Molecular Epigenetics and Genetics in Neuro-Oncology
Raman P. Nagarajan and Joseph F. Costello
Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center,
University of California San Francisco, San Francisco,
Summary: Gliomas arise through genetic and epigenetic alter-
ations of normal brain cells, although the exact cell of origin
for each glioma subtype is unknown. The alteration-induced
changes in gene expression and protein function allow uncon-
trolled cell division, tumor expansion, and infiltration into sur-
rounding normal brain parenchyma. The genetic and epigenetic
alterations are tumor subtype and tumor-grade specific. Partic-
ular alterations predict tumor aggressiveness, tumor response to
therapy, and patient survival. Genetic alterations include dele-
tion, gain, amplification, mutation, and translocation, which
result in oncogene activation and tumor suppressor gene inac-
tivation, or in some instances the alterations may simply be a
consequence of tumorigenesis. Epigenetic alterations in brain
tumors include CpG island hypermethylation associated with
tumor suppressor gene silencing, gene-specific hypomethyla-
tion associated with aberrant gene activation, and genome-wide
hypomethylation potentially leading to loss of imprinting, chro-
mosomal instability, and cellular hyperproliferation. Other epi-
genetic alterations, such as changes in the position of histone
variants and changes in histone modifications are also likely to
be important in the molecular pathology of brain tumors. Given
that histone deacetylases are targets for drugs that are already in
clinical trial, surprisingly little is known about histone acety-
lation in primary brain tumors. Although a majority of epige-
netic alterations are independent of genetic alterations, there is
interaction on specific genes, signaling pathways and within
chromosomal domains. Next-generation sequencing technol-
ogy is now the method of choice for genomic and epigenome
profiling, allowing more comprehensive understanding of ge-
netic and epigenetic contributions to tumorigenesis in the brain.
Key Words: Genomics, epigenomics, gliomas, methylation,
GENE REGULATION BY EPIGENETIC
Epigenetics is defined as mitotically heritable changes
in gene expression that are not due to changes in the
primary DNA sequence. Epigenetic mechanisms include
enzymatic modification of DNA and associated histone
proteins that regulate and maintain gene expression
states, and have important roles in chromosome structure
and stability. The discovery of altered epigenetic profiles
in human neoplasia has led to a new paradigm in which
both genetic and epigenetic mechanisms contribute sig-
nificantly to cancer and perhaps many other common
human diseases. Because of their reversible nature, epi-
genetic alterations are being targeted therapeutically in
cancer clinical trials.
Covalent modifications of DNA and amino acids on
histones are two major mechanisms of epigenetic gene
regulation. DNA methylation involves the addition of a
methyl group to cytosine to create 5-methylcytosine. In
mammals methylation occurs primarily at 5=-CpG-3=
dinucleotides, and occasionally at CpNpGs as well.1
DNA methylation is controlled by DNA methyltrans-
ferases (DNMT) that create (DNMT3A, DNMT3B) or
maintain (DNMT1) patterns of methylation.2,3DNA
methylation is required for maintaining gene silencing on
the inactive X chromosome,4–6parental allele-specific
expression of imprinted loci,7and tissue and cell-type-
specific gene expression. Methylation is also required for
silencing transposable elements and maintaining genome
stability8,9and is a critical regulator of pluripotency
A second type epigenetic mechanism is the post-trans-
lational modification of N-terminal tails of histone pro-
teins by acetylation, methylation, phosphorylation, ubiq-
uitylation, sumoylation, ADP ribosylation, biotinylation,
and potentially other modifications.13Like DNA meth-
ylation, specific enzymes also catalyze post-translational
Address correspondence and reprint requests to: Joseph F. Costello,
Ph.D., Brain Tumor Research Center, Department of Neurosurgery,
Helen Diller Family Comprehensive Cancer Center, University of Cal-
ifornia San Francisco, San Francisco, CA, 94143. E-mail: jcostello@
Neurotherapeutics: The Journal of the American Society for Experimental NeuroTherapeutics
Vol. 6, 436–446, July 2009 © The American Society for Experimental NeuroTherapeutics, Inc.
modifications of histones, and include acetyltransferases
and deacetylases, methyltransferases and demethylases,
among others. In contrast to DNA methylation, histone
methylation can be mono-, di-, or tri-methylated on a
single, specific lysine (i.e., at H3K4). Multiple types of
modifications are present on a single histone molecule,
increasing the combinatorial complexity, referred to as a
“histone code.” In addition to DNA methylation and
histone modifications, there are other interrelated, poten-
tially epigenetic mechanisms including specific deposi-
tion of histone variants, noncoding RNAs, chromatin
remodeling, and nuclear organization of DNA. These
mechanisms add additional layers of regulation and
maintenance of gene expression states in both normal
and diseased tissues.
EPIGENETIC MECHANISMS REGULATING
GENE EXPRESSION IN THE BRAIN
Epigenetic mechanisms are critical to the development
and function of the mammalian CNS). Global DNA
methylation levels change during brain development,14
and methylation of specific genes can vary among dif-
ferent brain regions, cell types, and potentially even be-
tween the same cell type from different brain regions.15
The relationship between brain-region-specific gene ex-
pression16and brain-region-specific DNA methylation
has not been fully explored. However, distinct CNS cell
types may be differentially marked by DNA methylation.
In murine astrogliogenesis, for example, DNA demeth-
ylation of the Gfap promoter including a critical STAT3
DNA binding site is associated with activation of Gfap
transcription, a known marker of the astroglial lineage.17
One particular CpG site within the Gfap promoter is
methylated in neural precursors and postmitotic neurons
but unmethylated in astrocytes.17–19
DNA methyltransferases are important in CNS devel-
opment and function. The maintenance methyltrans-
ferase DNMT1 is highly expressed in the mammalian
brain,20–22including in postmitotic neurons, despite its
proposed primary role in copying methylation during
DNA replication. DNA methylation changes in response
to neural activity may be one function of DNMT1 in
postmitotic neurons.23Conditional Dnmt1 deletion in
murine postmitotic neurons does not affect overall DNA
methylation levels or cell survival.24On the other hand,
conditional Dnmt1 deletion in embryonic day 12 neuro-
blasts resulted in DNA hypomethylation and lethality
immediately after birth due to CNS-associated respira-
tory failure, indicating a requirement for DNA methyl-
ation in these cells. Mosaic mice with ?30% Dnmt1-/-
cells survived into adulthood, but mutant cells were
rapidly eliminated from the brain within 3 weeks of birth,
further supporting the necessity of DNMT1 for CNS cell
survival. Dnmt3b is expressed in the murine CNS for a
short time during neurogenesis, whereas Dnmt3a is ex-
pressed in both prenatal and postnatal CNS.25Dnmt3b-/-
mice exhibit prenatal lethality and neural tube defects,
demonstrating a critical role for DNMT3b in neurode-
velopment.26Mice with conditional deletion of Dnmt3a
in the nervous system are apparently born healthy but die
prematurely, displaying hypoactivity, abnormal walking,
and poor performance on tests of neuromuscular function
and motor coordination.27Thus, the effects of Dnmt
deficiency on brain functions are significant, but the spe-
cific effects on neurons and glia require further investi-
Recent evidence indicates that neuronal differentiation
is regulated in part by DNA demethylation and polycomb-
mediated histone H3 K27 trimethylation (H3K27me3).28
DNA methylation contributes to repression of pluripo-
tency in lineage-committed neural progenitors. Also,
promoters marked by H3K27me3 in neural stem cells
often gain DNA methylation during differentiation.29
Thus, context-dependent interactions between different
epigenetic mechanisms guide neural differentiation, and
underscore the general importance of epigenetics in nor-
mal CNS development and maintenance of cellular iden-
Several human neurodevelopmental disorders are
caused by mutations in genes encoding proteins involved
in epigenetic mechanisms. Rett syndrome, for example,
is a severe neurodevelopmental disorder caused by mu-
tations in MECP2, which encodes a protein that can bind
to methylated DNA and regulate gene expression.30ICF
syndrome, which includes mental retardation, is caused
by mutations in the de novo DNA methyltransferase
DNMT3B.31–33Furthermore, the dependence of the CNS
on epigenetic regulation extends beyond DNA methyl-
ation and DNA methyltransferases, as mutations in genes
encoding other epigenetic regulatory proteins can cause
neurodevelopmental disorders. One example is JARID1/
SMCX, encoding a JmjC-domain-containing histone de-
methylase, which, when mutated, causes a form of X-
linked mental retardation.34–36These examples illustrate
the importance of epigenetic control of gene expression
in the development and function of the CNS. This knowl-
edge of the critical role of epigenetic mechanisms and
marks in the CNS provides a foundation for understand-
ing the role of epigenetic regulation in tumors arising
from CNS cells.
DNA HYPOMETHYLATION AND CPG
ISLAND HYPERMETHYLATION IN GLIOMAS
Genome-wide or “global” hypomethylation occurs
at a high frequency (?80%) in primary glioblastoma
(GBM).37–39The level of hypomethylation varies be-
tween tumors, ranging from near normal brain levels to
approximately 50% of normal in approximately 20% of
GLIOMA EPIGENOMICS AND GENOMICS437
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