Inhibitor-sensitive FGFR1 amplification in human non-small cell lung cancer.
ABSTRACT Squamous cell lung carcinomas account for approximately 25% of new lung carcinoma cases and 40,000 deaths per year in the United States. Although there are multiple genomically targeted therapies for lung adenocarcinoma, none has yet been reported in squamous cell lung carcinoma.
Using SNP array analysis, we found that a region of chromosome segment 8p11-12 containing three genes-WHSC1L1, LETM2, and FGFR1-is amplified in 3% of lung adenocarcinomas and 21% of squamous cell lung carcinomas. Furthermore, we demonstrated that a non-small cell lung carcinoma cell line harboring focal amplification of FGFR1 is dependent on FGFR1 activity for cell growth, as treatment of this cell line either with FGFR1-specific shRNAs or with FGFR small molecule enzymatic inhibitors leads to cell growth inhibition.
These studies show that FGFR1 amplification is common in squamous cell lung cancer, and that FGFR1 may represent a promising therapeutic target in non-small cell lung cancer.
Article: Focus on lung cancer.Cancer Cell 03/2002; 1(1):49-52. · 24.76 Impact Factor
- [show abstract] [hide abstract]
ABSTRACT: From biological, histopathologic, and clinical perspectives, lung cancer is a highly complex neoplasm probably having multiple preneoplastic pathways. The sequence of histopathologic changes in the bronchial mucosa that precedes the development of squamous carcinomas of the lung has been identified. For the other major forms of lung cancer, however, such sequences have been poorly documented. This review summarizes the current knowledge regarding the molecular and histopathologic pathogenesis of lung cancer and discusses the complexity of identifying novel molecular mechanisms involved in the development of the lung premalignant disease, and their relevance to the development of new strategies for early detection and chemoprevention. Although our current knowledge of the molecular pathogenesis of lung cancer is still meager, work over the last decade has taught several important lessons about the molecular pathogenesis of this tumor, including the following: a) Better characterization of the high-risk population is needed. b) There are several histopathologic and molecular pathways associated with the development of the major types of non-small cell lung cancer. c) Although there is a field effect phenomenon for lung preneoplastic lesions, recent data suggest that there are at least two distinct lung airway compartments (central and peripheral) for lung cancer pathogenesis. d) Inflammation may play an important role in lung cancer development and could be an important component of the field effect phenomenon. e) For lung adenocarcinoma, at least two pathways (smoking-related and nonsmoking-related) have been identified. f) Finally, the identification of deregulated molecular signaling pathways in lung cancer preneoplasias may provide a rationale for designing novel strategies for early detection and targeted chemoprevention of lung cancer.Current Molecular Medicine 03/2007; 7(1):3-14. · 4.20 Impact Factor
- [show abstract] [hide abstract]
ABSTRACT: Squamous cell carcinoma (SQCC) of the lung is thought to arise after the accumulation of multiple mutations, including p53. To better characterize when p53 mutations are acquired, 37 SQCC of the lung were examined by polymerase chain reaction and single-strand conformation polymorphism analysis. Somatic p53 mutations were detected in nine tumors (24.3%). There were no significant differences in the stage, sex, or race between patients with or without p53 mutations. However, the patients with SQCC and p53 mutations were significantly (P = 0.0006) younger (mean age, 54.3 years) compared with patients without p53 mutations (mean age, 65). The topographical tissue distributions of the p53 mutations were examined by selective ultraviolet radiation fractionation. In all nine cases, the specific p53 mutant alleles were homogeneously present throughout the primary tumors, in all three examples with in situ carcinoma, and in all four cases with metastases. In one case, squamous metaplasia contiguous with the primary tumor also contained the same p53 mutation. Normal or hyperplastic and metaplastic or dysplastic epithelium not contiguous with the primary tumors lacked the specific p53 mutations. These findings suggest that p53 mutations are commonly acquired at a relatively early age, before the bulk of clonal expansion, and usually persist throughout the progression of SQCC of the lung.American Journal Of Pathology 01/1995; 145(6):1444-9. · 4.52 Impact Factor
Inhibitor-Sensitive FGFR1 Amplification in Human Non-
Small Cell Lung Cancer
Amit Dutt1,2,8*, Alex H. Ramos1,2,7, Peter S. Hammerman1, Craig Mermel1,2, Jeonghee Cho1, Tanaz
Sharifnia1,2, Ajit Chande8, Kumiko Elisa Tanaka1,2, Nicolas Stransky2, Heidi Greulich1,2,3, Nathanael S.
Gray4,5, Matthew Meyerson1,2,6,7*
1Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America, 2The Broad Institute of Massachusetts Institute of
Technology and Harvard, Cambridge, Massachusetts, United States of America, 3Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School,
Boston, Massachusetts, United States of America, 4Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America,
5Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America, 6Center for Cancer
Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America, 7Department of Pathology, Harvard Medical School, Boston,
Massachusetts, United States of America, 8Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Kharghar, Navi Mumbai, India
Background: Squamous cell lung carcinomas account for approximately 25% of new lung carcinoma cases and 40,000
deaths per year in the United States. Although there are multiple genomically targeted therapies for lung adenocarcinoma,
none has yet been reported in squamous cell lung carcinoma.
Methodology/Principal Findings: Using SNP array analysis, we found that a region of chromosome segment 8p11-12
containing three genes–WHSC1L1, LETM2, and FGFR1–is amplified in 3% of lung adenocarcinomas and 21% of squamous cell
lung carcinomas. Furthermore, we demonstrated that a non-small cell lung carcinoma cell line harboring focal amplification
of FGFR1 is dependent on FGFR1 activity for cell growth, as treatment of this cell line either with FGFR1-specific shRNAs or
with FGFR small molecule enzymatic inhibitors leads to cell growth inhibition.
Conclusions/Significance: These studies show that FGFR1 amplification is common in squamous cell lung cancer, and that
FGFR1 may represent a promising therapeutic target in non-small cell lung cancer.
Citation: Dutt A, Ramos AH, Hammerman PS, Mermel C, Cho J, et al. (2011) Inhibitor-Sensitive FGFR1 Amplification in Human Non-Small Cell Lung Cancer. PLoS
ONE 6(6): e20351. doi:10.1371/journal.pone.0020351
Editor: Ming You, Medical College of Wisconsin, United States of America
Received December 30, 2010; Accepted April 30, 2011; Published June 7, 2011
Copyright: ? 2011 Dutt et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted
use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: Funding sources for this work include support from Novartis Pharmaceuticals, the American Lung Association, Uniting Against Lung Cancer, the Sarah
Thomas Monopoli Fund, the Seaman Foundation and Genentech to M.M. A.D. is supported by a Ramalingaswami fellowship from the Department of
Biotechnology, Ministry of Science, Government of India. P.S.H. is supported by a Young Investigator Award from the National Lung Cancer Partnership. The
funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing Interests: M.M. is a consultant to Novartis and receives research support from Novartis, receives research support from Genentech, and is a
founding advisor and consultant, and an equity holder in Foundation Medicine. N.G. laboratory receives sponsored research from Novartis. However, this does not
alter the authors’ adherence to all the PLoS ONE policies on sharing data and materials.
* E-mail: firstname.lastname@example.org (MM); email@example.com (AD)
Lung cancer is the leading cause of cancer-related death in
developed countries with deaths in 2009 estimated at approxi-
mately 160,000 in the United States, accounting for about 28% of
all cancer deaths . Non-small cell lung cancer (NSCLC)
accounts for 75% of all lung cancers and includes two
predominant subtypes, adenocarcinoma and squamous cell
carcinoma (SCC), which comprise 40% and 25% of NSCLCs,
respectively [2,3]. Despite clear histologic and biologic distinc-
tions, lung adenocarcinoma and squamous cell carcinoma are
largely treated with the same chemotherapeutic agents with the
exception of the antifolate agent pemetrexed which is approved for
the treatment of non-squamous NSCLC .
Significant advances in the treatment of lung adenocarcinoma
have stemmed from detailed genomic analyses and the deploy-
ment of molecularly targeted agents leading which have led to
improvements in patient outcomes. Examples include the use of
epidermal growth factor receptor (EGFR) inhibitors such as
gefitinib and erlotinib [5,6,7] for lung adenocarcinomas bearing
EGFR mutations [8,9,10], and of ALK inhibitors such as crizotinib
 for lung adenocarcinomas bearing EML4-ALK translocations
However, little is currently known about the targetable genetic
abnormalities underlying squamous cell lung cancer. In addition to
TP53 mutations , squamous cell lung carcinomas have been
shown to harbor amplifications of PIK3CA , SOX2 , and
EGFR  as well as EGFR variant III mutations  DDR2
mutations  and rare amplifications of PDGFRA/KIT [19,20]
and BRF2 . A recent study has demonstrated focal
amplification of the FGFR1 locus on chromosome 8p associated
with cellular dependency on FGFR1 and sensitivity to FGFR
inhibitors . At this time there are no FDA-approved targeted
therapies for squamous cell lung cancer.
Targeting amplified tyrosine kinases with antibodies or with
small molecule inhibitors has led to dramatic improvements in
PLoS ONE | www.plosone.org 1June 2011 | Volume 6 | Issue 6 | e20351
response rates and overall survival of cancer patients whose tumors
harbor specific genomic abnormalities. Amplifications of EGFR
and ERBB2 have been reported in a variety of malignancies,
including head and neck, esophageal, gastric, breast and colon
cancers as well as NSCLC . Targeting of these tyrosine
kinases, such as the use of cetuximab to target EGFR in colorectal
and head and neck cancer [24,25] and the use of trastuzumab to
target ERBB2 in breast cancer , has resulted in significant
improvement in patient outcomes in each of these diseases, though
not all patients with these amplifications respond to targeted
agents [27,28], likely due to additional genomic alterations within
the tumor that result in primary resistance to specific agents
The fibroblast growth factor receptor type 1 gene (FGFR1) is
one of the most commonly amplified genes in human cancer .
The fibroblast growth factor receptor (FGFR) tyrosine kinase
family is comprised of four kinases, FGFR1, 2, 3, and 4, that play
crucial role in development, and have been shown to be targets
for deregulation by either amplification, point mutation, or
translocation (reviewed in ). Translocations involving FGFR3,
as well as activating somatic mutations in FGFR3 have been
identified in multiple myeloma and bladder cancer [32,33,34].
We and others have identified activating mutations in FGFR2 in
endometrial cancer [35,36]. Amplification or activation of FGFR1
has been reported in oral squamous carcinoma , esophageal
squamous cell carcinomas , ovarian cancer , bladder
cancer , prostate cancer , rhabodomyosarcoma , and
lung cancer [16,43,44,45,46]. Consistent with this, a pan-FGFR
tyrosine kinase inhibitor has been shown to block tumor
proliferation in a subset of NSCLC cell lines with activated
FGFR signaling but has no effect on cells that do not activate the
pathway . FGFR1 has been identified as the driver event in
breast carcinomas and NSCLC, especially squamous cell lung
carcinomas, harboring similar amplifications of the 8p11
chromosomal segment [22,48]
Based on SNP array copy number analysis of 732 samples, we
report that FGFR1 is somatically amplified in 21% of lung
squamous cell carcinomas as compared to 3.4% of lung
adenocarcinomas. We validate FGFR1 as a potential therapeutic
target by showing that at least one FGFR1-amplified NSCLC
tumor cell line is sensitive to FGFR enzymatic inhibition and
dependent on FGFR1 expression for cell viability as evidenced by
shRNA treatment. Together with previous reports reviewed
above, these results suggest that FGFR1 may be an attractive
therapeutic target in NSCLC.
Materials and Methods
NSCLC primary samples and cell lines
NSCLC cell lines, NCI-H1703 (squamous), NCI-H2444
(pulmonary), NCI-H520 (squamous), HCC95 (squamous), NCI-
1581 (large cell carcinoma), Calu3 (not otherwise specified), NCI-
H1734 (not otherwise specified), Colo699 (adenocarcinoma),
NCI-H2170 (squamous), NCI-H226 (squamous), A427 (adeno-
carcinoma), NCI-H1563 (adenocarcinoma), NCI-H1781 (adeno-
carcinoma) and HCC15 (squamous) were obtained from the
collection of A.F. Gazdar, J. Minna, and colleagues [49,50,51],
from ATCC (Manassas, Virginia, United States) and/or DSMZ
(Braunschweig, Germany). Cells were maintained in RPMI 1640
complete media supplemented with 10% calf serum (Gibco/
Invitrogen, Carlsbad, California, United States) and penicillin/
streptomycin (Gibco/Invitrogen). The NSCLC tumor/normal
pairs analyzed in this study have been described earlier
SNP array data analysis
SNP array experiments were performed on 732 NSCLC
tumor and cell line samples and data analyzed as described
previously [16,20,45,50,52]. The boundaries of the 8p11
amplicon defined by GISTIC analysis  were identified as
the Integrative Genomics Viewer (http://www.broadinstitute.org/
has been performedusing
Transfection and infection
Phoenix 293T packaging cell line (Orbigen, San Diego,
California, United States) were transfected with pBabe-Puro-
based gateway vectors using FuGENEH 6 Transfection Reagent
(Roche, Indianapolis, United States) to generate replication
incompetent retroviruses. Target cells were infected with these
retroviruses in the presence of 8 mg/ml polybrene. Two days post
infection, cells were treated with 2 mg/ml puromycin (Sigma, St.
Louis, Missouri, United States) for two days. The resulting stable
cell lines were used for experimental studies.
shRNA mediated FGFR1 knockdown
shRNA vectors were obtained from TRC (The RNAi
Consortium). The target sequences of the shRNA constructs are:
FGFR1#1 (TRCN 0000121307): 59- AGTGGCTTATTAA-
FGFR1 #2 (TRCN 0000121308): 59- GCTTGCCAATGGCG-
FGFR1 #3 (TRCN 0000121309): 59- CTTGTATGTCATC-
FGFR1 #4 (TRCN 0000121310): 59- CAAGATGAAGAG-
FGFR1 #5 (TRCN 0000121311): 59- GAATGAGTACGGCA-
LETM2 #1 (TRCN 0000040243): 59- CGCACCTTCTACC-
LETM2 #2 (TRCN 0000040244): 59- CCCAGCACAAAG-
LETM2 #3 (TRCN 0000040245): 59- CCAGTTACATCAT-
LETM2 #4 (TRCN 0000040246): 59- CCAGGAACTAGAC-
LETM2 #4 (TRCN 0000040247): 59- GCATTGAGTGTAT-
WHSC1L1#1 (TRCN 0000015613): 59- CGAGAGTATAA-
WHSC1L1 #2 (TRCN 0000015614): 59- CCATCATCAAT-
WHSC1L1 #3 (TRCN 0000015615): 59- CGAGAATATC-
WHSC1L1 #4 (TRCN 0000015616): 59- GCTTCCATTAC-
WHSC1L1 #5 (TRCN 0000015617): 59- GCAGGGAATT-
The sequence targeted by the GFP shRNA is 59-GCAAGCT-
GACCCTGAAGTTCAT-39. Lentiviruses were made by trans-
fection of 293T packaging cells with these constructs using a
three-plasmid system as previously described . Target
cells were incubated with lentiviruses for 6 hours in the
presence of 8 mg/ml polybrene and left in fresh media. Cells
were grown for two days. Fifty micrograms of total cell lysates
prepared from the infected cell lines was analyzed by Western
FGFR1 Amplification in Squamous Cell Lung Cancer
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FGFR1 Amplification in Squamous Cell Lung Cancer
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Growth and Proliferation assays
For survival assays, 26106cells for each tumor cell line
expressing shRNAs constructs targeting FGFR1, WHSC1L1,
LETM2 or GFP along with uninfected cells were seeded in 3
replicates on a 6 well plate. Cell viability was determined at
24 hour time points for 4 consecutive days by counting the cells
using Beckman Coulter Vi-Cell Automated Cell Viability
Analyzer following trypan blue dye staining. The percentage of
cell viability was plotted for each cell line of readings obtained on
day 4 relative to day 1.
Soft agar anchorage-independent growth assay
For soft agar assays, 26104NSCLC cells expressing shFGFR1
and shGFP were suspended in a top layer of RPMI1640 containing
10% calf serum and 0.4% Select agar (Gibco/Invitrogen,
Carlsbad, California, United States) and plated on a bottom layer
of RPMI1640 containing 10% calf serum and 0.5% Select agar on
a 6 well plate. PD173074 or FIIN-1  was added as described to
the top agar. After 3–5 weeks incubation colonies were counted in
triplicate. IC50s were determined by nonlinear regression using
Prism 5 software (GraphPad Software).
Depending on the growth curves for each cell line, between 800
and 2000 NSCLC cells were seeded in 6 replicates in 96- well
plate. One day after plating, increasing doses of FGFR inhibitors
PD173074 or FIIN-1 were added and proliferation of cells was
assessed 4 days later using the WST-1 assay (Roche Applied
Science). Each data point represents the median of six replicate
wells for each tumor cell line and inhibitor concentration. IC50s
were determined by nonlinear regression using the Prism
Total protein was extracted and separated by gel electrophoresis
by lysing cells in a buffer containing 50 mM Tris-HCl (pH 7.4),
150 mM NaCl, 2.5 mM EDTA, 1% Triton X-100, and 0.25%
IGEPAL. Protease inhibitors (Roche Applied Science) and
phosphatase inhibitors (Calbiochem) were added prior to use.
Before loading to the gel, samples were normalized for total
protein content. Total protein lysates were boiled in sample buffer,
separated by SDS-PAGE on 8% polyacrylamide gels, transferred
to PVDF membrane, and probed overnight using the appropriate
primary antibodies. Antibodies used for immunoblotting were:
anti- FGFR1 antibody (# 3472, Cell Signaling Technologies,
Danvers, MA, United States), anti- phospho FRS2 Y436 (#3861,
Cell Signaling Technologies, Danvers, MA, United States), anti-
phospho-FRS2 Y196 (#3864, Cell Signaling Technologies,
Danvers, MA, United States), anti-FRS2 (# sc-17841, Santa
Cruz Biotechnology, Santa Cruz, CA, United States). anti-
WHSC1L1 monoclonal antibody (# sc-130009, Santa Cruz
Biotechnology), anti-LETM2 monoclonal antibody (# ab84626,
Abcam), and anti-Actin monoclonal antibody (# sc-1615, Santa
Comparisons between SNP array copy number data for lung
adenocarcinoma (AC) and squamous cell carcinoma (SCC) tumors
were performed using Fisher’s exact T test to calculate two-tailed
p-values among samples harboring high level amplification,
defined as log2 ratio .0.7 or 3.25 normalized DNA copies. P
values,0.05 were considered significant.
To determine the IC50 for FGFR inhibitors, the cell viability
measurements of six replicates at varying concentrations of
inhibitors were normalized to untreated control cells. Sigmoidal
dose response curves were fitted to the data by non linear
regression using GraphPad Prism software. Standard deviations
were determined for the mean of each value using an inbuilt
module of the software.
For shRNA experiments, performed in three replicates, the cell
number was counted and the mean and standard deviation were
determined using functions in Microsoft Excel.
FGFR1 is amplified in non-small cell lung cancer
We examined the 8p11-12 genomic region using Affymetrix
250K SNP array copy number data in a previously reported data
set of 732 NSCLC samples, (628 primary tumors and 104 cell
lines) (Table S1) [16,20,45,50,52]. We observed high level
amplification, defined as log2 ratio .0.7 or 3.25 normalized
DNA copies, of the 8p11-12 chromosomal segment encompassing
the FGFR1 locus in 44 (6%) of NSCLC samples (Figure 1a; Table
S2). The majority (93%; 41/44) of these amplifications were
relatively focal events (,50% of the length of chromosome 8p)
indicating preferential selection of the specific target genes within
the region of amplification . The inferred copy number of the
amplifications, normalized to a copy number of 2 for each sample,
ranged from 3.25 to 25 copies (median=2.8 copies). The
estimated extent of the region of focal amplifications ranged from
0.47 to 112.7 Mb (median=2.74 Mb).
To identify regions of significant copy-number alteration, we
applied GISTIC (Genomic Identification of Significant Targets In
Cancer) , and identified a 170 Kb region on 8p11 (38.28 to
38.45 Mb) as significantly amplified. While the overall pattern of
8p11 amplification was consistent with the literature on lung
cancer as reported, our sample size and resolution provided more
power to accurately identify and localize both large-scale and focal
chromosomal alterations as compared to earlier reports [45,52].
The sole genes within the region of amplification identified in our
analysis across all samples were FGFR1 and LETM2. In our copy
number data, WHSC1L1 was generally amplified with FGFR1 and
LETM2 (41/44 samples) but the whole WHSC1L1 gene did not fall
Figure 1. Amplifications of FGFR1 locus in NSCLC. (A) Copy number estimates at chromosome arm 8p11-12q for 44 NSCLC samples (columns;
ordered by amplification of 8p11) having amplification greater than 3.25 copies (log2 ratio of 0.7) from a collection of 732 NSCLC primary samples
and cell lines. The horizontal line indicates the region containing FGFR1, LETM2 and WHSC1L1 genes. The color scale ranges from blue (deletion) to red
(amplification) with estimated copy numbers shown. Grey regions represent the absence of SNP copy number data. (B) Bar graph depicting
percentages of samples harboring 8p11-12 amplification in lung adenocarcinomas (AC) and squamous cell carcinoma (SCC) demonstrates that FGFR1
amplification is observed in SCC at much higher frequency than AC. (C) FGFR1 expression (upper panel) shown in ten NSCLC cells; eight cell lines
harboring FGFR1 amplification—HCC1734, HCC95, NCI-H2444, Calu3, NCI-H2077, NCI-H1703, NCI-H1581 and NCI-H520 (indicated by red horizontal
bar below)—one NSCLC cell line harboring deletion of the region HCC15 (indicated by blue horizontal bar below)– and three NSCLC cells with no
amplification—A427, NCI-H226, NCI-H2170 (indicated by black horizontal bar below)– using actin as a loading control (shown in lower panel). FGFR1
copy number status and 8p11-12 amplicon length determined by SNP array is indicated below cells harboring amplification. Of note, NCI-H2077 and
NCI-1581 were found to be genotypically identical by fingerprinting analysis.
FGFR1 Amplification in Squamous Cell Lung Cancer
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within the GISTIC peak (chr8:38,284,229–38,451,475). Specifi-
cally, three primary tumor samples with amplified FGFR1 and
LETM2 genes had amplicon breakpoints within WHSC1L1,
explaining the exclusion of WHSC1L1 from the GISTIC
amplification peak (Figure S1; Figure S2). The amplicon break-
points within WHSC1L1 are consistent with a lack of amplification
of the functional SET domain (chr8:38,265,630–38,255,125)
associated with histone methyltransferase enzymatic activity of
the gene product . These results do not exclude WHSC1L1 as
the target of amplification on 8p11 along with FGFR1 but suggest
that its histone methyltransferase activity is not likely to be
specifically targeted for amplification.
In comparing subtypes of NSCLC primary tumors and cell
lines, 3.4% (20/588) of adenocarcinomas and 21% (12/57) of
squamous cell carcinomas harbored 8p11 amplifications, indicat-
ing that while 8p11 is amplified at appreciable frequencies across
both major NSCLC subtypes, it is preferentially amplified in SCCs
(p,0.001, Fisher exact test) (Figure 1b). No statistically significant
correlations were observed between the presence of 8p11
amplifications and available clinical parameters including histol-
ogy, degree of histological differentiation, stage at surgical
resection of the tumors and the age, gender, or reported ethnicity
of the patients (Table S3). Additionally, targeted sequencing of the
kinase domain of FGFR1 in 52 NSCLC cell lines and of the entire
FGFR1 coding sequence in three cell lines (NCI-H1581, NCI-
H1703, NCI-H2170) did not reveal any evidence of kinase domain
mutations (data not shown).
The SNP array data revealed an elevated FGFR1 gene copy
number in 11 NSCLC cell lines out of 104 NSCLC cell lines
analyzed (Figure S3) with amplifications observed in 36% (4/11) of
squamous NSCLC cell lines assayed. We examined FGFR1
protein expression by immunoblot analysis in 8 primary NSCLC
cell lines that harbor focal or broad 8p11 amplification above a
log2 ratio of 1.6 or 6.0 normalized DNA copies (NCI-H1703,
NCI-H2444, NCI-H520, NCI-1581, NCH-H2077, Calu3, NCI-
H1734, and HCC 95), 3 that have approximately neutral FGFR1
copy number (NCI-2170, NCI-H226 and A427) and 3 that harbor
FGFR1 deletion (NCI-H1781, NCI-H1563 and HCC15) by
immunoblot analysis. We found 6 out of 8 FGFR1 amplified
NSCLC cell lines overexpress FGFR1 as compared to cell lines
that do not harbor amplification, with the exceptions of the NCI-
H1703 and Calu3 cells (Figure S4; Figure 1c). Consistent with this
finding, NCI-H1703, which harbors a 8p11 amplification, has
been shown not to be dependent on FGFR1  but on amplified
PDGFRA [19,20]. Furthermore, an elevated level of phosphory-
lation of the FGFR1 substrate FRS2 was observed in NCI-H1581
large cell carcinoma cells carrying focal amplification of FGFR1,
but not in cells harboring relatively broader levels of FGFR1
amplification (Figure S4).
FGFR1 is required for survival of an NSCLC cell line
harboring focal amplification
Based on our copy number analysis, FGFR1 and LETM2 fell
within the GISTIC-defined region of statistically significant
amplification with WHSC11 immediately adjacent. To determine
the cellular requirement for genes in the region targeted by the
amplification, we assessed the requirement of WHSC1L1, LETM2
and FGFR1 expression for tumor maintenance by depleting them
individually using shRNA. Transfection with five shRNA
constructs targeting either WHSC1L1 or LETM2 had no
differential effect on the survival of cells harboring focal or broad
8p11-12 amplification as compared to control cells without the
amplification (data not shown).
In contrast, three out of five shRNA constructs targeting FGFR1,
all of which led to a 3- to 5-fold decrease in FGFR1 protein levels
relative to shRNA controls (Figure 2a), significantly inhibited cell
survival inan NSCLC cell linecarrying a focal FGFR1amplification
(NCI-H1581; Figure 2b). shRNA constructs #3 and #4, which did
not lead to significant knockdown of FGFR1 protein levels, did not
affect the survival of cells harboring 8p11 amplification (Figure 2b).
There were no observed survival effects of FGFR1 shRNA on cell
lines harboring relatively broader FGFR1 amplification (NCI-
H1703, HCC95, HCC1734, Calu3; not shown) or without FGFR1
amplification (NCI-H2170; Figure 2c. HCC15, NCI-H1563 and
NCI-H1781; not shown). Overall, these results argue that FGFR1
expression is required for the viability of at least one NSCLC cell
line carrying an FGFR1 amplification.
To further validate the specificity of cell viability changes
associated with shRNA-induced FGFR1-depletion, we examined
the ability of ectopic expression of FGFR1 cDNA to rescue the
effects of FGFR1 knock down. Wild-type FGFR1 cDNA, lacking
the 39-untranslated region (UTR) of the endogenous FGFR1
mRNA targeted by FGFR1 shRNA #1, was over-expressed in
NCI-H1581 cells transfected with this shRNA construct. Recon-
stituted levels of wild type FGFR1 protein resulted in significant
rescue of the survival inhibition phenotype (Figure 3a, c) but had
noimpact on the
(Figure 3b). Collectively, these experiments implicate FGFR1 as
a critical oncogenic target of 8p11-12 amplification.
Interestingly, one NSCLC cell line carrying a focal FGFR1
amplification, NCI-H2444 (Figure S3), was not sensitive to
knockdown of FGFR1 (data not shown). This cell line also
harbors an activating KRAS G12V mutation [57,58], which is
associated with resistance of colorectal cancers to the EGFR-
directed therapy cetuximab . NCI-H2444 does not show
FRS2 phosphorylation (Figure S4). This observation suggests that
co-occurrence of other activating oncogenes may relieve FGFR1
dependence and specifically that primary resistance to FGFR1
inhibition may be governed by KRAS mutation status.
FGFR kinase Inhibitors inhibits growth of FGFR1 amplified
To evaluate the possibility that targeting FGFR1 in 8p11
amplified SCCs could represent a new therapeutic strategy in
SCCs, we studied the effects of the pan-FGFR inhibitor PD173074
on NSCLC cell lines. The FGFR1-amplified NCI-H1581 cells
were sensitive to treatment with PD173074 as assayed by colony
formation in soft agar with IC50s in the range of 10–20 nM
(Figure 4a and Figure S5). In contrast, NCI-H2170 cells with wild
type FGFR1 copy number were insensitive to PD173074
(Figure 4a). We also performed PD173074 dose response curves
on cell survival in liquid culture to compare the sensitivity of cells
harboring FGFR1 amplification and those without and again
found that NCI-H1581 cells were killed at IC50 values of 14 nM,
while those without amplification required more than 100-fold
higher doses of PD173074 to inhibit proliferation (Figure 4b). In
agreement with these results, we also observed that a second
FGFR irreversible inhibitor, FIIN-1, inhibits proliferation of NCI-
H1581 cells with focal FGFR1 amplification as compared to NCI-
H2170 without FGFR1 amplification, with IC50 values of 2.5 nM
versus greater than 10 micromolar, respectively (Figure S6).
Here we have shown that FGFR1 is frequently amplified in lung
carcinomas and that this amplification is enriched in lung SCCs.
At least one NSCLC cell line with focally amplified FGFR1
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PLoS ONE | www.plosone.org5 June 2011 | Volume 6 | Issue 6 | e20351
requires the gene as demonstrated by shRNA depletion, and is also
sensitive to inhibition with FGFR kinase inhibitors.
GenesotherthanFGFR1 havebeen proposedtobe thefunctional
target of amplification on chromosome segment 8p11-8p12, most
notably WHSC1L1  and BRF2 . However, we believe that
the evidence presented here as well as in a recent report  argues
for FGFR1 as the functional target of amplification in at least one
NSCLC cell line. Additionally, in our data set WHSC1L1 is not
amplified in all the FGFR1 amplified samples, arguing that it is
unlikely to be the only relevant amplified gene in the 8p11-12
amplicon. The cell line that was shown to require WHSC1L1 for its
survival, NCI-H1703, does
(Figure 1c), does not show FRS2 phosphorylation (Figure S4) and
is dependent on another amplified tyrosine kinase oncogene,
PDGFRA [19,20]. In contrast, knockdown of WHSC1L1 had no
impact on FGFR1-amplified, FGFR1-expressing NCI-H1581 cells,
suggesting that amplification of either gene may contribute to
cellular transformation in the appropriate cellular context.
A recent study characterizing DNA amplification in NSCLC
suggested that BRF2, encoding a transcription initiation complex
subunit of RNA polymerase III, is the target of amplification in the
8p11 amplicon . We compared FGFR1 amplification to BRF2
amplification in light of this report and found that of 12 samples
with the highest amplification of FGFR1 in our dataset (log2 ratio
.2.5), only 4 samples include BRF2 in the amplified region,
suggesting that BRF2 is not the predominant target of 8p11
amplification in SCC (Figure S7a). We also found that of the 12
samples with highest amplification of BRF2 (log 2 ratio .1.8), all
have FGFR1 amplification (in one case, with what appears to be a
translocation within FGFR1) (Figure S7b). We believe that these
data argue in favor of FGFR1 instead of BRF2 as the more
commonly amplified gene in this region.
Our study and a recent report  identify FGFR1 as a
potential therapeutic target in NSCLC, where 8p11-12 amplifi-
cation is common, suggesting that high levels of expression of
FGFR1 may contribute to tumorigenesis or progression in
NSCLC. Interestingly, we did not find evidence of FGFR1
mutation in 52 samples which argues in favor of amplification
rather than mutation being the preferred mechanism of FGFR1
activation in a subset of NSCLCs. As FGFR1 amplification has
been reported in other tumor types, it may be the case that
FGFR1 inhibition will be a successful therapeutic strategy in a
variety of settings. As several FGFR kinase inhibitors are now in
clinical trials, including brivanib , dovitinib , BIBF 1120
, and SU-6668 , it could be useful to test these inhibitors
on NSCLC patients bearing focal FGFR1 amplifications. Given
Figure 2. NCI-H1581 cells are sensitive to knock-down of FGFR1 expression. (A) Effects of five FGFR1 shRNA constructs on FGFR1 protein
expression in NCI-H1581 cells as assayed by immunoblotting. shRNAs #1, #2 and #5 efficiently knock down endogenous FGFR1 expression in NCI-
H1581 cells infected with shRNA-expressing lentiviruses while shRNAs #3 and #4 do not. Actin is shown as a loading control (lower panel). (B and C),
infection with three independent FGFR1-suppressing hairpins (#1, #2 and #5) inhibits survival of NCI-H1581 cells over expressing FGFR1 (B) but did
not inhibit survival of cells not harboring FGFR1 amplification, NCI-H2170 (C) as assessed by WST assay. NI, no infection. shGFP, control hairpin specific
for green fluorescent protein used as a negative control. All results normalized to survival of cells infected with shGFP.
FGFR1 Amplification in Squamous Cell Lung Cancer
PLoS ONE | www.plosone.org6 June 2011 | Volume 6 | Issue 6 | e20351
Figure 3. Ectopic expression of FGFR1 coding region rescues lethality of an shRNA targeting the FGFR1 39 UTR. (A) Bar graph for rescue
assay. Lethality due to depleted levels on endogenous FGFR1 level in NCI-H1581 is rescued by over expression of wild type (Wt) full length FGFR1
coding sequence . (B) No effect on the survival of NCI-H2170 cells was observed due to over expression of wild type form of FGFR1. NCI-H2170 is not
dependent on FGFR1 activity. NI, no infection. shGFP, control hairpin specific for green fluorescent protein used as a negative control. All results are
normalized to survival of cells infected with shGFP. Data shown is as mean of three replicates. (C) Validation of FGFR1 rescue by immunoblotting.
Depleted levels of endogenous FGFR1 level in NCI-H1581 cells infected with FGFR1 shRNA-expressing lentiviruses targeting the FGFR1 39UTR (lane 1)
is rescued by overexpression of wild type form of FGFR1 cDNA lacking the 39UTR (lane 2) with concomitant modest rescue in the levels tyrosine
residue phosphorylation of the FGFR1 substrate FRS2 (middle panel). Actin is shown as a loading control (lower panel).
Figure 4. FGFR1 tyrosine kinase activity is essential in NCI-H1581 cells. (A) Treatment with the indicated concentrations of pan FGFR
inhibitor PD173074 inhibited soft agar colony formation by the NCI-H1581 NSCLC cell lines harboring FGFR1 amplification, as compared with the NCI-
H2170 line, which does not harbor FGFR1 amplification. Colonies were photographed and quantitated after 4 weeks. (B) Treatment with the indicated
concentrations of PD173074 inhibited survival of NCI-H1581 cells, but not of NCI-H2170 cells, as determined by WST assay performed after 4 days
treatment. IC50s are indicated.
FGFR1 Amplification in Squamous Cell Lung Cancer
PLoS ONE | www.plosone.org7June 2011 | Volume 6 | Issue 6 | e20351
that our results suggest that amplification alone will not always
predict sensitivity to FGFR1 inhibition, additional work is needed
to fully characterize the genetic alterations involved in NSCLC
carcinogenesis and dependency on FGFR1.
domain is not likely to be specifically targeted for
amplification at 8p11-12q. Heat map representation of SNP
array based segmented copy number on chromosome arm 8p11-
12q for 34 NSCLC samples (rows; ordered by amplification of a
170 kb chromosomal segment spanning WHSC1L1, LETM2 and
FGFR1) having amplification greater than 3.25 copies (log2 ratio of
0.7) from a collection of 732 NSCLC primary samples and cell
lines. Three primary tumor samples marked * harbor amplicon
with breakpoints within WHSC1L1 and only amplify FGFR1 and
LETM2 genes. The sample marked # appears to be a
translocation within FGFR1 removing its first exon. The locations
of WHSC1L1 SET domain and FGFR1 kinase domain are
indicated. The color scale ranges from blue (deletion) to red
(amplification) with estimated copy numbers as shown. Grey
denotes a region for which no SNPs are present on the array and
therefore represents indeterminate copy number.
WHSC1L1 histone methyltransferase activity
among primary tumors harboring amplified FGFR1 and
LETM2. Bar graph representation of unsegmented probe-level
copy number values for amplicons in 3 primary tumor samples
harboring break points within WHSC1L1. Estimated copy number
values (y axis) are plotted for individual SNPs at 8p11-12 locus (x
axis). Copy number of SNPs defining boundary of breakpoint are
indicated. Genomic positions of genes in region are shown along
the x axis.
Exclusion of WHSC1L1 functional domain
cell lines. SNP array based segmented copy number on
chromosome arm 8p11-12q for 18 NSCLC cell lines (rows;
ordered by amplification) from telomere (left) to centromere
(right). The color scale ranges from blue (deletion) to red
(amplification) with estimated copy numbers shown.
Elevated FGFR1 gene copy number in NSCLC
H1581 cells. Western blot analysis of FGFR1 in five different
NCIH1581, NCI-H520 and NCIH1703) indicated by red
horizontal bar below and in three NSCLC cell lines harboring
deletion of the region (NCI-H1781, NCI-H1563 and HCC15)
indicated by blue horizontal bar below. NCI-H1581 cells show
increased tyrosine residue phosphorylation of FGFR1 substrate
FRS2 as compared to other NSCLC cell lines using actin as a
loading control (shown in lower panel).
Activation of FGFR1 substrate FRS2 in NCI-
NCI-H1581 anchorage independent growth. Inhibition of
soft agar colony formation by the NCI-H1581 NSCLC cell line
harboring FGFR1 amplification, in the presence of increasing
concentrations of FGFR inhibitor PD173074, compared with
HCC15 and NCI-H2170 cells without FGFR1 amplification, and
NCI-H1703 cells that harbor FGFR1 amplification but do not
over-express FGFR1. Cells were seeded in soft agar and treated
with different concentrations of PD173074. Representative plates
from two independent experiments are presented. Colonies were
photographed and quantitated after 4 weeks.
FGFR1 tyrosine kinase activity is essential for
proliferation of NCI-H1581 cells. Treatment with the
indicated concentrations of irreversible FGFR inhibitor FIIN-1
inhibited survival of NCI-H1581 cells, but not of NCI-H2170
cells, as determined by WST assay performed after 4 days
treatment. IC50s are indicated.
FGFR1 tyrosine kinase activity is essential in
amplified gene at 8p11. Copy-number data from chromosome
8p11-12 in 12 samples sorted by highest copy number on the top.
The view is sorted by FGFR1 amplification (A) and BRF2
amplification (B). (A) Of the 12 samples with highest amplification
at FGFR1 of log2 ratio above 2.5, only 4 samples amplify BRF2 at
similar levels. (B) Out of 12 samples with log2ratio above 1.8 at
BRF2, all samples include FGFR1 amplification. Each sample is
represented as a horizontal row from telomere (left) to telomere
(right). Areas of red indicate gain; blue indicates loss. The positions
of FGFR1 and BRF2 are indicated with vertical lines.
FGFR1 instead of BRF2 is the more commonly
List of NSCLC Samples Analyzed by SNP
LETM2 and FGFR1.
Amplicons at 8p11-12 overlapping WHSC1L1,
8p11 Amplification Status and Clinical Features.
Categorization of 628 Primary Samples by
The authors thank Dr. Robin Mukhopadhyaya for use of the lentiviral
facility of his laboratory at Advanced Centre for Treatment, Research and
Education in Cancer, Tata Memorial Center, Mumbai, India.
Conceived and designed the experiments: AD MM. Performed the
experiments: KT AC. Provided samples and performed the genomic and
bioinformatic analysis: AD AHR CM PH JC NS HG KET. Provided cell
lines for assays: KET HG. Provided FGFR irreversible inhibitor
compound FIIN-1: NSG. Wrote and edited the AD PH MM.Reviewed
the manuscript: AD AHR PH CM JC TS AC KT NS HG NSG MM.
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