Cross Species Genomic Analysis Identifies a Mouse
Model as Undifferentiated Pleomorphic Sarcoma/
Malignant Fibrous Histiocytoma
Jeffrey K. Mito1, Richard F. Riedel2, Leslie Dodd3, Guy Lahat4, Alexander J. Lazar5, Rebecca D. Dodd6,
Lars Stangenberg7, William C. Eward8, Francis J. Hornicek7, Sam S. Yoon7, Brian E. Brigman8, Tyler
Jacks9,10, Dina Lev3, Sayan Mukherjee11,12, David G. Kirsch1,6*
1Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, United States of America, 2Division of Medical Oncology,
Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America, 3Department of Pathology, Duke University Medical Center,
Durham, North Carolina, United States of America, 4Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
of America, 5Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America, 6Department of Radiation
Oncology, Duke University Medical Center, Durham, North Carolina, United States of America, 7Department of Surgery, Massachusetts General Hospital and Harvard
Medical School, Boston, Massachusetts, United States of America, 8Division of Orthopaedic Surgery, Department of Surgery, Duke University Medical Center, Durham,
North Carolina, United States of America, 9Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America,
10Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America, 11Department of Statistical Sciences, Duke University, Durham, North Carolina,
United States of America, 12Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, North Carolina, United States of America
Undifferentiated pleomorphic sarcoma/Malignant Fibrous Histiocytoma (MFH) is one of the most common subtypes of
human soft tissue sarcoma. Using cross species genomic analysis, we define a geneset from the LSL-KrasG12D; Trp53Flox/Flox
mouse model of soft tissue sarcoma that is highly enriched in human MFH. With this mouse geneset as a filter, we identify
expression of the RAS target FOXM1 in human MFH. Expression of Foxm1 is elevated in mouse sarcomas that metastasize to
the lung and tissue microarray analysis of human MFH correlates overexpression of FOXM1 with metastasis. These results
suggest that genomic alterations present in human MFH are conserved in the LSL-KrasG12D; p53Flox/Floxmouse model of soft
tissue sarcoma and demonstrate the utility of this pre-clinical model.
Citation: Mito JK, Riedel RF, Dodd L, Lahat G, Lazar AJ, et al. (2009) Cross Species Genomic Analysis Identifies a Mouse Model as Undifferentiated Pleomorphic
Sarcoma/Malignant Fibrous Histiocytoma. PLoS ONE 4(11): e8075. doi:10.1371/journal.pone.0008075
Editor: Syed A. Aziz, Health Canada, Canada
Received October 9, 2009; Accepted November 3, 2009; Published November 30, 2009
Copyright: ? 2009 Mito 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: This study was supported by the Howard Hughes Medical Institute (TJ) and by KO8 CA 114176 and RO1 CA 138265 (DGK), T32 GM-07171 (JM), and the
Maria Garcia-Estrada Foundation (RR). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests exist.
* E-mail: firstname.lastname@example.org
Malignant Fibrous Histiocytoma was first described in the 1960s
and quickly became the most commonly diagnosed adult soft
tissue sarcoma . Because these tumors do not appear to arise
from histiocytes, the term Malignant Fibrous Histiocytoma has
recently fallen out of favor and many pathologists now classify
these tumors as undifferentiated pleomorphic sarcomas. Despite
this change in nomenclature, undifferentiated pleomorphic
sarcoma (referred to here as MFH) remains one of the most
common adult soft tissue sarcomas encountered in the clinic.
However, the cell(s) of origin of MFH is unknown. Indeed, some
have suggested that MFH is a collection of undifferentiated
mesenchymal tumors sharing a common morphology rather than
a single clinical entity [2,3,4]. This debate could be clarified by
identifying the cell(s) of origin of a mouse model for MFH.
Whether MFH describes a cancer that is a single pathogenic entity
or an undifferentiated state shared by several sarcoma subtypes,
the survival of patients with MFH has not improved for decades.
Therefore, identifying a mouse model of MFH may also lead to
better treatments for patients with this diagnosis.
Human MFH is characterized by a propensity to metastasize to
the lungs and by a range of histologic appearances including spindle
and pleomorphic cells. Although these features are recapitulated in
a mouse model of soft tissue sarcoma initiated by conditional
mutations in Kras and Trp53 , it is not clear whether this model is
most similar to human MFH or another soft tissue sarcoma.
Therefore, we sought to more accurately classify the sarcoma
subtype for this mouse model using gene expression profiling.
Mouse Genotyping, Tumor Generation, and
Determination of Metastatic Potential
Both mouse genotyping and generation of tumors was carried
out as described previously  in accordance with Duke
University and MIT Institutional Animal Care and Use
Committee approved protocols. Sarcomas were induced in the
lower left limb and allowed to grow until ,200 mm3in volume.
Tumors were then surgically excised via amputation of the limb
and animals followed for a minimum of 4 months to determine the
metastatic potential of the primary tumor.
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RNA was extracted from LSL-KrasG12D; Trp53Flox/Floxtumors or
normal muscle using TRIzol reagent (Invitrogen) and was purified
using RNeasy mini kit (Qiagen).
Microarray Processing and Analysis
Full details can be found in supplementary methods S1. Briefly,
gene expression was determined using Affymetrix 430A 2.0 arrays
(Affymetrix) as described in detail online (http://www.genome.
duke.edu/cores/microarray/). CEL files were processed using the
RMA algorithm [6,7] to normalize the data. Genesets were
identified using a signal-to-noise metric.
Human and Mouse datasets [8,9,10] were downloaded from
GEO (GSE6461, GSE6481, GSE2553, and GDS1209), normal-
ized with RMA (when appropriate). Genesets and array data were
used in GSEA as described previously . Classes were defined
as one soft tissue sarcoma subtype versus controls (other sarcoma
or normal muscle) present in their respective datasets.
Database Accession Numbers
Microarray data was generated in conformity to MIAME
guidelines and has been deposited in the GEO database under
accession number GSE16779.
Oncogenic Pathway Predictors
Human soft tissue sarcoma datasets [9,10] were combined using
ComBat  and normal tissue samples removed from the
combined dataset. An oncogenic pathway classifier for Ras
pathway activity was developed as described previously . This
classifier was used to compare undifferentiated pleiomorphic
sarcoma/MFH samples (n=29) against all other soft tissue
sarcomas. Significance was determined using a non-parametric
Histology and Immunohistochemistry and Image Analysis
All human samples were obtained from tissue repositories at
Duke and MD Anderson. These samples were used in accordance
with Duke and MD Anderson Cancer Center Institutional Review
Board (IRB) approved protocols under a waiver of consent. Five
micron thick sections were cut from formalin fixed paraffin
embedded samples. Samples were subjected to standard hema-
toyxlin and eosin staining or immunohistochemistry. Immunohis-
tochemistry was performed with the following antibodies:
ab47808), using the Vectastain ABC Rabbit IgG kit with
Vectastain Elite ABC Reagent (Vector Labs).
Brightfield images of slides taken at 40x were used for analysis using
Image Pro AMS v6.1. The counting module was trained using both
positive and negative nuclear staining for phospho-ERK. A minimum
of 3000 nuclei were counted per sample and a ratio between total
nuclei with positive nuclei to total nuclei was determined using a
minimal and maximal area of 100 and 1000 pixels respectively.
Tissue Microarrays (TMAs)
TMAs were generated at MD Anderson Cancer Center and
contained a clinically annotated set of 214 soft tissue sarcoma
samples including: 166 MFH/Unclassified sarcomas, 19 synovial
sarcomas, 6 leiomyosarcomas, 8 pleomorphic liposarcomas, 8
myxoid liposarcomas, 6 atypical lipomatous tumors, and 1
dedifferentiated liposarcoma. TMAs were stained as above and
scored semiquantitatively on a scale from 0-3+ by a musculoskel-
etal pathologist (L.D.) blinded to patient outcome. Scores were
correlated with both diagnosis and clinical outcome.
Statistical Analysis of TMAs
Scoring of TMAs was correlated with diagnosis, and metastasis-
Correlation of immunohistochemical staining with diagnosis was
tested for normality using a chi-square test. This did not reach statistical
significance, therefore comparison between MFH and other soft tissue
Metastasis free survival analysis was performed on MFH samples
comparing 3+ staining to 0-2+ staining. Survival was determined by
Cross-Species Genomic Analysis of LSL-KRasG12D;
Trp53Flox/FloxMouse Model of Soft Tissue Sarcoma
We hypothesized that genes most differentially expressed
between mouse sarcoma and normal muscle would provide a
useful molecular signature to interrogate human sarcoma datasets
(Fig. 1A). To test this approach, we first analyzed published gene
expression data from a previously validated mouse model of
synovial sarcoma . After identifying a geneset of 100 genes
highly overexpressed in synovial sarcoma compared to normal
muscle (Table S1) we used Gene Set Enrichment Analysis (GSEA)
 to probe gene expression data from three studies of human soft
tissue sarcomas [8,9,10]. We demonstrated strong statistical
enrichment (p,0.001, FDR,0.02) of this geneset in human
synovial sarcomas, but not in other subtypes of soft tissue sarcoma
(Fig. S1, Table S2). This result is in agreement with GSEA for the
mouse model of synovial sarcoma that was previously reported .
Having validated this approach, we identified a geneset of 100
genes highlyoverexpressedinthe LSL-KrasG12D; Trp53Flox/Floxmouse
model of soft tissue sarcoma (n=17) compared to normal muscle
(n=4) (Table S3). When this geneset was analyzed in the three
human datasets of soft tissue sarcoma [8,9,10], only MFH samples
showed statistical enrichment (p=0.001; FDR=0.012) (Table 1,
Fig. 1B). Enrichment was seen in all three datasets [8,9,10], which
represent 325 sarcoma samples and two types of array platforms.
Moreover, genesets derived from human MFH (Table S4) also
enriched in the mouse sarcoma data (p,0.001; FDR,0.001)
(Fig. 1C). These data indicate that this mouse sarcoma model and
human MFH share common genomic features.
Ras Pathway Activity Is Enriched in Human MFH
The initiating events of human MFH are not well understood.
Previous studies have shown mutations in p53 occur in 36% of
human MFH  while the rate of canonical RAS mutations in
human MFH varies from 0–50% [16,17]. We hypothesized that the
RASpathway maybeactivated inhumanMFHeven inthe absence
of canonical RAS mutations. To explore a link between MFH and
Ras, we utilized previously described oncogenic pathway predictors
that correlatewithRASactivity.TheRasoncogenicsignature is
enriched in human MFH samples compared to a panel of other soft
tissue sarcomas (p=0.002) (Fig. 2A). Moreover, in human MFH
(n=8) lacking canonical RAS mutations, we observed nuclear
staining of phospho-ERK by immunohistochemistry in greater than
30% of tumor cells in 7 of 8 samples (Fig. S2).
FoxM1 Is a Novel Marker of Metastasis in MFH
Because human MFH and the LSL-KrasG12D; Trp53Flox/Floxmouse
model of soft tissue sarcoma share common genomic features, we
wanted to determine if these shared features could be used to identify
diagnostic or prognostic factors for human MFH. As MFH is
considered a diagnosis of exclusion, we initially attempted to identify a
marker that is specific to MFH. We identified a panel of 10 candidate
A Mouse Model of UPS/MFH
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Figure 1. Cross-species genomic comparison. A, Schematic for cross species genomic comparison using GSEA. B, The LSL-KrasG12D; Trp53FloxFlox
sarcoma geneset (Table S3) is highly enriched in human MFH in the Nakayama et al. soft tissue sarcoma dataset  [p=0.0014; False Discovery Rate
(FDR)=0.012; Enrichment Score (ES)=0.74; Normalized Enrichment Score (NES)=2.09]. C, Conversely, a human MFH geneset (Table S4) is strongly
enriched in the mouse model of soft tissue sarcoma (p,0.001, FDR,0.001, ES=0.637 NES=2.78).
Table 1. GSEA results for the LSL-KrasG12D; Trp53Flox/Floxgeneset derived from the mouse model of soft tissue sarcoma (Table S3).
Nakayama Detwiller Baird 
Malignant Fibrous Histiocytoma0.001 (0.012)0.014 (0.149) 0.024 (0.190)
Fibrosarcoma0.177 (0.326) 0.159 (0.784)DNE
Leiomyosarcoma0.262 (0.673) 0.854 (0.981) 0.401 (0.715)
Synovial Sarcoma DNEDNEDNE
Rhabdomyosarcoma-- 0.586 (0.781)
Ewing’s Sarcoma-- DNE
The mouse sarcoma geneset was used to examine three human soft tissue sarcoma datasets [8,9,10]. Only undifferentiated pleomorphic sarcoma/MFH demonstrated
statistically significant enrichment. Table denotes p-values with FDR in parentheses. Bolded results note significance with p,0.05; FDR,0.25. DNE=Did Not Enrich, dash
marks represent insufficient data points to do comparison.
A Mouse Model of UPS/MFH
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and the mouse sarcoma model (Table S5). Expression of 9 of these
candidates was validated in an independent cohort of mouse sarcomas
by Q-RT-PCR (Fig. S3).
FOXM1, which is a member of the forkhead transcription
factor family that enhances tumorigenesis in other solid tumors
, was selected for further analysis because it is downstream of
Ras . Immunohistochemistry for FOXM1 in a panel of 8
human MFH samples demonstrated nuclear staining for FOXM1
in all 8 tumors (Fig. S2). We next analyzed the expression of
FOXM1 in a clinically annotated tissue microarray (TMA)
containing 166 MFH samples and 48 other soft tissue sarcomas.
Although 84% of the MFH samples stained positive for FOXM1
(p=0.02, Fig. S4), this marker was also expressed, but to a lesser
degree, in other sarcoma subtypes. Therefore, FOXM1 may not
be a useful diagnostic marker for human MFH.
Because FoxM1 has previously been shown to regulate the
expression of matrix metalloproteases MMP-2 and -9, which are
key mediators of cell invasion , we hypothesized that high
FOXM1 expression may correlate with metastasis. We measured
Foxm1 gene expression in murine soft tissue sarcomas and found a
correlation with the development of lung metastases (Fig. 2B,
p=0.01). Likewise, human MFH with high FOXM1 expression
correlated with decreased metastasis-free survival compared to
sarcomas with low to no FOXM1 expression (Fig. 2C). In contrast,
overexpression of another candidate marker MELK (Table S5) did
not correlate with metastasis-free survival (Fig. S5).
We used cross species genomic analysis to determine which
human sarcoma subtype is represented by the LSL-KrasG12D;
Trp53Flox/Floxmouse model of soft tissue sarcoma. We identified a
geneset in the mouse sarcomas that is highly enriched in human
MFH. This geneset was not enriched in other human sarcomas,
such as fibrosarcoma or leiomyosarcoma, which can be difficult to
of Ras pathway activity in human MFH compared to other types of
soft-tissue sarcoma. Additionally, the LSL-KrasG12D; Trp53Flox/Flox
mouse model of soft tissue sarcoma has a propensity to metastasize
to the lungs much like human MFH . Based on this genomic
analysis, the pattern of lung metastasis, and the similarity of the
mouse sarcomas to human MFH at the histological level (Fig. S6),
we conclude that this model closely resembles MFH.
We recognize that the diagnosis of undifferentiated pleomorphic
[2,3,4]. Our results do not exclude the possibility that MFH is a
collection of mesenchymal tumorsderived fromdifferent celltypesthat
share an undifferentiated state. However, our finding of a sarcoma
that this subtype of human sarcoma shares an underlying biology
beyond a common histologic appearance. Moreover, the use of cross-
species analysis to identify FOXM1 as a marker of metastasis-free
survival in human MFH supports the use of this mouse model to
and to develop novel therapies for human MFH.
Supplementary Methods S1
Found at: doi:10.1371/journal.pone.0008075.s001 (0.07 MB
sarcoma versus control (normal muscle). Geneset was derived
using signal-to-noise metric.
Found at: doi:10.1371/journal.pone.0008075.s002 (0.04 MB
Geneset derived from mouse model of synovial
Figure 2. The LSL-KrasG12D; Trp53Flox/Floxmouse model of soft
tissue sarcoma provides insight into human MFH. A, An
oncogenic Ras signature is enriched in human MFH samples compared
to other types of soft tissue sarcoma (p=0.002, non-parametric Mann-
Whitney test). B, Q-RT-PCR for Foxm1 in murine soft tissue sarcomas
correlates with metastatic potential of primary tumors (p=0.01, two-
tailed student’s T-test, scale bars represent one standard deviation). C,
FOXM1 expression in a tissue microarray correlates with metastasis free
survival in human MFH (p=0.038).
A Mouse Model of UPS/MFH
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from mouse model of synovial sarcoma (Table S1). The mouse
synovial sarcoma geneset was used to examine three datasets of
human soft tissue sarcomas. Table denotes p-values with FDR in
parentheses. Bolded results note significance with p,0.05;
FDR,0.25. DNE=Did Not Enrich, dash marks represent
insufficient data points to do comparison.
Found at: doi:10.1371/journal.pone.0008075.s003 (0.04 MB
GSEA results for synovial sarcoma geneset derived
mouse model of soft tissue sarcoma compared to control (normal
muscle). Genes were identified using signal-to-noise metric with
the top 100 genes used in the geneset.
Found at: doi:10.1371/journal.pone.0008075.s004 (0.04 MB
Geneset derived from LSL-KrasG12D; Trp53Flox/Flox
Nakayama et al  using signal-to-noise metric comparing
MFH versus control (other soft tissue sarcomas).
Found at: doi:10.1371/journal.pone.0008075.s005 (0.05 MB
Geneset used in Figure 1c was derived from
identified using differentially expressed genes between human
MFH and other sarcomas (T-test, p,0.001) [9–10]. This list of
genes was then cross referenced against the LSL-KrasG12D;
Trp53Flox/Floxsoft tissue sarcoma geneset (Table S3) and ten
overlapping genes were identified.
Found at: doi:10.1371/journal.pone.0008075.s006 (0.03 MB
Candidate marker genes of human MFH were
shows strong enrichment for human synovial sarcoma (Enrich-
ment Score(ES)=0.67, Normalized
(NES)=2.21) in a human soft tissue sarcoma dataset
Found at: doi:10.1371/journal.pone.0008075.s007 (0.21 MB
The mouse synovial sarcoma geneset (Table S1)
pho-ERK and B FOXM1 show strong nuclear staining from the
same human tumor sample. All scale bars represent 100 microns.
Found at: doi:10.1371/journal.pone.0008075.s008 (9.18 MB
Representative immunohistochemistry for A phos-
selected for Q-RT-PCR using an independent set of mouse soft
tissue sarcomas (n=5) and normal muscle samples (n=3). Relative
fold expression determined to lowest expressing normal muscle
sample. Significance of differentially expressed genes was deter-
mined by two-tailed student’s T-test.
Found at: doi:10.1371/journal.pone.0008075.s009 (0.31 MB
Box and whisker plots of nine candidate genes
FOXM1 and MELK identifies expression in MFH. Tissue
Microarrays (TMAs) containing 214 soft tissue sarcomas were
stained for FOXM1 and scored semi-quantitatively. The degree of
staining for A FOXM1 (p=0.0017, non-parametric Mann-
Whitney test) and B MELK (p=0.02, non-parametric Mann-
Whitney test) was correlated with MFH.
Found at: doi:10.1371/journal.pone.0008075.s010 (0.20 MB
Immunostaining of tissue microarrays (TMAs) for
metastasis free survival (p=0.46) in MFH patients. MFH patients
were segregated based on high (3+) or low (0-2+) staining on
TMAs and survival of the cohorts was compared by Kaplan-Meier
Found at: doi:10.1371/journal.pone.0008075.s011 (0.28 MB
Potential biomarker MELK does not correlate with
tissue sarcoma mimics human undifferentiated pleomorphic
sarcoma/Malignant Fibrous Histiocytoma (MFH). A, The gross
appearance of mouse sarcomas includes areas of necrosis and
hemorrhage. The microscopic appearance of these tumors
includes high grade sarcomas with B spindle cells and C more
pleomorphic cells with D epitheloid like cells and frequent atypical
nuclei (arrow). All scale bars represent 100 mm.
Found at: doi:10.1371/journal.pone.0008075.s012 (1.05 MB JPG)
The LSL-KrasG12D; Trp53Flox/Floxmouse model of soft
Conceived and designed the experiments: DL SM DGK. Performed the
experiments: JKM RDD LMS WCE FJH SY BEB. Analyzed the data:
JKM RFR LD GL AJFL. Contributed reagents/materials/analysis tools:
LD TJ DL. Wrote the paper: JKM DGK.
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