Genes make proteins and you need the right amount in the right place
at the right time.
I should
start this post by confessing to not having carried out genetic testing on
Monty, now aged 18 with autism. When I
did mention this to one autism doctor at a conference, I was surprised by her
reply:- “ You did not need to. Now there’s no point doing it”.
I got lucky
and treated at least some of Monty’s Differentially Expressed Genes (DEGs) by
approaching the problem from a different direction.
People do
often ask me about what diagnostic tests to run and in particular about genetic
testing. In general, people have far too
high expectations regarding such tests and assume that there will be definitive
answers, leading to effective therapeutic interventions.
I do include
an interesting example today where parent power is leading a drive towards
an effective therapeutic intervention in one single gene type of autism. The approach has been to start with the
single gene that has the mutation and look downstream at the resulting Differentially
Expressed Genes (DEGs). The intervention targets one of the DEGs and not the mutated
gene itself.
This is a
really important lesson.
It can be
possible to repurpose existing drugs to treat DEGs quite cheaply. Many DEGs encode ion channels and there are very many existing drugs that affect ion channels.
Entirely
different types of autism may share some of the same DEGs and so benefit from
the same interventions.
Genetic
Testing
Genetic
testing has not proved to be the holy grail in diagnosing and treating autism,
but it remains a worthwhile tool at a population level (i.e. maybe not in your specific case). What matters most of all are Differentially
Expressed Genes (DEGs), which is something different.
A paper was
recently published that looked into commercially available genetic
testing. Its conclusion was similar to my
belief that you risk getting a “false negative” from these tests, in other
words they falsely conclude that there is no genetic basis for the person’s
symptoms of autism.
Brief Report: Evaluating the Diagnostic Yield of Commercial
Gene Panels in Autism
Autism is a prevalent neurodevelopmental
condition, highly heterogenous in both genotype and phenotype. This
communication adds to existing discussion of the heterogeneity of clinical
sequencing tests, “gene panels”, marketed for application in autism. We
evaluate the clinical utility of available gene panels based on existing
genetic evidence. We determine that diagnostic yields of these gene panels
range from 0.22% to 10.02% and gene selection for the panels is variable in
relevance, here measured as percentage overlap with SFARI Gene and ranging from
15.15% to 100%. We
conclude that gene panels marketed for use in autism are currently of limited
clinical utility, and that sequencing with greater coverage may be more
appropriate.
To save time
and money, the commercial gene panels only test genes that the company defines
as autism genes. There is no approved
list of autism genes.
You have
more than 20,000 genes and very many are implicated directly, or indirectly, in
autism and its comorbities. To be thorough you need Whole Exome Sequencing (WES), where you check them all.
There are tiny mutations called SNPs ("snips") which you inherit from your parents; there are more than 300 million known SNPs and most people will carry 4-5 million. Some SNPs are important but clearly most are not. Some SNPs are very common and some are very rare.
Even WES only analyses 2% of your DNA, it does not consider the other 98% which is beyond the exome. Whole Genome Sequencing (WGS) which looks at
100% of your DNA will be the ideal solution, but at some time in the
future. The interpretation of WES data
is often very poor and adding all the extra data from WGS is going to overwhelm most people involved.
Today we
return to the previous theme of treating autism by treating the downstream
effects caused by Differentially Expressed
Genes (DEGS).
Genetics is
very complicated and so people assume that is must be able to provide answers.
For a minority of autism current genetics does indeed provide an answer, but
for most people it does not.
Early on in
this blog I noted so many overlaps between the genes and signaling
pathways that drive cancer and autism,
that is was clear that to understand autism you probably first have to
understand cancer; and who has time to do that!
Some
people’s cancer is predictable. Chris Evert, the American former world No. 1 tennis player,
announced that she has ovarian cancer.
Her sister had exactly the same cancer.
Examining family history can often yield useful information and it is a
lot less expensive that genetic testing.
Most people’s cancer is not so predictable; sure if you expose yourself
to known environmental triggers you raise its chances, but much appears to be
random. Cancer, like much autism, is usually a multiple hit process. Multiple events need to occur and you may only need to block one of them to avoid cancer. We saw this with a genetic childhood leukemia that you can prevent with a gut bacteria.
What is not random in cancer
are the Differentially Expressed Genes (DEGs).
We all carry
highly beneficial tumor suppressing genes, like the autism/cancer gene
PTEN. You would not want to have a
mutation in one of these genes.
What happens
in many cancers is that the individual carries two good copies of the gene like
PTEN, but the gene is turned off. For example, in many people with prostate
cancer, the tumor suppressor gene PTEN is turned off in that specific part of
the body. There is no genetic mutation,
but there is a harmful Differentially Expressed
Gene (DEG). If you could promptly turn PTEN expression back on, you would suppress the cancer.
Not surprisingly, daily use of drugs that increase PTEN expression is associated with reduced incidence of PTEN associated cancer. Atorvastatin is one such drug.
DEGs are
what matter, not simply mutations
In many
cases genetic mutations are of no clinical relevance, we all carry several on average. In some cases they are of immediate critical
relevance. In most cases mutations are
associated with a chance of something happening, there is no certainty and
quite often further hits/events/triggers are required.
A good
example is epilepsy. Epilepsy is usually caused by an ion channel dysfunction
(sodium, potassium or calcium) that is caused by a defect in the associated
gene. Most people are not born with epilepsy, the onset can be many years later. Some parents of a child with autism/epilepsy
carry the same ion channel mutation but remain unaffected.
Follow
the DEGs from a known mutation
There is a
vanishingly small amount of intelligent translation of autism science to
therapy, or even attempts to do so. I
set out below an example of what can be done.
Pitt Hopkins (Haploinsufficiency of TCF4)
The syndrome
is caused by a reduction in Transcription factor 4, due to mutation in the TCF4
gene. One recently proposed therapy is to
repurpose the cheap calcium channel blocker Nicardipine. Follow the rationale below.
↓
means down regulated
↑ means up regulated
1. Gene/Protein TCF4 (Transcription Factor 4) ↓↓↓↓
2. Genes SCN10a ↑↑ KCNQ1 ↑↑
3. Encoding ion channels Nav1.8 ↑↑ Kv7.1 ↑↑
4. Repurpose approved drugs as inhibitors
of Kv7.1 and Nav1.8
5. High throughput screen (HTS) of
1280 approved drugs.
6. The HTS delivered 55 inhibitors of
Kv7.1 and 93 inhibitors of Nav1.8
7. Repurposing the Calcium Channel
Inhibitor Nicardipine as a Nav1.8 inhibitor
The
supporting science:
Highlights
•TCF4
loss of function alters the intrinsic excitability of prefrontal neurons
•TCF4-dependent excitability
deficits are rescued by SCN10a and KCNQ1 antagonists
•TCF4 represses the expression of
SCN10a and KCNQ1 ion channels in central neurons
•SCN10a
is a potential therapeutic target for Pitt-Hopkins syndrome
Nav1.8 is
a sodium ion channel subtype that in humans is encoded by
the SCN10A gene
Kv7.1 (KvLQT1)
is a potassium channel protein whose
primary subunit in humans is encoded by the KCNQ1 gene.
Transcription Factor 4 (TCF4) is a clinically
pleiotropic gene associated with schizophrenia and Pitt-Hopkins syndrome
(PTHS).
SNPs in a genomic locus containing TCF4 were
among the first to reach genome-wide significance in clinical genome-wide association studies (GWAS) for schizophrenia These neuropsychiatric
disorders are each characterized by prominent cognitive deficits, which suggest not only genetic
overlap between these disorders but a potentially overlapping pathophysiology.
We propose that these intrinsic excitability phenotypes may
underlie some aspects of pathophysiology observed in PTHS and schizophrenia and
identify potential ion channel therapeutic targets.
Given that TCF4 dominant-negative or haploinsufficiency results
in PTHS, a syndrome with much more profound neurodevelopmental deficits than
those observed in schizophrenia, the mechanism of schizophrenia risk associated
with TCF4 is
presumably due to less extreme alterations in TCF4 expression at some unknown
time point in development
The pathological expression of these peripheral ion channels in
the CNS may create a unique opportunity to target these channels with
therapeutic agents without producing unwanted off-target effects on normal
neuronal physiology, and we speculate that targeting these ion channels may ameliorate cognitive
deficits observed in PTHS and potentially schizophrenia.
Pitt-Hopkins syndrome (PTHS)
is a rare autism spectrum-like disorder characterized by intellectual
disability, developmental delays, and breathing problems involving episodes of
hyperventilation followed by apnea. PTHS is caused by functional
haploinsufficiency of the gene encoding transcription factor 4 (Tcf4). Despite
the severity of this disease, mechanisms contributing to PTHS behavioral abnormalities
are not well understood. Here, we show that a Tcf4 truncation (Tcf4tr/+)
mouse model of PTHS exhibits breathing problems similar to PTHS patients. This
behavioral deficit is associated with selective loss of putative expiratory
parafacial neurons and compromised function of neurons in the retrotrapezoid
nucleus that regulate breathing in response to tissue CO2/H+.
We also show that central Nav1.8 channels can be targeted pharmacologically to
improve respiratory function at the cellular and behavioral levels in Tcf4tr/+ mice,
thus establishing Nav1.8 as a high priority target with therapeutic potential
in PTHS.
Purpose:
Pitt Hopkins Syndrome
(PTHS) is a rare genetic disorder caused by mutations of a specific gene,
transcription factor 4 (TCF4), located on chromosome 18. PTHS results in
individuals that have moderate to severe intellectual disability, with most
exhibiting psychomotor delay. PTHS also exhibits features of autistic spectrum
disorders, which are characterized by the impaired ability to communicate and
socialize. PTHS is comorbid with a higher prevalence of epileptic seizures
which can be present from birth or which commonly develop in childhood.
Attenuated or absent TCF4 expression results in increased translation of
peripheral ion channels Kv7.1 and Nav1.8 which triggers
an increase in after-hyperpolarization and altered firing properties.
Methods:
We now describe a high
throughput screen (HTS) of 1280 approved drugs and machine learning models
developed from this data. The ion channels were expressed in either CHO (KV7.1)
or HEK293 (Nav1.8) cells and the HTS used either 86Rb+ efflux
(KV7.1) or a FLIPR assay (Nav1.8).
Results:
The HTS delivered 55
inhibitors of Kv7.1 (4.2% hit rate) and 93 inhibitors of Nav1.8
(7.2% hit rate) at a screening concentration of 10 μM. These datasets also
enabled us to generate and validate Bayesian machine learning models for these
ion channels. We also describe a structure activity relationship for several
dihydropyridine compounds as inhibitors of Nav1.8.
Conclusions:
This work could lead
to the potential repurposing of nicardipine or other dihydropyridine calcium
channel antagonists as potential treatments for PTHS acting via Nav1.8,
as there are currently no approved treatments for this rare disorder.
Individuals with the rare genetic disorder Pitt
Hopkins Syndrome (PTHS) do not have sufficient expression of the transcription
factor 4 (TCF4) which is located on chromosome 18. TCF4 is a basic
helix-loop-helix E protein that is critical for the normal development of the
nervous system and the brain in humans. PTHS patients lacking sufficient TCF4
frequently display gastrointestinal issues, intellectual disability and
breathing problems. PTHS patients also commonly do not speak and display
distinctive facial features and seizures. Recent research has proposed that
decreased TCF4 expression can lead to the increased translation of the sodium
channel Nav1.8. This in turn results in increased
after-hyperpolarization as well as altered firing properties. We have recently
identified an FDA approved dihydropyridine calcium antagonist nicardipine used
to treat angina, which inhibited Nav1.8 through a drug repurposing
screen.
All of the
above was a parent driven process. Well done,
Audrey!
Questions
remain.
Is Nicardipine
actually beneficial to people with Pitt Hopkins Syndrome? Does it matter at what age
therapy is started? What about the Kv7.1 inhibitor?
Conclusion
Genetics is
complicated, ion channel dysfunctions are complicated; but just a superficial
understanding can take you a long way to understand autism, epilepsy and many
other health issues.
There is a great deal in this blog about channelopathies/ion channel dysfunctions.
https://epiphanyasd.blogspot.com/search/label/Channelopathy
Almost everyone with autism has one or more channelopathies. Most channelopathies are potentially treatable.
Parents of
children with rare single gene autisms should get organized and make sure there
is basic research into their specific biological condition. They need to ensure that there is an animal
model created and it is then used to screen for existing drugs that may be
therapeutic. I think they also need to
advocate for gene therapy to be developed.
This all takes years, but the sooner you start, the sooner you will make
an impact.
Very likely, therapies developed for some
single gene autisms will be applicable more broadly. A good example may be the IGF-1 derivative Trofinetide, for girls
with Rett Syndrome. IGF-1 (Insulin-like growth factor 1) is an important growth factor that is required for proper brain
development. In the brain, IGF-1 is broken down into a protein fragment called
glypromate (GPE). Trofinetide is an orally available version of GPE.
The
MeCP2 protein controls the expression of several genes, such as Insulin-like Growth
Factor 1 (IGF1), brain-derived neurotrophic factor (BDNF) and
N-methyl-D-aspartate (NMDA). All three
are implicated in broader autism.
https://rettsyndromenews.com/trofinetide-nnz-2566/
In
girls with Rett Syndrome the genetic mutation is in the gene MeCP2, but one of
the key DEGs (differentially expressed genes) is the FXYD1; it is over-expressed. IGF-1 supresses the activity of FXYD1 and
hopefully so does Trofinetide. Not so
complicated, after all!
Medicine is often driven by the imperative to do no harm.
In otherwise severely impaired people, perhaps the imperative should be to try and do some good.
In medicine, time is of the essence; doctors in the ER can be heard to say "Stat!", from the Latin word for immediately, statim.
How about some urgency in translating autism science into therapy? But then, what's the hurry? Why rock the boat?
On an individual basis, much is already possible, but you will have to do most of the work yourself - clearly a step too far for most people.