Characterization of Human Cancer Cell Lines by Reverse-phase Protein Arrays

Jun Li; Wei Zhao; Rehan Akbani; Wenbin Liu; Zhenlin Ju; Shiyun Ling; Christopher P. Vellano; Paul Roebuck; Qinghua Yu; A. Karina Eterovic; Lauren A. Byers; Michael A. Davies; Wanleng Deng; Y. N.Vashisht Gopal; Guo Chen; Erika M. von Euw; Dennis Slamon; Dylan Conklin; John V. Heymach; Adi F. Gazdar; John D. Minna; Jeffrey N. Myers; Yiling Lu; Gordon B. Mills; Han Liang

doi:10.1016/j.ccell.2017.01.005

Characterization of Human Cancer Cell Lines by Reverse-phase Protein Arrays

Jun Li, Wei Zhao, Rehan Akbani, Wenbin Liu, Zhenlin Ju, Shiyun Ling, Christopher P. Vellano, Paul Roebuck, Qinghua Yu, A. Karina Eterovic, Lauren A. Byers, Michael A. Davies, Wanleng Deng, Y. N.Vashisht Gopal, Guo Chen, Erika M. von Euw, Dennis Slamon, Dylan Conklin, John V. Heymach, Adi F. GazdarJohn D. Minna, Jeffrey N. Myers, Yiling Lu, Gordon B. Mills, Han Liang

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

141 Scopus citations

Abstract

Cancer cell lines are major model systems for mechanistic investigation and drug development. However, protein expression data linked to high-quality DNA, RNA, and drug-screening data have not been available across a large number of cancer cell lines. Using reverse-phase protein arrays, we measured expression levels of ∼230 key cancer-related proteins in >650 independent cell lines, many of which have publically available genomic, transcriptomic, and drug-screening data. Our dataset recapitulates the effects of mutated pathways on protein expression observed in patient samples, and demonstrates that proteins and particularly phosphoproteins provide information for predicting drug sensitivity that is not available from the corresponding mRNAs. We also developed a user-friendly bioinformatic resource, MCLP, to help serve the biomedical research community.

Original language	English (US)
Pages (from-to)	225-239
Number of pages	15
Journal	Cancer Cell
Volume	31
Issue number	2
DOIs	https://doi.org/10.1016/j.ccell.2017.01.005
State	Published - Feb 13 2017
Externally published	Yes

Keywords

biomarker
cancer cell lines
data portal
drug sensitivity
proteomics
reverse-phase protein array
signaling pathways

ASJC Scopus subject areas

Oncology
Cell Biology
Cancer Research

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10.1016/j.ccell.2017.01.005

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Li, J., Zhao, W., Akbani, R., Liu, W., Ju, Z., Ling, S., Vellano, C. P., Roebuck, P., Yu, Q., Eterovic, A. K., Byers, L. A., Davies, M. A., Deng, W., Gopal, Y. N. V., Chen, G., von Euw, E. M., Slamon, D., Conklin, D., Heymach, J. V., ... Liang, H. (2017). Characterization of Human Cancer Cell Lines by Reverse-phase Protein Arrays. Cancer Cell, 31(2), 225-239. https://doi.org/10.1016/j.ccell.2017.01.005

Li, J, Zhao, W, Akbani, R, Liu, W, Ju, Z, Ling, S, Vellano, CP, Roebuck, P, Yu, Q, Eterovic, AK, Byers, LA, Davies, MA, Deng, W, Gopal, YNV, Chen, G, von Euw, EM, Slamon, D, Conklin, D, Heymach, JV, Gazdar, AF, Minna, JD, Myers, JN, Lu, Y, Mills, GB & Liang, H 2017, 'Characterization of Human Cancer Cell Lines by Reverse-phase Protein Arrays', Cancer Cell, vol. 31, no. 2, pp. 225-239. https://doi.org/10.1016/j.ccell.2017.01.005

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title = "Characterization of Human Cancer Cell Lines by Reverse-phase Protein Arrays",

abstract = "Cancer cell lines are major model systems for mechanistic investigation and drug development. However, protein expression data linked to high-quality DNA, RNA, and drug-screening data have not been available across a large number of cancer cell lines. Using reverse-phase protein arrays, we measured expression levels of ∼230 key cancer-related proteins in >650 independent cell lines, many of which have publically available genomic, transcriptomic, and drug-screening data. Our dataset recapitulates the effects of mutated pathways on protein expression observed in patient samples, and demonstrates that proteins and particularly phosphoproteins provide information for predicting drug sensitivity that is not available from the corresponding mRNAs. We also developed a user-friendly bioinformatic resource, MCLP, to help serve the biomedical research community.",

keywords = "biomarker, cancer cell lines, data portal, drug sensitivity, proteomics, reverse-phase protein array, signaling pathways",

author = "Jun Li and Wei Zhao and Rehan Akbani and Wenbin Liu and Zhenlin Ju and Shiyun Ling and Vellano, {Christopher P.} and Paul Roebuck and Qinghua Yu and Eterovic, {A. Karina} and Byers, {Lauren A.} and Davies, {Michael A.} and Wanleng Deng and Gopal, {Y. N.Vashisht} and Guo Chen and {von Euw}, {Erika M.} and Dennis Slamon and Dylan Conklin and Heymach, {John V.} and Gazdar, {Adi F.} and Minna, {John D.} and Myers, {Jeffrey N.} and Yiling Lu and Mills, {Gordon B.} and Han Liang",

note = "Funding Information: This study was supported by the NIH (CA168394, CA098258, CA143883, and HG008100 to G.B.M.; CA175486 to H.L.; CA209851 to H.L. and G.B.M.; CA176284 and CA70907 to A.F.G. and J.D.M.; and Cancer Center Support Grants CA016672); the R. Lee Clark Fellow Award from The Jeanne F. Shelby Scholarship Fund (to H.L.); a grant from the Cancer Prevention and Research Institute of Texas (RP140462 to H.L.); the Lorraine Dell Program in Bioinformatics for Personalization of Cancer Medicine (to H.L.); and the Adelson Medical Research Foundation (to G.B.M.). We thank the MDACC high-performance computing core facility for computing, and LeeAnn Chastain for editorial assistance. G.B.M. has sponsored research support from AstraZeneca and is on the Scientific Advisory Board for AstraZeneca, ImmunoMet, Nuevolution, and Precision Medicine. Publisher Copyright: {\textcopyright} 2017 Elsevier Inc.",

year = "2017",

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day = "13",

doi = "10.1016/j.ccell.2017.01.005",

language = "English (US)",

volume = "31",

pages = "225--239",

journal = "Cancer Cell",

issn = "1535-6108",

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T1 - Characterization of Human Cancer Cell Lines by Reverse-phase Protein Arrays

AU - Li, Jun

AU - Zhao, Wei

AU - Akbani, Rehan

AU - Liu, Wenbin

AU - Ju, Zhenlin

AU - Ling, Shiyun

AU - Vellano, Christopher P.

AU - Roebuck, Paul

AU - Yu, Qinghua

AU - Eterovic, A. Karina

AU - Byers, Lauren A.

AU - Davies, Michael A.

AU - Deng, Wanleng

AU - Gopal, Y. N.Vashisht

AU - Chen, Guo

AU - von Euw, Erika M.

AU - Slamon, Dennis

AU - Conklin, Dylan

AU - Heymach, John V.

AU - Gazdar, Adi F.

AU - Minna, John D.

AU - Myers, Jeffrey N.

AU - Lu, Yiling

AU - Mills, Gordon B.

AU - Liang, Han

N1 - Funding Information: This study was supported by the NIH (CA168394, CA098258, CA143883, and HG008100 to G.B.M.; CA175486 to H.L.; CA209851 to H.L. and G.B.M.; CA176284 and CA70907 to A.F.G. and J.D.M.; and Cancer Center Support Grants CA016672); the R. Lee Clark Fellow Award from The Jeanne F. Shelby Scholarship Fund (to H.L.); a grant from the Cancer Prevention and Research Institute of Texas (RP140462 to H.L.); the Lorraine Dell Program in Bioinformatics for Personalization of Cancer Medicine (to H.L.); and the Adelson Medical Research Foundation (to G.B.M.). We thank the MDACC high-performance computing core facility for computing, and LeeAnn Chastain for editorial assistance. G.B.M. has sponsored research support from AstraZeneca and is on the Scientific Advisory Board for AstraZeneca, ImmunoMet, Nuevolution, and Precision Medicine. Publisher Copyright: © 2017 Elsevier Inc.

PY - 2017/2/13

Y1 - 2017/2/13

N2 - Cancer cell lines are major model systems for mechanistic investigation and drug development. However, protein expression data linked to high-quality DNA, RNA, and drug-screening data have not been available across a large number of cancer cell lines. Using reverse-phase protein arrays, we measured expression levels of ∼230 key cancer-related proteins in >650 independent cell lines, many of which have publically available genomic, transcriptomic, and drug-screening data. Our dataset recapitulates the effects of mutated pathways on protein expression observed in patient samples, and demonstrates that proteins and particularly phosphoproteins provide information for predicting drug sensitivity that is not available from the corresponding mRNAs. We also developed a user-friendly bioinformatic resource, MCLP, to help serve the biomedical research community.

AB - Cancer cell lines are major model systems for mechanistic investigation and drug development. However, protein expression data linked to high-quality DNA, RNA, and drug-screening data have not been available across a large number of cancer cell lines. Using reverse-phase protein arrays, we measured expression levels of ∼230 key cancer-related proteins in >650 independent cell lines, many of which have publically available genomic, transcriptomic, and drug-screening data. Our dataset recapitulates the effects of mutated pathways on protein expression observed in patient samples, and demonstrates that proteins and particularly phosphoproteins provide information for predicting drug sensitivity that is not available from the corresponding mRNAs. We also developed a user-friendly bioinformatic resource, MCLP, to help serve the biomedical research community.

KW - biomarker

KW - cancer cell lines

KW - data portal

KW - drug sensitivity

KW - proteomics

KW - reverse-phase protein array

KW - signaling pathways

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AN - SCOPUS:85012908020

SN - 1535-6108

VL - 31

SP - 225

EP - 239

JO - Cancer Cell

JF - Cancer Cell

IS - 2

ER -

Characterization of Human Cancer Cell Lines by Reverse-phase Protein Arrays

Abstract

Keywords

ASJC Scopus subject areas

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