Online citations, reference lists, and bibliographies.
← Back to Search

Proteomic Profiling Of The NCI-60 Cancer Cell Lines Using New High-density Reverse-phase Lysate Microarrays

S. Nishizuka, L. Charboneau, Lynn M Young, S. Major, W. Reinhold, M. Waltham, H. Kouros-Mehr, K. Bussey, J. Lee, V. Espina, P. Munson, E. Petricoin, L. Liotta, J. Weinstein
Published 2003 · Biology, Medicine

Save to my Library
Download PDF
Analyze on Scholarcy
Share
Because most potential molecular markers and targets are proteins, proteomic profiling is expected to yield more direct answers to functional and pharmacological questions than does transcriptional profiling. To aid in such studies, we have developed a protocol for making reverse-phase protein lysate microarrays with larger numbers of spots than previously feasible. Our first application of these arrays was to profiling of the 60 human cancer cell lines (NCI-60) used by the National Cancer Institute to screen compounds for anticancer activity. Each glass slide microarray included 648 lysate spots representing the NCI-60 cell lines plus controls, each at 10 two-fold serial dilutions to provide a wide dynamic range. Mouse monoclonal antibodies and the catalyzed signal amplification system were used for immunoquantitation. The signal levels from the >30,000 data points for our first 52 antibodies were analyzed by using p-scan and a quantitative dose interpolation method. Clustered image maps revealed biologically interpretable patterns of protein expression. Among the principal early findings from these arrays were two promising pathological markers for distinguishing colon from ovarian adenocarcinomas. When we compared the patterns of protein expression with those we had obtained for the same genes at the mRNA level by using both cDNA and oligonucleotide arrays, a striking regularity appeared: cell-structure-related proteins almost invariably showed a high correlation between mRNA and protein levels across the NCI-60 cell lines, whereas non-cell-structure-related proteins showed poor correlation.
This paper references
Cancer Res
S Nishizuka (2003)
10.1016/S1471-4892(02)00185-6
'Omic' and hypothesis-driven research in the molecular pharmacology of cancer.
J. Weinstein (2002)
10.1002/(SICI)1098-2744(200005)28:1<12::AID-MC3>3.0.CO;2-Q
Development of a prostate cDNA microarray and statistical gene expression analysis package
A. J. Carlisle (2000)
Genome Biol
K J Bussey (2003)
J. Natl. Cancer Inst
A Monks (1991)
Nat. Genet
U Scherf (2000)
J. Natl. Cancer Inst
K D Paull (1989)
Curr. Opin. Pharmacol
J N Weinstein (2002)
10.1126/SCIENCE.275.5298.343
An Information-Intensive Approach to the Molecular Pharmacology of Cancer
J. Weinstein (1997)
Biochim. Biophys. Acta
D Barilá (1995)
10.1093/JNCI/83.11.757
Feasibility of a high-flux anticancer drug screen using a diverse panel of cultured human tumor cell lines.
A. Monks (1991)
N. & Kirsch, I. R. Cancer Res
A V Roschke
Diagnostic markers that distinguish colon and ovarian adenocarcinomas: identification by genomic, proteomic, and tissue array profiling.
S. Nishizuka (2003)
10.1038/73432
Systematic variation in gene expression patterns in human cancer cell lines
D. T. Ross (2000)
10.1002/1615-9861(200110)1:10<1271::AID-PROT1271>3.0.CO;2-6
Proteomic profiling of the cancer microenvironment by antibody arrays
V. Knezevic (2001)
10.1126/SCIENCE.292.5518.929
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.
T. Ideker (2001)
10.1038/sj.onc.1204265
Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front
C. Paweletz (2001)
10.1016/0092-8674(93)90586-F
Cell
AC Tose (1993)
Feasibility of drug screening with panels of human tumor cell lines using a microculture tetrazolium assay.
M. Alley (1988)
10.1128/MCB.19.3.1720
Correlation between Protein and mRNA Abundance in Yeast
S. Gygi (1999)
Mol. Cell. Biol
S P Gygi (1999)
Nat. Genet
D T Ross (2000)
Proc. Natl. Acad. Sci. USA 88
W T Lankes (1991)
10.1016/0092-8674(80)90330-X
Villin is a major protein of the microvillus cystoskeleton which binds both G and F actin in a calcium-dependent manner
A. Bretscher (1980)
10.1038/73439
A gene expression database for the molecular pharmacology of cancer
U. Scherf (2000)
Anticancer Res
S F Stinson (1992)
10.1073/pnas.191368598
Chemosensitivity prediction by transcriptional profiling
J. E. Staunton (2001)
EMBO J
E Pringault (1986)
Cytometry
J N Weinstein (2002)
10.1073/PNAS.91.5.1858
E-cadherin gene mutations in human gastric carcinoma cell lines.
T. Oda (1994)
10.1016/S1535-6108(03)00086-2
Protein microarrays: meeting analytical challenges for clinical applications.
Lance A. Liotta (2003)
10.5694/j.1326-5377.1924.tb66156.x
THE CANCER CELL
A. Chadli (1963)
Genome Biol
B B Haab (2001)
10.1002/j.1460-2075.1986.tb04618.x
A human villin cDNA clone to investigate the differentiation of intestinal and kidney cells in vivo and in culture.
E. Pringault (1986)
10.1016/0167-4781(95)00090-4
Transcriptional regulation of the ezrin gene during rat intestinal development and epithelial differentiation.
D. Barilà (1995)
Cancer Res
M C Alley (1988)
Genome Res
J K Lee
10.1111/J.1432-0436.1993.TB00649.X
Differential localization by in situ hybridization of distinct keratin mRNA species during intestinal epithelial cell development and differentiation.
D. Calnek (1993)
10.1093/JNCI/81.14.1088
Display and analysis of patterns of differential activity of drugs against human tumor cell lines: development of mean graph and COMPARE algorithm.
K. Paull (1989)
Mol. Carcinog
A J Carlisle (2000)
J. Biol. Chem
O Farrell (1975)
10.1002/ELPS.1150180333
A comparison of selected mRNA and protein abundances in human liver
L. Anderson (1997)
10.1016/s0021-9258(19)41496-8
High resolution two-dimensional electrophoresis of proteins.
P. O'Farrell (1975)
Morphological and immunocytochemical characteristics of human tumor cell lines for use in a disease-oriented anticancer drug screen.
S. Stinson (1992)
Oncogene
C P Paweletz (1981)
Www
10.6013/jbrewsocjapan1988.86.425
基礎講座 電気泳動(Electrophoresis)
大房 健 (2005)
10.1073/PNAS.88.19.8297
Moesin: a member of the protein 4.1-talin-ezrin family of proteins.
W. Lankes (1991)
10.1002/ELPS.1150180351
A protein expression database for the molecular pharmacology of cancer
T. G. Myers (1997)
10.1038/219305b0
Differentiation
J. Bonner (1968)
Proc. Natl. Acad. Sci. USA 98
J E Staunton (2001)
10.1002/CYTO.10041
The bioinformatics of microarray gene expression profiling.
J. Weinstein (2002)
Proc. Natl. Acad. Sci. USA 91
T Oda (1994)



This paper is referenced by
10.1126/scisignal.294er9
A Correction to the Perspective Titled: "Emerging Miniaturized Proteomic Technologies to Study Cell Signaling in Clinical Samples" by Taranjit S. Gujral and Gavin MacBeath
T. S. Gujral (2009)
10.1016/S0166-526X(05)46016-X
Chapter 16 Clinical cancer proteomics
A. Alaiya (2005)
10.1201/B13912-7
Proteomics of breast cancer
E. Petricoin (2006)
10.3390/s150511972
A Highly Sensitive Porous Silicon (P-Si)-Based Human Kallikrein 2 (hK2) Immunoassay Platform toward Accurate Diagnosis of Prostate Cancer
S. Lee (2015)
10.1002/prca.200780035
Reverse‐phase protein arrays for application‐orientated cancer research
U. Korf (2009)
10.1016/j.febslet.2009.03.042
Challenges in cancer research and multifaceted approaches for cancer biomarker quest
J. Martínková (2009)
10.2217/17435889.4.1.83
Inorganic nanoparticles for predictive oncology of breast cancer.
M. Yezhelyev (2009)
10.1038/nprot.2008.179
Reverse-phase protein lysate microarrays for cell signaling analysis
Brett Spurrier (2008)
10.1101/SQB.2005.70.016
"Lineage addiction" in human cancer: lessons from integrated genomics.
L. Garraway (2005)
10.1002/9781119187547.ch24
Computational Biology Approaches to Support Biomarker Discovery and Development
B. Li (2020)
10.1021/acs.langmuir.0c01306
Functional Microarray Platform with Self-Assembled Monolayers on 3C-Silicon Carbide.
Oren Cooper (2020)
10.1093/bioinformatics/btv529
Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel
I. Cortés-Ciriano (2016)
10.1002/ELPS.200700539
Protein microchips in biomedicine and biomarker discovery
S. Spisák (2007)
10.4137/BMI.S689
Proteomics Discovery of Disease Biomarkers
M. Ahram (2008)
10.1177/153303460600500601
Dissection of Signaling Pathways in Fourteen Breast Cancer Cell Lines Using Reverse-Phase Protein Lysate Microarray
M. Akkiprik (2006)
10.4137/CIN.S9055
Surface Adjustment of Reverse Phase Protein Arrays using Positive Control Spots
E. Neeley (2012)
10.1074/mcp.M113.033845
Alternative Mammalian Target of Rapamycin (mTOR) Signal Activation in Sorafenib-resistant Hepatocellular Carcinoma Cells Revealed by Array-based Pathway Profiling*
M. Masuda (2014)
10.1158/0008-5472.CAN-12-1370
CellMiner: a web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set.
W. Reinhold (2012)
10.1016/j.isci.2019.10.059
Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines
Tiannan Guo (2019)
10.1186/1471-2105-10-272
Correlating gene and protein expression data using Correlated Factor Analysis
Chuen Seng Tan (2008)
10.1186/1471-2105-11-495
An integrated analysis of molecular aberrations in NCI-60 cell lines
C. Yeang (2010)
10.1002/9780470048672.WECB645
Microarrays in Chemical Biology
A. N. Koehler (2008)
10.1002/PMIC.200401294
Printing of protein microarrays via a capillary‐free fluid jetting mechanism
J. Barron (2005)
10.3233/BD-2004-19103
Integromic analysis of the NCI-60 cancer cell lines.
J. Weinstein (2004)
10.1186/1471-2164-11-364
Systematic investigation of global coordination among mRNA and protein in cellular society
Haiyun Wang (2009)
10.1007/978-1-61779-286-1_2
Impact of blocking and detection chemistries on antibody performance for reverse phase protein arrays.
Kristi L H Ambroz (2011)
10.1586/14789450.2.4.499
Multiplex approaches in protein microarray technology
B. Kersten (2005)
10.2202/1544-6115.1638
Sparse Canonical Covariance Analysis for High-throughput Data
Woojoo Lee (2011)
10.1158/0008-5472.CAN-04-1554
Expression profiling of homocysteine junction enzymes in the NCI60 panel of human cancer cell lines.
W. Zhang (2005)
10.1007/978-981-32-9755-5_13
Utility of Reverse-Phase Protein Array for Refining Precision Oncology.
M. Masuda (2019)
10.1186/s12859-016-1273-5
Handling missing rows in multi-omics data integration: multiple imputation in multiple factor analysis framework
V. Voillet (2016)
10.1007/s13206-017-2109-8
Development of a Sol-gel-assisted Reverse-phase Microarray Platform for Simple and Rapid Detection of Prostate-specific Antigen from Serum
S. W. Lee (2018)
See more
Semantic Scholar Logo Some data provided by SemanticScholar