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The spatial transcriptomic landscape of the healing mouse intestine following damage

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The spatial transcriptomic landscape of the healing mouse intestine following damage. / Parigi, Sara M; Larsson, Ludvig; Das, Srustidhar; Ramirez Flores, Ricardo O; Frede, Annika; Tripathi, Kumar P; Diaz, Oscar E; Selin, Katja; Morales, Rodrigo A; Luo, Xinxin; Monasterio, Gustavo; Engblom, Camilla; Gagliani, Nicola; Saez-Rodriguez, Julio; Lundeberg, Joakim; Villablanca, Eduardo J.

In: NAT COMMUN, Vol. 13, No. 1, 828, 11.02.2022.

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

Harvard

Parigi, SM, Larsson, L, Das, S, Ramirez Flores, RO, Frede, A, Tripathi, KP, Diaz, OE, Selin, K, Morales, RA, Luo, X, Monasterio, G, Engblom, C, Gagliani, N, Saez-Rodriguez, J, Lundeberg, J & Villablanca, EJ 2022, 'The spatial transcriptomic landscape of the healing mouse intestine following damage', NAT COMMUN, vol. 13, no. 1, 828. https://doi.org/10.1038/s41467-022-28497-0

APA

Parigi, S. M., Larsson, L., Das, S., Ramirez Flores, R. O., Frede, A., Tripathi, K. P., Diaz, O. E., Selin, K., Morales, R. A., Luo, X., Monasterio, G., Engblom, C., Gagliani, N., Saez-Rodriguez, J., Lundeberg, J., & Villablanca, E. J. (2022). The spatial transcriptomic landscape of the healing mouse intestine following damage. NAT COMMUN, 13(1), [828]. https://doi.org/10.1038/s41467-022-28497-0

Vancouver

Parigi SM, Larsson L, Das S, Ramirez Flores RO, Frede A, Tripathi KP et al. The spatial transcriptomic landscape of the healing mouse intestine following damage. NAT COMMUN. 2022 Feb 11;13(1). 828. https://doi.org/10.1038/s41467-022-28497-0

Bibtex

@article{787232492d014586a8d395b78667b38a,
title = "The spatial transcriptomic landscape of the healing mouse intestine following damage",
abstract = "The intestinal barrier is composed of a complex cell network defining highly compartmentalized and specialized structures. Here, we use spatial transcriptomics to define how the transcriptomic landscape is spatially organized in the steady state and healing murine colon. At steady state conditions, we demonstrate a previously unappreciated molecular regionalization of the colon, which dramatically changes during mucosal healing. Here, we identified spatially-organized transcriptional programs defining compartmentalized mucosal healing, and regions with dominant wired pathways. Furthermore, we showed that decreased p53 activation defined areas with increased presence of proliferating epithelial stem cells. Finally, we mapped transcriptomics modules associated with human diseases demonstrating the translational potential of our dataset. Overall, we provide a publicly available resource defining principles of transcriptomic regionalization of the colon during mucosal healing and a framework to develop and progress further hypotheses.",
keywords = "Animals, Colon/metabolism, Disease Models, Animal, Epithelial Cells, Female, Intestinal Mucosa/metabolism, Intestines/metabolism, Mice, Mice, Inbred C57BL, Mice, Neurologic Mutants, Signal Transduction, Transcriptome, Wound Healing",
author = "Parigi, {Sara M} and Ludvig Larsson and Srustidhar Das and {Ramirez Flores}, {Ricardo O} and Annika Frede and Tripathi, {Kumar P} and Diaz, {Oscar E} and Katja Selin and Morales, {Rodrigo A} and Xinxin Luo and Gustavo Monasterio and Camilla Engblom and Nicola Gagliani and Julio Saez-Rodriguez and Joakim Lundeberg and Villablanca, {Eduardo J}",
note = "{\textcopyright} 2022. The Author(s).",
year = "2022",
month = feb,
day = "11",
doi = "10.1038/s41467-022-28497-0",
language = "English",
volume = "13",
journal = "NAT COMMUN",
issn = "2041-1723",
publisher = "NATURE PUBLISHING GROUP",
number = "1",

}

RIS

TY - JOUR

T1 - The spatial transcriptomic landscape of the healing mouse intestine following damage

AU - Parigi, Sara M

AU - Larsson, Ludvig

AU - Das, Srustidhar

AU - Ramirez Flores, Ricardo O

AU - Frede, Annika

AU - Tripathi, Kumar P

AU - Diaz, Oscar E

AU - Selin, Katja

AU - Morales, Rodrigo A

AU - Luo, Xinxin

AU - Monasterio, Gustavo

AU - Engblom, Camilla

AU - Gagliani, Nicola

AU - Saez-Rodriguez, Julio

AU - Lundeberg, Joakim

AU - Villablanca, Eduardo J

N1 - © 2022. The Author(s).

PY - 2022/2/11

Y1 - 2022/2/11

N2 - The intestinal barrier is composed of a complex cell network defining highly compartmentalized and specialized structures. Here, we use spatial transcriptomics to define how the transcriptomic landscape is spatially organized in the steady state and healing murine colon. At steady state conditions, we demonstrate a previously unappreciated molecular regionalization of the colon, which dramatically changes during mucosal healing. Here, we identified spatially-organized transcriptional programs defining compartmentalized mucosal healing, and regions with dominant wired pathways. Furthermore, we showed that decreased p53 activation defined areas with increased presence of proliferating epithelial stem cells. Finally, we mapped transcriptomics modules associated with human diseases demonstrating the translational potential of our dataset. Overall, we provide a publicly available resource defining principles of transcriptomic regionalization of the colon during mucosal healing and a framework to develop and progress further hypotheses.

AB - The intestinal barrier is composed of a complex cell network defining highly compartmentalized and specialized structures. Here, we use spatial transcriptomics to define how the transcriptomic landscape is spatially organized in the steady state and healing murine colon. At steady state conditions, we demonstrate a previously unappreciated molecular regionalization of the colon, which dramatically changes during mucosal healing. Here, we identified spatially-organized transcriptional programs defining compartmentalized mucosal healing, and regions with dominant wired pathways. Furthermore, we showed that decreased p53 activation defined areas with increased presence of proliferating epithelial stem cells. Finally, we mapped transcriptomics modules associated with human diseases demonstrating the translational potential of our dataset. Overall, we provide a publicly available resource defining principles of transcriptomic regionalization of the colon during mucosal healing and a framework to develop and progress further hypotheses.

KW - Animals

KW - Colon/metabolism

KW - Disease Models, Animal

KW - Epithelial Cells

KW - Female

KW - Intestinal Mucosa/metabolism

KW - Intestines/metabolism

KW - Mice

KW - Mice, Inbred C57BL

KW - Mice, Neurologic Mutants

KW - Signal Transduction

KW - Transcriptome

KW - Wound Healing

U2 - 10.1038/s41467-022-28497-0

DO - 10.1038/s41467-022-28497-0

M3 - SCORING: Journal article

C2 - 35149721

VL - 13

JO - NAT COMMUN

JF - NAT COMMUN

SN - 2041-1723

IS - 1

M1 - 828

ER -