Neighbor-specific gene expression revealed from physically interacting cells during mouse embryonic development

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Standard

Neighbor-specific gene expression revealed from physically interacting cells during mouse embryonic development. / Kim, Junil; Rothová, Michaela Mrugala; Madan, Esha; Rhee, Siyeon; Weng, Guangzheng; Palma, António M.; Liao, Linbu; David, Eyal; Amit, Ido; Hajkarim, Morteza Chalabi; Vudatha, Vignesh; Gutiérrez-García, Andrés; Moreno, Eduardo; Winn, Robert; Trevino, Jose; Fisher, Paul B.; Brickman, Joshua M.; Gogna, Rajan; Won, Kyoung Jae.

I: Proceedings of the National Academy of Sciences of the United States of America, Bind 120, Nr. 2, e2205371120, 2023.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Kim, J, Rothová, MM, Madan, E, Rhee, S, Weng, G, Palma, AM, Liao, L, David, E, Amit, I, Hajkarim, MC, Vudatha, V, Gutiérrez-García, A, Moreno, E, Winn, R, Trevino, J, Fisher, PB, Brickman, JM, Gogna, R & Won, KJ 2023, 'Neighbor-specific gene expression revealed from physically interacting cells during mouse embryonic development', Proceedings of the National Academy of Sciences of the United States of America, bind 120, nr. 2, e2205371120. https://doi.org/10.1073/pnas.2205371120

APA

Kim, J., Rothová, M. M., Madan, E., Rhee, S., Weng, G., Palma, A. M., Liao, L., David, E., Amit, I., Hajkarim, M. C., Vudatha, V., Gutiérrez-García, A., Moreno, E., Winn, R., Trevino, J., Fisher, P. B., Brickman, J. M., Gogna, R., & Won, K. J. (2023). Neighbor-specific gene expression revealed from physically interacting cells during mouse embryonic development. Proceedings of the National Academy of Sciences of the United States of America, 120(2), [e2205371120]. https://doi.org/10.1073/pnas.2205371120

Vancouver

Kim J, Rothová MM, Madan E, Rhee S, Weng G, Palma AM o.a. Neighbor-specific gene expression revealed from physically interacting cells during mouse embryonic development. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(2). e2205371120. https://doi.org/10.1073/pnas.2205371120

Author

Kim, Junil ; Rothová, Michaela Mrugala ; Madan, Esha ; Rhee, Siyeon ; Weng, Guangzheng ; Palma, António M. ; Liao, Linbu ; David, Eyal ; Amit, Ido ; Hajkarim, Morteza Chalabi ; Vudatha, Vignesh ; Gutiérrez-García, Andrés ; Moreno, Eduardo ; Winn, Robert ; Trevino, Jose ; Fisher, Paul B. ; Brickman, Joshua M. ; Gogna, Rajan ; Won, Kyoung Jae. / Neighbor-specific gene expression revealed from physically interacting cells during mouse embryonic development. I: Proceedings of the National Academy of Sciences of the United States of America. 2023 ; Bind 120, Nr. 2.

Bibtex

@article{3b08eb9597b8413888c45610eecba14e,

title = "Neighbor-specific gene expression revealed from physically interacting cells during mouse embryonic development",

abstract = "Development of multicellular organisms is orchestrated by persistent cell–cell communication between neighboring partners. Direct interaction between different cell types can induce molecular signals that dictate lineage specification and cell fate decisions. Current single-cell RNA-seq technology cannot adequately analyze cell–cell contact-dependent gene expression, mainly due to the loss of spatial information. To overcome this obstacle and resolve cell–cell contact-specific gene expression during embryogenesis, we performed RNA sequencing of physically interacting cells (PIC-seq) and assessed them alongside similar single-cell transcriptomes derived from developing mouse embryos between embryonic day (E) 7.5 and E9.5. Analysis of the PIC-seq data identified gene expression signatures that were dependent on the presence of specific neighboring cell types. Our computational predictions, validated experimentally, demonstrated that neural progenitor (NP) cells upregulate Lhx5 and Nkx2-1 genes, when exclusively interacting with definitive endoderm (DE) cells. Moreover, there was a reciprocal impact on the transcriptome of DE cells, as they tend to upregulate Rax and Gsc when in contact with NP cells. Using individual cell transcriptome data, we formulated a means of computationally predicting the impact of one cell type on the transcriptome of its neighboring cell types. We have further developed a distinctive spatial-t-distributed stochastic neighboring embedding to display the pseudospatial distribution of cells in a 2-dimensional space. In summary, we describe an innovative approach to study contact-specific gene regulation during embryogenesis.",

keywords = "contact-specific expression, mouse embryonic development, PIC-seq, single-cell RNA sequencing, spatial-tSNE",

author = "Junil Kim and Rothov{\'a}, {Michaela Mrugala} and Esha Madan and Siyeon Rhee and Guangzheng Weng and Palma, {Ant{\'o}nio M.} and Linbu Liao and Eyal David and Ido Amit and Hajkarim, {Morteza Chalabi} and Vignesh Vudatha and Andr{\'e}s Guti{\'e}rrez-Garc{\'i}a and Eduardo Moreno and Robert Winn and Jose Trevino and Fisher, {Paul B.} and Brickman, {Joshua M.} and Rajan Gogna and Won, {Kyoung Jae}",

note = "Publisher Copyright: Copyright {\textcopyright} 2023 the Author(s).",

year = "2023",

doi = "10.1073/pnas.2205371120",

language = "English",

volume = "120",

journal = "Proceedings of the National Academy of Sciences of the United States of America",

issn = "0027-8424",

publisher = "The National Academy of Sciences of the United States of America",

number = "2",

}

RIS

TY - JOUR

T1 - Neighbor-specific gene expression revealed from physically interacting cells during mouse embryonic development

AU - Kim, Junil

AU - Rothová, Michaela Mrugala

AU - Madan, Esha

AU - Rhee, Siyeon

AU - Weng, Guangzheng

AU - Palma, António M.

AU - Liao, Linbu

AU - David, Eyal

AU - Amit, Ido

AU - Hajkarim, Morteza Chalabi

AU - Vudatha, Vignesh

AU - Gutiérrez-García, Andrés

AU - Moreno, Eduardo

AU - Winn, Robert

AU - Trevino, Jose

AU - Fisher, Paul B.

AU - Brickman, Joshua M.

AU - Gogna, Rajan

AU - Won, Kyoung Jae

PY - 2023

Y1 - 2023

N2 - Development of multicellular organisms is orchestrated by persistent cell–cell communication between neighboring partners. Direct interaction between different cell types can induce molecular signals that dictate lineage specification and cell fate decisions. Current single-cell RNA-seq technology cannot adequately analyze cell–cell contact-dependent gene expression, mainly due to the loss of spatial information. To overcome this obstacle and resolve cell–cell contact-specific gene expression during embryogenesis, we performed RNA sequencing of physically interacting cells (PIC-seq) and assessed them alongside similar single-cell transcriptomes derived from developing mouse embryos between embryonic day (E) 7.5 and E9.5. Analysis of the PIC-seq data identified gene expression signatures that were dependent on the presence of specific neighboring cell types. Our computational predictions, validated experimentally, demonstrated that neural progenitor (NP) cells upregulate Lhx5 and Nkx2-1 genes, when exclusively interacting with definitive endoderm (DE) cells. Moreover, there was a reciprocal impact on the transcriptome of DE cells, as they tend to upregulate Rax and Gsc when in contact with NP cells. Using individual cell transcriptome data, we formulated a means of computationally predicting the impact of one cell type on the transcriptome of its neighboring cell types. We have further developed a distinctive spatial-t-distributed stochastic neighboring embedding to display the pseudospatial distribution of cells in a 2-dimensional space. In summary, we describe an innovative approach to study contact-specific gene regulation during embryogenesis.

AB - Development of multicellular organisms is orchestrated by persistent cell–cell communication between neighboring partners. Direct interaction between different cell types can induce molecular signals that dictate lineage specification and cell fate decisions. Current single-cell RNA-seq technology cannot adequately analyze cell–cell contact-dependent gene expression, mainly due to the loss of spatial information. To overcome this obstacle and resolve cell–cell contact-specific gene expression during embryogenesis, we performed RNA sequencing of physically interacting cells (PIC-seq) and assessed them alongside similar single-cell transcriptomes derived from developing mouse embryos between embryonic day (E) 7.5 and E9.5. Analysis of the PIC-seq data identified gene expression signatures that were dependent on the presence of specific neighboring cell types. Our computational predictions, validated experimentally, demonstrated that neural progenitor (NP) cells upregulate Lhx5 and Nkx2-1 genes, when exclusively interacting with definitive endoderm (DE) cells. Moreover, there was a reciprocal impact on the transcriptome of DE cells, as they tend to upregulate Rax and Gsc when in contact with NP cells. Using individual cell transcriptome data, we formulated a means of computationally predicting the impact of one cell type on the transcriptome of its neighboring cell types. We have further developed a distinctive spatial-t-distributed stochastic neighboring embedding to display the pseudospatial distribution of cells in a 2-dimensional space. In summary, we describe an innovative approach to study contact-specific gene regulation during embryogenesis.

KW - contact-specific expression

KW - mouse embryonic development

KW - PIC-seq

KW - single-cell RNA sequencing

KW - spatial-tSNE

U2 - 10.1073/pnas.2205371120

DO - 10.1073/pnas.2205371120

M3 - Journal article

C2 - 36595695

AN - SCOPUS:85145429535

VL - 120

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

SN - 0027-8424

IS - 2

M1 - e2205371120

ER -

ID: 372960045