kofler, Florian

AU - Todorov, Mihail Ivilinov

AU - Molbay, Muge

AU - Kolabas, Zeynep Ilgin

AU - Negwer, Moritz

AU - Hoeher, Luciano

AU - Steinke, Hanno

AU - Dima, Alina

AU - Gupta, Basavdatta

AU - Kaltenecker, Doris

AU - Caliskan, Özüm Sehnaz

AU - Brandt, Daniel

AU - Krahmer, Natalie

AU - Müller, Stephan

AU - Lichtenthaler, Stefan Frieder

AU - Hellal, Farida

AU - Bechmann, Ingo

AU - Menze, Bjoern

AU - Theis, Fabian

AU - Mann, Matthias

AU - Ertürk, Ali

N1 - Copyright © 2022 Elsevier Inc. All rights reserved.

PY - 2022

Y1 - 2022

N2 - Spatial molecular profiling of complex tissues is essential to investigate cellular function in physiological and pathological states. However, methods for molecular analysis of large biological specimens imaged in 3D are lacking. Here, we present DISCO-MS, a technology that combines whole-organ/whole-organism clearing and imaging, deep-learning-based image analysis, robotic tissue extraction, and ultra-high-sensitivity mass spectrometry. DISCO-MS yielded proteome data indistinguishable from uncleared samples in both rodent and human tissues. We used DISCO-MS to investigate microglia activation along axonal tracts after brain injury and characterized early- and late-stage individual amyloid-beta plaques in a mouse model of Alzheimer's disease. DISCO-bot robotic sample extraction enabled us to study the regional heterogeneity of immune cells in intact mouse bodies and aortic plaques in a complete human heart. DISCO-MS enables unbiased proteome analysis of preclinical and clinical tissues after unbiased imaging of entire specimens in 3D, identifying diagnostic and therapeutic opportunities for complex diseases. VIDEO ABSTRACT.

AB - Spatial molecular profiling of complex tissues is essential to investigate cellular function in physiological and pathological states. However, methods for molecular analysis of large biological specimens imaged in 3D are lacking. Here, we present DISCO-MS, a technology that combines whole-organ/whole-organism clearing and imaging, deep-learning-based image analysis, robotic tissue extraction, and ultra-high-sensitivity mass spectrometry. DISCO-MS yielded proteome data indistinguishable from uncleared samples in both rodent and human tissues. We used DISCO-MS to investigate microglia activation along axonal tracts after brain injury and characterized early- and late-stage individual amyloid-beta plaques in a mouse model of Alzheimer's disease. DISCO-bot robotic sample extraction enabled us to study the regional heterogeneity of immune cells in intact mouse bodies and aortic plaques in a complete human heart. DISCO-MS enables unbiased proteome analysis of preclinical and clinical tissues after unbiased imaging of entire specimens in 3D, identifying diagnostic and therapeutic opportunities for complex diseases. VIDEO ABSTRACT.

KW - Mice

KW - Humans

KW - Animals

KW - Proteome/analysis

KW - Proteomics/methods

KW - Alzheimer Disease/pathology

KW - Amyloid beta-Peptides

KW - Mass Spectrometry

KW - Plaque, Amyloid

U2 - 10.1016/j.cell.2022.11.021

DO - 10.1016/j.cell.2022.11.021

M3 - Journal article

C2 - 36563667

VL - 185

SP - 5040-5058.e19

JO - Cell

JF - Cell

SN - 0092-8674

IS - 26

ER -

ID: 331590588