Molecular Psychiatry (2014) 19, 156–158

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PERSPECTIVE
Brain somatic mutations: the dark matter of
psychiatric genetics?
TR Insel

Although inherited DNA sequences have a well-demonstrated role in psychiatric disease risk, for even the most heritable mental
disorders, monozygotic twins are discordant at a significant rate. The genetic variation associated with mental disorders has
heretofore been based on the search for rare or common variation in blood cells. This search is based on the premise that every
somatic cell shares an identical DNA sequence, so that variation found in lymphocytes should reflect variation present in brain cells.
Evidence from the study of cancer cells, stem cells and now neurons demonstrate that this premise is false. Somatic mutation is
common in human cells and has been implicated in a range of diseases beyond cancer. The exuberant proliferation of cortical
precursors during fetal development provides a likely environment for somatic mutation in neuronal and glial lineages. Studies of
rare neurodevelopmental disorders, such as hemimegencephaly, demonstrate somatic mutations in affected cortical cells that
cannot be detected in unaffected parts of the brain or in peripheral cells. This perspective argues for the need to investigate
somatic variation in the brain as an explanation of the discordance in monozygotic twins, a proximate cause of mental disorders in
individuals with inherited risk, and a potential guide to novel treatment targets.

Molecular Psychiatry (2014) 19, 156–158; doi:10.1038/mp.2013.168; published online 17 December 2013
Keywords: mosaicism; single-cell biology; somatic mutation

Now my own suspicion is that the Universe is not only queerer
than we suppose, but queerer than we can suppose; 'JBS Haldane,
Possible Worlds, 1927, p 286'.
What Haldane suggested of the universe certainly seems to be
emerging as an undeniable fact about the brain. Looking at recent
reports on transcription within the mammalian brain, the findings
are indeed surprising beyond what we would have or could have
suspected from studying other organs. Best estimates from the
human brain suggest that 86% of the genome is expressed in the
brain, with over 90% of these genes showing different patterns of
expression prenatally1,2 (http://www.brainspan.org). Molecular
phenomena, such as genomic imprinting, that are tightly
controlled in peripheral organs appear to run rampant in the
mouse brain with as many as 1000 genes showing mono-allelic
expression.3 Even the rules for epigenomics seem to be
re-written in brain. Whereas methylation in most of the body
occurs at cytosine–guanine dinucleotide sites, in the brain
methylation is found mostly at dinucleotide sites of cytosine with
adenine, thymine or cytosine.4,5
These remarkable and unexpected aspects of gene expression
in the brain have emerged from studies of the transcriptome.
What has been largely overlooked until recently has been the
brain’s genome. Why should we look at DNA sequence in the
brain? After all, every cell is derived from a single progenitor,
yielding each person’s inherited genetic blueprint. Therefore,
sequencing from a blood cell or buccal smear should yield a
faithful representation of the DNA of every neuron and every
other somatic cell. Except it does not. Recent sequencing of
prefrontal cortical neurons suggest high variability, with 18 000
retrotransposons identified6,7 (although also see ref. 8). That is,
DNA from blood or buccal cells is not always identical with DNA in
the brain and DNA sequence in one neuron may not be identical
to a neighboring neuron or neighboring brain regions. These are
somatic mutations as opposed to germline mutations that are
inherited and found in every cell.
Somatic mutations are believed to be the cause of most
cancers.9 A spontaneous mutation in a tumor suppressor or cell
cycle driver gene alters the normal regulation of cell division
leading to unregulated growth. These mutations are not only the
proximate cause of cancer, they have become the preferred targets
for drug development allowing oncology to move from broad cell
cycle toxins to targeted therapies with much better outcomes.
And they explain the limited heritability of several cancers. What
may be inherited in the germline is not the specific causal muta-
tion but the more general capacity for genomic surveillance that
detects somatic changes or genomic stability that protects against
such mutations. Importantly, the germline variant is the basis for
heritable risk, whereas the causal gene is unique to the tumor.
How often does somatic variation occur outside of cancer cells?
Changes in DNA sequence have been an important concern in
stem cell biology as it has become evident that cells in culture are
prone to de novo mutations as they divide. In an attempt to
reduce this variation, Vaccarino and colleagues10 studied the
process by which fibroblasts undergoing de-differentiation to iPS
cells developed these mutations. To their surprise, the sequence
variation was present before the cells were manipulated. Indeed,
mosaicism or DNA sequence variation within an individual is a
well-known phenomenon ranging from duplication of a chromo-
some (aneuploidy) to single-base changes, associated with at least
30 Mendelian diseases.11 Our singular focus on DNA from blood or

National Institute of Mental Health, Bethesda, MD, USA. Correspondence: Dr TR Insel, Office of the Director, National Institute of Mental Health, 6001 Executive Boulevard, Room
8129, Bethesda, MD 20892, USA.
E-mail: tinsel@mail.nih.gov
Received 23 September 2013; revised 10 October 2013; accepted 21 October 2013; published online 17 December 2013

buccal smears assumes that these cells are identical to all somatic
cells, when, in fact, they may not even be similar to each other.
Somatic mutations may seem unlikely for brain disorders
because outside of the dentate gyrus of the hippocampus and
the rostral migratory stream, nearly all forebrain neurons are post-
mitotic. Although most neurons in the adult do not divide, during
the first half of human gestation the proliferation of cells may be
higher than in any organ at any period of development. By week
24 of gestation, the human brain has generated 1010 neurons from
a few progenitors at week 4 (www.translatingtime.org). Even by a
conservative estimate, proliferation during this 20-week interval
(roughly 105 min) clocks out at over 105 divisions per minute,
faster than any cancer or other somatic cell. If one were looking for
an organ and a time with the highest risk for somatic mutations,
early brain development fits the bill. Indeed, given the high rate of
mutation, it seems implausible that somatic mutations are not
abundant in the human brain.
There are, in fact, several brain diseases due to mutations
that would be lethal in the zygote but are tolerated when they
emerge later in development as somatic mutations. The disease is
not inherited in the classic sense, as the mutation is embryonic
lethal. But emergence later in development is compatible with
survival although it is not likely to be transmitted, and therefore is
under powerful negative selection. Poduri and colleagues12
recently reviewed several examples of somatic mutations
detected in brain as well as multiple peripheral tissues. These
are generally rare neurodevelopmental syndromes that are not
inherited in a classic sense.
Are there functional somatic mutations found only in the
human brain? A recent paper demonstrated AKT3 mutations in
brain tissue from children with hemimegalencephaly, a develop-
mental brain disorder characterized by an enlarged, malformed
cerebral hemisphere, intractable epilepsy and intellectual
deficits.13 These mutations were found in brain tissue resected
surgically from hemimegalencephaly patients but, in some cases,
not in their blood cells and, importantly, not in cells from the
unaffected part of the brain. Surprisingly, the mutation was found
in as few as 8% and generally o 35% of cells (both neurons and
glia) in the affected tissue. The presence in both neurons and glia
demonstrate that this mutation occurred in a common progenitor.
The low fraction of affected cells reminds us that somatic
mutations in such a clone can still be enough to disturb cortical
architecture.
Could forebrain somatic mutations be a factor in mental illness?
Somatic mutations would be consistent with the discordance
found in monozygotic twins in every psychiatric disorder, the
higher prevalence in males for most neurodevelopmental
disorders (X-linked mutations would be more penetrant in males),
and the high rates of de novo events in neurodevelopmental
disorders suggesting a predisposition to somatic mutations.
Although the data for schizophrenia remain inconclusive, children
with autism and intellectual disability are clearly more likely to
have de novo mutations, either as single-base changes or as larger
structural variants.14 These de novo mutations in affected children
are presumably due to transmission from an affected sperm or
egg but not present in the blood of either parent. Such de novo
events would be transmitted to every cell in the child. They are
thus different from somatic mutations that occur during mitosis
following fertilization and formation of the zygote and result in
mosaicism in the developing fetus. These de novo mutations may
still be important clues for brain somatic changes. Neurofibroma-
tosis and tuberous sclerosis are examples of ‘two hit’ syndromes in
which a mutation on one allele is inherited and the second allele is
altered only in the affected tissue.15–17
Although we have long known about brain mosaicism from
mitochondrial DNA mutations,18 there are only limited data to
support the hypothesis that somatic mutations within genomic
DNA are involved in psychiatric disorders, mostly from case
© 2014 Macmillan Publishers Limited
Brain somatic mutations
TR Insel
157
studies of aneuploidy.19,20 We have postmortem studies of
transcriptional profiles but there are few studies that have looked
for DNA sequence differences in identified cell lineages selected
in psychiatric populations.21 The key to finding a difference is
knowing where to look. A cubic mm of neocortex homogenized
for DNA will contain nearly 100 000 neurons of many different
types along with an equal number of glia and additional vascular
cells. In such a heterogeneous mix of cell types of diverse origins,
one might not find a difference that is unique to a single-cell
lineage. Again, think of the cancer model. To find the driver
mutation, one must sequence the malignant cell and experimen-
tally demonstrate a functional role of the mutation. Doing this in
cancer has demonstrated multiple mutations and often different
mutations within the same tumor, driven by continuing
proliferation in the presence of defective DNA repair.22 In that
sense, tumor biology may be an imperfect model, as somatic
mutations in brain would presumably be limited by the end of
cell division. Furthermore, in the brain, we will need to go beyond
brain regions to interrogate unique cell lineages implicated in the
pathophysiology of the disease, such as a specific clone of
parvalbumin-positive interneurons in schizophrenia, to test the
hypothesis.
The technology is becoming available from the single-cell
biology program.21 The brain samples exist to look for these muta-
tions, aided by DNA being more stable than RNA. Although trans-
criptional differences might indicate cortical regions of interest, it
will not be sufficient to test genomic DNA in tissue samples from
different brain regions alone. The use of single-cell technology or
laser capture of a given lineage should focus the search. For much
of the neocortex, the columnar organization constrains cell
lineage, providing a rough localization of the proliferative path.
But even within columns or minicolumns, there may overlapping
pyramidal cell populations representing independent lineages.
The migratory pathways for interneurons, possibly most important
for mental illness, are complex and still being resolved.23 And for
glia, the migratory pathways in development (and the timing) may
be quite different from neurons.
Which cell lineage to test is a difficult question, but one could
start simply comparing several populations from the same tissue
sample of a single individual and referencing those to germline
DNA. With a concurrent measure of the transcriptome, the
functional implications of a DNA difference should be apparent.
Somatic mutations will require brain tissue for analysis and will
not be detected by germline, iPS cell or whole-brain genetics. This
is not an argument for abandoning these other approaches. There
will likely be many informative avenues to study the full genetic
architecture and its related molecular pathophysiology of brain
disorders. A search for somatic mutations is simply a different
pathway that has yet to be pursued as a possible approach to
pathophysiology. Given the surprises recently revealed from
studies of the brain transcriptome and mindful of Haldane’s
maxim, the brain’s genome or more accurately genomes, may
prove to be even stranger than we have imagined.
CONFLICT OF INTEREST
The author declares no conflict of interest.
ACKNOWLEDGMENTS
I am grateful to Andrea Beckel-Michener, Thomas Lehner, Francis McMahon, David
Panchision and Nenad Sestan for helpful comments on this manuscript.
NOTE ADDED TO THE PROOF
Since the acceptance of this commentary, the first single-cell analysis of
endogenous human frontal cortex neurons was published, revealing that 13–
41% of neurons have at least one megabase-scale de novo CNV, that deletions
Molecular Psychiatry (2014), 156 – 158
 Brain somatic mutations
TR Insel
158
are twice as common as duplications, and that a subset of neurons have highly
aberrant genomes marked by multiple alterations (McConnell MJ, Lindberg MR,
Brennan KJ, Piper JC, Voet T, Cowing-Zitron C et al. Mosaic copy number
variation in human neurons. Science 2013; 342: 632–637).
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