Conservation and divergence in the transcriptional programs of the human and mouse immune systems

Tal Shay; Vladimir Jojic; Or Zuk; Katherine Rothamel; David Puyraimond-Zemmour; Ting Feng; Ei Wakamatsu; Christophe Benoist; Daphne Koller; Aviv Regev; Paul Monach; Susan A Shinton; Richard R Hardy; Radu Jianu; David H Laidlaw; Jim J Collins; Roi Gazit; Brian S Garrison; Derrick J Rossi; Kavitha Narayan; Katelyn Sylvia; Joonsoo Kang; Anne Fletcher; Kutlu G Elpek; Angelique Bellemare-Pelletier; Deepali Malhotra; Shannon J Turley; Adam J Best; Jamie Knell; Ananda W Goldrath; Nadia R Cohen; Patrick J Brennan; Michael B Brenner; Taras Kreslavsky; Natalie A Bezman; Joseph C Sun; Charlie C Kim; Lewis L Lanier; Jennifer C Miller; Brian D Brown; Miriam Merad; Emmanuel L Gautier; Claudia V Jakubzick; Gwendalyn J Randolph; Francis S Kim; Tata N Rao; Amy Wagers; Tracy S P Heng; Michio W Painter; Jeffrey A Ericson; Scott P Davis; Ayla Ergun; Michael Mingueneau; Diane Mathis

doi:10.1073/pnas.1222738110

Conservation and divergence in the transcriptional programs of the human and mouse immune systems

Tal Shay, Vladimir Jojic, Or Zuk, Katherine Rothamel, David Puyraimond-Zemmour, Ting Feng, Ei Wakamatsu, Christophe Benoist, Daphne Koller, Aviv Regev, Paul Monach, Susan A Shinton, Richard R Hardy, Radu Jianu, David H Laidlaw, Jim J Collins, Roi Gazit, Brian S Garrison, Derrick J Rossi, Kavitha NarayanKatelyn Sylvia, Joonsoo Kang, Anne Fletcher, Kutlu G Elpek, Angelique Bellemare-Pelletier, Deepali Malhotra, Shannon J Turley, Adam J Best, Jamie Knell, Ananda W Goldrath, Nadia R Cohen, Patrick J Brennan, Michael B Brenner, Taras Kreslavsky, Natalie A Bezman, Joseph C Sun, Charlie C Kim, Lewis L Lanier, Jennifer C Miller, Brian D Brown, Miriam Merad, Emmanuel L Gautier, Claudia V Jakubzick, Gwendalyn J Randolph, Francis S Kim, Tata N Rao, Amy Wagers, Tracy S P Heng, Michio W Painter, Jeffrey A Ericson, Scott P Davis, Ayla Ergun, Michael Mingueneau, Diane Mathis

Research output: Contribution to journal › Article › Research › peer-review

292 Citations (Scopus)

Abstract

Much of the knowledge about cell differentiation and function in the immune system has come from studies in mice, but the relevance to human immunology, diseases, and therapy has been challenged, perhaps more from anecdotal than comprehensive evidence. To this end, we compare two large compendia of transcriptional profiles of human and mouse immune cell types. Global transcription profiles are conserved between corresponding cell lineages. The expression patterns of most orthologous genes are conserved, particularly for lineage-specific genes. However, several hundred genes show clearly divergent expression across the examined cell lineages, and among them, 169 genes did so even with highly stringent criteria. Finally, regulatory mechanisms--reflected by regulators differential expression or enriched cis-elements--are conserved between the species but to a lower degree, suggesting that distinct regulation may underlie some of the conserved transcriptional responses.

Original language	English
Pages (from-to)	2946 - 2951
Number of pages	6
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	110
Issue number	8
DOIs	https://doi.org/10.1073/pnas.1222738110
Publication status	Published - 2013
Externally published	Yes

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1073/pnas.1222738110

Cite this

Shay, T., Jojic, V., Zuk, O., Rothamel, K., Puyraimond-Zemmour, D., Feng, T., Wakamatsu, E., Benoist, C., Koller, D., Regev, A., Monach, P., Shinton, S. A., Hardy, R. R., Jianu, R., Laidlaw, D. H., Collins, J. J., Gazit, R., Garrison, B. S., Rossi, D. J., ... Mathis, D. (2013). Conservation and divergence in the transcriptional programs of the human and mouse immune systems. Proceedings of the National Academy of Sciences of the United States of America, 110(8), 2946 - 2951. https://doi.org/10.1073/pnas.1222738110

@article{29a6e7817d9c45e8816d95e6dd48fde1,

title = "Conservation and divergence in the transcriptional programs of the human and mouse immune systems",

abstract = "Much of the knowledge about cell differentiation and function in the immune system has come from studies in mice, but the relevance to human immunology, diseases, and therapy has been challenged, perhaps more from anecdotal than comprehensive evidence. To this end, we compare two large compendia of transcriptional profiles of human and mouse immune cell types. Global transcription profiles are conserved between corresponding cell lineages. The expression patterns of most orthologous genes are conserved, particularly for lineage-specific genes. However, several hundred genes show clearly divergent expression across the examined cell lineages, and among them, 169 genes did so even with highly stringent criteria. Finally, regulatory mechanisms--reflected by regulators differential expression or enriched cis-elements--are conserved between the species but to a lower degree, suggesting that distinct regulation may underlie some of the conserved transcriptional responses.",

author = "Tal Shay and Vladimir Jojic and Or Zuk and Katherine Rothamel and David Puyraimond-Zemmour and Ting Feng and Ei Wakamatsu and Christophe Benoist and Daphne Koller and Aviv Regev and Paul Monach and Shinton, \{Susan A\} and Hardy, \{Richard R\} and Radu Jianu and Laidlaw, \{David H\} and Collins, \{Jim J\} and Roi Gazit and Garrison, \{Brian S\} and Rossi, \{Derrick J\} and Kavitha Narayan and Katelyn Sylvia and Joonsoo Kang and Anne Fletcher and Elpek, \{Kutlu G\} and Angelique Bellemare-Pelletier and Deepali Malhotra and Turley, \{Shannon J\} and Best, \{Adam J\} and Jamie Knell and Goldrath, \{Ananda W\} and Cohen, \{Nadia R\} and Brennan, \{Patrick J\} and Brenner, \{Michael B\} and Taras Kreslavsky and Bezman, \{Natalie A\} and Sun, \{Joseph C\} and Kim, \{Charlie C\} and Lanier, \{Lewis L\} and Miller, \{Jennifer C\} and Brown, \{Brian D\} and Miriam Merad and Gautier, \{Emmanuel L\} and Jakubzick, \{Claudia V\} and Randolph, \{Gwendalyn J\} and Kim, \{Francis S\} and Rao, \{Tata N\} and Amy Wagers and Heng, \{Tracy S P\} and Painter, \{Michio W\} and Ericson, \{Jeffrey A\} and Davis, \{Scott P\} and Ayla Ergun and Michael Mingueneau and Diane Mathis",

year = "2013",

doi = "10.1073/pnas.1222738110",

language = "English",

volume = "110",

pages = "2946 -- 2951",

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

issn = "0027-8424",

publisher = "National Academy of Sciences",

number = "8",

}

Shay, T, Jojic, V, Zuk, O, Rothamel, K, Puyraimond-Zemmour, D, Feng, T, Wakamatsu, E, Benoist, C, Koller, D, Regev, A, Monach, P, Shinton, SA, Hardy, RR, Jianu, R, Laidlaw, DH, Collins, JJ, Gazit, R, Garrison, BS, Rossi, DJ, Narayan, K, Sylvia, K, Kang, J, Fletcher, A, Elpek, KG, Bellemare-Pelletier, A, Malhotra, D, Turley, SJ, Best, AJ, Knell, J, Goldrath, AW, Cohen, NR, Brennan, PJ, Brenner, MB, Kreslavsky, T, Bezman, NA, Sun, JC, Kim, CC, Lanier, LL, Miller, JC, Brown, BD, Merad, M, Gautier, EL, Jakubzick, CV, Randolph, GJ, Kim, FS, Rao, TN, Wagers, A, Heng, TSP, Painter, MW, Ericson, JA, Davis, SP, Ergun, A, Mingueneau, M & Mathis, D 2013, 'Conservation and divergence in the transcriptional programs of the human and mouse immune systems', Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 8, pp. 2946 - 2951. https://doi.org/10.1073/pnas.1222738110

TY - JOUR

T1 - Conservation and divergence in the transcriptional programs of the human and mouse immune systems

AU - Shay, Tal

AU - Jojic, Vladimir

AU - Zuk, Or

AU - Rothamel, Katherine

AU - Puyraimond-Zemmour, David

AU - Feng, Ting

AU - Wakamatsu, Ei

AU - Benoist, Christophe

AU - Koller, Daphne

AU - Regev, Aviv

AU - Monach, Paul

AU - Shinton, Susan A

AU - Hardy, Richard R

AU - Jianu, Radu

AU - Laidlaw, David H

AU - Collins, Jim J

AU - Gazit, Roi

AU - Garrison, Brian S

AU - Rossi, Derrick J

AU - Narayan, Kavitha

AU - Sylvia, Katelyn

AU - Kang, Joonsoo

AU - Fletcher, Anne

AU - Elpek, Kutlu G

AU - Bellemare-Pelletier, Angelique

AU - Malhotra, Deepali

AU - Turley, Shannon J

AU - Best, Adam J

AU - Knell, Jamie

AU - Goldrath, Ananda W

AU - Cohen, Nadia R

AU - Brennan, Patrick J

AU - Brenner, Michael B

AU - Kreslavsky, Taras

AU - Bezman, Natalie A

AU - Sun, Joseph C

AU - Kim, Charlie C

AU - Lanier, Lewis L

AU - Miller, Jennifer C

AU - Brown, Brian D

AU - Merad, Miriam

AU - Gautier, Emmanuel L

AU - Jakubzick, Claudia V

AU - Randolph, Gwendalyn J

AU - Kim, Francis S

AU - Rao, Tata N

AU - Wagers, Amy

AU - Heng, Tracy S P

AU - Painter, Michio W

AU - Ericson, Jeffrey A

AU - Davis, Scott P

AU - Ergun, Ayla

AU - Mingueneau, Michael

AU - Mathis, Diane

PY - 2013

Y1 - 2013

N2 - Much of the knowledge about cell differentiation and function in the immune system has come from studies in mice, but the relevance to human immunology, diseases, and therapy has been challenged, perhaps more from anecdotal than comprehensive evidence. To this end, we compare two large compendia of transcriptional profiles of human and mouse immune cell types. Global transcription profiles are conserved between corresponding cell lineages. The expression patterns of most orthologous genes are conserved, particularly for lineage-specific genes. However, several hundred genes show clearly divergent expression across the examined cell lineages, and among them, 169 genes did so even with highly stringent criteria. Finally, regulatory mechanisms--reflected by regulators differential expression or enriched cis-elements--are conserved between the species but to a lower degree, suggesting that distinct regulation may underlie some of the conserved transcriptional responses.

AB - Much of the knowledge about cell differentiation and function in the immune system has come from studies in mice, but the relevance to human immunology, diseases, and therapy has been challenged, perhaps more from anecdotal than comprehensive evidence. To this end, we compare two large compendia of transcriptional profiles of human and mouse immune cell types. Global transcription profiles are conserved between corresponding cell lineages. The expression patterns of most orthologous genes are conserved, particularly for lineage-specific genes. However, several hundred genes show clearly divergent expression across the examined cell lineages, and among them, 169 genes did so even with highly stringent criteria. Finally, regulatory mechanisms--reflected by regulators differential expression or enriched cis-elements--are conserved between the species but to a lower degree, suggesting that distinct regulation may underlie some of the conserved transcriptional responses.

UR - http://www.ncbi.nlm.nih.gov/pubmed/23382184

U2 - 10.1073/pnas.1222738110

DO - 10.1073/pnas.1222738110

M3 - Article

SN - 0027-8424

VL - 110

SP - 2946

EP - 2951

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

IS - 8

ER -

Conservation and divergence in the transcriptional programs of the human and mouse immune systems

Abstract

UN SDGs

Access to Document

Other files and links

Cite this