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>Gene
expression comparison of biopsies from DMD and normal
skeletal muscle
(2002) Gene expression comparison of biopsies from Duchenne
muscular dystrophy (DMD) and normal skeletal muscle. Proceedings
of the National Academy of Sciences U S A 99:15000-15005
Abstract
The primary cause of Duchenne muscular dystrophy (DMD)
is a mutation in the dystrophin gene leading to absence
of the corresponding RNA transcript and protein. Absence
of dystrophin leads to disruption of the dystrophin-associated
protein complex (DAPC) and substantial changes in skeletal
muscle pathology. Although the histological pathology
of dystrophic tissue has been well documented, the underlying
molecular pathways remain poorly understood. In order
to examine the pathogenic pathways and identify new or
modifying factors involved in muscular dystrophy, expression
microarrays were used to compare individual gene expression
profiles of skeletal muscle biopsies from twelve DMD patients
and twelve unaffected control patients. Two separate statistical
analysis methods were used to interpret the resulting
data; t-test analysis to determine the statistical significance
of differential expression and geometric fold change analysis
to determine the extent of differential expression. These
analyses identified 105 genes that differ significantly
in expression level between unaffected and DMD muscle.
Many of the differentially expressed genes reflect changes
in histological pathology. For instance, immune response
signals and extracellular matrix genes are overexpressed
in DMD muscle, an indication of the infiltration of inflammatory
cells and connective tissue. Significantly more genes
are overexpressed than underexpressed in dystrophic muscle,
with dystrophin underexpressed while other genes encoding
muscle structure and regeneration processes are overexpressed,
reflecting the regenerative nature of the disease.
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•PNAS Data
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>Molecular
profiles of inflammatory myopathies
(Oct 2002) S.A. Greenberg, D. Sanoudou, J.N. Haslett,
I.S. Kohane, L.M. Kunkel, A.H. Begss, A.A. Amato. Molecular
profiles of inflammatory myopathies. Neurology
59: 1170 - 1182.
Abstract
Objective: To describe the use of large-scale gene
expression profiles to distinguish broad categories of
myopathy and subtypes of inflammatory myopathies (IM)
and to provide insight into the pathogenesis of inclusion
body myositis (IBM), polymyositis (PM), and dermatomyositis
(DM). Methods: Using Affymetrix GeneChip microarrays,
we measured the simultaneous expression of approximately
10,000 genes in muscle specimens from 45 patients in 4
major disease categories (dystrophy, congenital myopathy,
inflammatory myopathy, and normal). We separately analyzed
gene expression in 14 patients limited to the three major
subtypes of IM. We used bioinformatics techniques to classify
specimens with similar expression profiles based on global
patterns of gene expression and to identify genes with
significant differential gene expression compared to normal.
Results: Ten of 11 patients with IM, all normals and nemaline
myopathies, and 10 of 12 patients with Duchenne muscular
dystrophy were correctly classified by this approach.
The various subtypes of inflammatory myopathies have distinct
gene expression signatures. Specific sets of immune-related
genes allow for molecular classification of patients with
IBM, PM, and DM. Analysis of differential gene expression
identifies as relevant to disease pathogenesis previously
reported cytokines, major histocompatibility complex class
I and II molecules, granzymes, and adhesion molecules
as well as newly identified members of these categories.
Increased expression of actin cytoskeleton genes is also
identified. Conclusions: The molecular profiles of muscle
tissue in patients with inflammatory myopathies are distinct
and represent molecular signatures from which diagnostic
insight may follow. Large numbers of differentially expressed
genes are rapidly identified. |
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To download data we recommend
using a high-speed connection because of the large file
sizes.
•The microarray data set for 16 experiments (6
IBM, 6 DM, 2 PM, and 2 NORM) can be downloaded as an
Excel file from: http://potato.chip.org/~steveng1/Greenberg-et-al-IM-Dataset.xls
(9.5 MB).
• Various database analyses performed on this data
set can be downloaded as an Access database from: http://potato.chip.org/~steveng1/Greenberg-et-al-IM-Analyses.mdb
(9.3 MB).
• Studies on the effect of patient age, gender,
and muscle on clustering of expression profiles: Because
of their potentially confounding influences, we have
studied the effects of patient age, gender, and choice
of muscle on molecular profiles. Fifteen normals (mean
age 25 years, range 1-72) showed no substantial tendency
for an age-related or gender clustering effect (Figure
1), though some effect may be present, particularly
for gender. Similar analysis for choice of muscle (e.g.,
quadriceps, biceps brachii) showed no effect on clustering.
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Figure 1.
(Below) Effect of age and gender on clustering in 15 normal
muscle specimens. Hierarchical clustering across 12,600
genes, filtered for variation, resulting in 2491 genes
across 15 normal specimens. No substantial age-related
clustering effect is evident, though some effect may be
present. The cluster consisting of H207, H239, and H126
may be an age effect or related to the fact that these
3 specimens are the only autopsy specimens from the group.
Similarly for gender, among the 4 major clusters present,
2 contain a mixture of male and female specimens. One
cluster, S93-3678, Ema2, S93-482, and H029, may be a gender
related effect. |
Figure 1. |
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>Gene
Expression Profiling of Duchenne Muscular Dystrophy Skeletal
Muscle
(March 2003) In Press in Neurogenetics Haslett J. N.,
Sanoudou D., Kho A. T., Han, M., Bennett R. R., Kohane
I. S., Beggs A. H. and Kunkel L. M.
Abstract
The primary cause of Duchenne muscular dystrophy is a
mutation in the dystrophin gene, leading to absence of
the corresponding protein, disruption of the dystrophin-associated
protein complex and substantial changes in skeletal muscle
pathology. Although the primary defect is known and the
histological pathology well documented, the underlying
molecular pathways remain in question. To clarify these
pathways, we used expression microarrays to compare individual
gene expression profiles for skeletal muscle biopsies
from DMD patients and unaffected controls. We have previously
published expression data for the 12,500 known genes and
full-length ESTs on the Affymetrix HG-U95Av2 chips. Here
we present comparative expression analysis of the 50,000
EST clusters represented on the remainder of the Affymetrix
HG-U95 set. Individual expression profiles were generated
for biopsies from ten DMD patients and ten unaffected
control patients. Two statistical analysis methods were
used to interpret the resulting data; t-test analysis
to determine the statistical significance of differential
expression and geometric fold change analysis to determine
the extent of differential expression. These analyses
identified 183 probe sets (59 of which represent known
genes) that differ significantly in expression level between
unaffected and disease muscle. This study adds to our
knowledge of the molecular pathways that are altered in
the dystrophic state. In particular it suggests that signaling
pathways might be substantially involved in the disease
process. In addition it highlights a large number of unknown
genes whose expression is altered and whose identity therefore
becomes important in understanding the pathogenesis of
muscular dystrophy.
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The
data files below are in an Excel PDF format. To download
data we recommend using a high-speed connection because
of the large file sizes.
Adobe Acrobat Required
Click
here to download |
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•Neurogenetics
U95B
•Neurogenetics
U95C
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•Neurogenetics
U95D
•Neurogenetics
U95E
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To view other publications that Harvard Neuromuscular Disease
Project researchers participated in, please click here.
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