Single-cell transcriptomes reveal the mechanism for a breast cancer prognostic gene panel

Shengwen Calvin Li; Andres Stucky; Xuelian Chen; Mustafa H. Kabeer; William G. Loudon; Ashley S. Plant; Lilibeth Torno; Chaitali S. Nangia; Jin Cai; Gang Zhang; Jiang F. Zhong

doi:10.18632/oncotarget.26044

Single-cell transcriptomes reveal the mechanism for a breast cancer prognostic gene panel

Shengwen Calvin Li^*, Andres Stucky, Xuelian Chen, Mustafa H. Kabeer, William G. Loudon, Ashley S. Plant, Lilibeth Torno, Chaitali S. Nangia, Jin Cai, Gang Zhang, Jiang F. Zhong

^*Corresponding author for this work

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

1 Scopus citations

Abstract

The clinical benefits of the MammaPrint® signature for breast cancer is well documented; however, how these genes are related to cell cycle perturbation have not been well determined. Our single-cell transcriptome mapping (algorithm) provides details into the fine perturbation of all individual genes during a cell cycle, providing a view of the cell-cycle-phase specific landscape of any given human genes. Specifically, we identified that 38 out of the 70 (54%) MammaPrint® signature genes are perturbated to a specific phase of the cell cycle. The MammaPrint® signature panel derived its clinical prognosis power from measuring the cell cycle activity of specific breast cancer samples. Such cell cycle phase index of the MammaPrint® signature suggested that measurement of the cell cycle index from tumors could be developed into a prognosis tool for various types of cancer beyond breast cancer, potentially improving therapy through targeting a specific phase of the cell cycle of cancer cells.

Original language	English (US)
Pages (from-to)	33290-33301
Number of pages	12
Journal	Oncotarget
Volume	9
Issue number	70
DOIs	https://doi.org/10.18632/oncotarget.26044
State	Published - Sep 1 2018
Externally published	Yes

Keywords

Cell cycle
Cell cycle phase
Cell-cycle-staged therapy
Single-cell
Transcriptome

ASJC Scopus subject areas

Oncology

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@article{d439ed02d1bf4795a9720101c8dab4d1,

title = "Single-cell transcriptomes reveal the mechanism for a breast cancer prognostic gene panel",

abstract = "The clinical benefits of the MammaPrint{\textregistered} signature for breast cancer is well documented; however, how these genes are related to cell cycle perturbation have not been well determined. Our single-cell transcriptome mapping (algorithm) provides details into the fine perturbation of all individual genes during a cell cycle, providing a view of the cell-cycle-phase specific landscape of any given human genes. Specifically, we identified that 38 out of the 70 (54%) MammaPrint{\textregistered} signature genes are perturbated to a specific phase of the cell cycle. The MammaPrint{\textregistered} signature panel derived its clinical prognosis power from measuring the cell cycle activity of specific breast cancer samples. Such cell cycle phase index of the MammaPrint{\textregistered} signature suggested that measurement of the cell cycle index from tumors could be developed into a prognosis tool for various types of cancer beyond breast cancer, potentially improving therapy through targeting a specific phase of the cell cycle of cancer cells.",

keywords = "Cell cycle, Cell cycle phase, Cell-cycle-staged therapy, Single-cell, Transcriptome",

author = "Li, {Shengwen Calvin} and Andres Stucky and Xuelian Chen and Kabeer, {Mustafa H.} and Loudon, {William G.} and Plant, {Ashley S.} and Lilibeth Torno and Nangia, {Chaitali S.} and Jin Cai and Gang Zhang and Zhong, {Jiang F.}",

note = "Funding Information: We thank Meng Li (USC Bioinformatics Core Facility) for bioinformatic analysis, and Dr. Bridget Samuels (PhD, Caltech) for editing the manuscript. This work was supported in part by the National Institutes of Health (NCI, R01CA164509; NIEHS, R01ES021801-04S1) and by CHOC Children's Foundation, CHOC-UCI Joint Research Awards (2014, 2015, 2016). Publisher Copyright: {\textcopyright} Li et al.",

year = "2018",

month = sep,

day = "1",

doi = "10.18632/oncotarget.26044",

language = "English (US)",

volume = "9",

pages = "33290--33301",

journal = "Oncotarget",

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Single-cell transcriptomes reveal the mechanism for a breast cancer prognostic gene panel. / Li, Shengwen Calvin; Stucky, Andres; Chen, Xuelian; Kabeer, Mustafa H.; Loudon, William G.; Plant, Ashley S.; Torno, Lilibeth; Nangia, Chaitali S.; Cai, Jin; Zhang, Gang; Zhong, Jiang F.

In: Oncotarget, Vol. 9, No. 70, 01.09.2018, p. 33290-33301.

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

TY - JOUR

T1 - Single-cell transcriptomes reveal the mechanism for a breast cancer prognostic gene panel

AU - Li, Shengwen Calvin

AU - Stucky, Andres

AU - Chen, Xuelian

AU - Kabeer, Mustafa H.

AU - Loudon, William G.

AU - Plant, Ashley S.

AU - Torno, Lilibeth

AU - Nangia, Chaitali S.

AU - Cai, Jin

AU - Zhang, Gang

AU - Zhong, Jiang F.

N1 - Funding Information: We thank Meng Li (USC Bioinformatics Core Facility) for bioinformatic analysis, and Dr. Bridget Samuels (PhD, Caltech) for editing the manuscript. This work was supported in part by the National Institutes of Health (NCI, R01CA164509; NIEHS, R01ES021801-04S1) and by CHOC Children's Foundation, CHOC-UCI Joint Research Awards (2014, 2015, 2016). Publisher Copyright: © Li et al.

PY - 2018/9/1

Y1 - 2018/9/1

N2 - The clinical benefits of the MammaPrint® signature for breast cancer is well documented; however, how these genes are related to cell cycle perturbation have not been well determined. Our single-cell transcriptome mapping (algorithm) provides details into the fine perturbation of all individual genes during a cell cycle, providing a view of the cell-cycle-phase specific landscape of any given human genes. Specifically, we identified that 38 out of the 70 (54%) MammaPrint® signature genes are perturbated to a specific phase of the cell cycle. The MammaPrint® signature panel derived its clinical prognosis power from measuring the cell cycle activity of specific breast cancer samples. Such cell cycle phase index of the MammaPrint® signature suggested that measurement of the cell cycle index from tumors could be developed into a prognosis tool for various types of cancer beyond breast cancer, potentially improving therapy through targeting a specific phase of the cell cycle of cancer cells.

AB - The clinical benefits of the MammaPrint® signature for breast cancer is well documented; however, how these genes are related to cell cycle perturbation have not been well determined. Our single-cell transcriptome mapping (algorithm) provides details into the fine perturbation of all individual genes during a cell cycle, providing a view of the cell-cycle-phase specific landscape of any given human genes. Specifically, we identified that 38 out of the 70 (54%) MammaPrint® signature genes are perturbated to a specific phase of the cell cycle. The MammaPrint® signature panel derived its clinical prognosis power from measuring the cell cycle activity of specific breast cancer samples. Such cell cycle phase index of the MammaPrint® signature suggested that measurement of the cell cycle index from tumors could be developed into a prognosis tool for various types of cancer beyond breast cancer, potentially improving therapy through targeting a specific phase of the cell cycle of cancer cells.

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JF - Oncotarget

SN - 1949-2553

IS - 70

ER -

Single-cell transcriptomes reveal the mechanism for a breast cancer prognostic gene panel

Abstract

Keywords

ASJC Scopus subject areas

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