Genetic Mutations vs Differentially Expressed Genes (DEGs) in Autism

 

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. 

Learning about Autism from the 3 Steps to Childhood Leukaemia

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  Na_v1.8   ↑↑     K_v7.1   ↑↑

4.     Repurpose approved drugs as inhibitors of K_v7.1 and Na_v1.8 

5.     High throughput screen (HTS) of 1280 approved drugs.

6.     The HTS delivered 55 inhibitors of K_v7.1 and 93 inhibitors of Na_v1.8

7.     Repurposing the Calcium Channel Inhibitor Nicardipine as a Na_v1.8 inhibitor 

           

The supporting science: 

Psychiatric Risk Gene Transcription Factor 4 Regulates Intrinsic Excitability of Prefrontal Neurons via Repression of SCN10a and KCNQ1

  

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

  

Na_v1.8 is a sodium ion channel subtype that in humans is encoded by the SCN10A gene

K_v7.1 (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.

 

 

Disordered breathing in a Pitt-Hopkins syndrome model involves Phox2b-expressing parafacial neurons and aberrant Nav1.8 expression

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 (Tcf4^tr/+) 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 Tcf4^tr/+ mice, thus establishing Nav1.8 as a high priority target with therapeutic potential in PTHS. 

 

Repurposing Approved Drugs as Inhibitors of K_v7.1 and Na_v1.8 To Treat Pitt Hopkins Syndrome

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 K_v7.1 and Na_v1.8 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 (K_V7.1) or HEK293 (Na_v1.8) cells and the HTS used either ⁸⁶Rb⁺ efflux (K_V7.1) or a FLIPR assay (Na_v1.8).

Results:

The HTS delivered 55 inhibitors of K_v7.1 (4.2% hit rate) and 93 inhibitors of Na_v1.8 (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 Na_v1.8.

Conclusions:

This work could lead to the potential repurposing of nicardipine or other dihydropyridine calcium channel antagonists as potential treatments for PTHS acting via Na_v1.8, as there are currently no approved treatments for this rare disorder.

  

Repurposing the Dihydropyridine Calcium Channel Inhibitor Nicardipine as a Na_v1.8 inhibitor in vivo for Pitt Hopkins Syndrome

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 Na_v1.8. 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 Na_v1.8 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 K_v7.1 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.

   

 

It’s a Small World – IGF-1 and NNZ-2566 in Autism

You may or may not believe in fate, but some strange things have been happening related to Australia, growth hormones and TBI.

Last week I took Monty, aged 10 with ASD, to have his IGF-1 (insulin-like growth factor) measured.  At the time, this had nothing to do with autism, rather just what the Endocrinologist had requested.  Then I start doing my research on hormones and autism and found, surprisingly, there is an ongoing clinical trial in autism using IGF-1.  Then I start looking again at TBI (Traumatic Brain Injury), which I see as having much in common with ASD.  I looked for similarities in hormone disruptions found in TBI and ASD; I found there are many and they are mainly related to GH (growth hormone) and IGF-1.  The problem with IGF-1 therapy is that it is intravenous; I had told the Endocrinologist that I was not going to measure IGF-1, because I was not very keen on giving Monty intravenous drugs.  In the end, I did the test anyway and I am glad I did.

As I researched TBI, I saw a great deal of interest in using GH as a therapy and the US military is providing a great deal of funding to develop therapies.

Today the postman brings me my first post from Australia in several years.  It contains some children books for Monty (Thank you Lisa).

Now I come across NNZ-2566;  it is a synthetic analogue of a naturally occurring neurotropic peptide derived from IGF-1.   NNZ-2566 is being developed both in intravenous and oral formulations for a range of acute and chronic conditions including TBI, Fragile X and Retts syndrome.  NNZ-2566 exhibits a wide range of important effects including inhibiting neuroinflammation, normalizing the role of microglia and correcting deficits in synaptic function.  NNZ-2566 is being developed guess where? Australia, by Neuren Pharmaceuticals.

Just 10 days ago the company made the following announcement:-

Melbourne, Australia, 18 October 2013: Neuren Pharmaceuticals (ASX: NEU) announced today that the U.S. Food and Drug Administration (FDA) has granted Fast Track designation for Neuren’s programme to develop NNZ-2566 for Fragile X Syndrome. Fast Track designation is designed to expedite the development and review of important new medicines that are intended to treat serious diseases and meet unmet medical needs.

A different group of researchers are poised to begin clinical trials of IGF-1 in children with autism early next year. Because IGF-1 is already approved in the United States for use in children with short stature, the U.S. Food and Drug Administration is allowing the researchers to proceed directly to clinical trials for its use as an autism treatment.

What a lot of coincidences.

For those scientists among you, here are more details.

First of all it has been shown that in autism there are elevated levels of growth hormones.  Here is an American study.

Elevated levels of growth-related hormones in autism and autism spectrum disorder

 The Australians quote research from Finland that looks to me to contradict the above paper.  One difference is that the US researchers were testing blood and the Finns were testing spinal fluid.  What is clear is that in autism IGF-1 is not normal.

Neurotrophic Factors in the Pathogenesis of Rett Syndrome

Abstract

Rett syndrome is characterized by disruption of a period of vigorous brain growth with synapse development. Neurotrophic factors are important regulators of neuronal growth, differentiation, and survival during early brain development. The aims of this study were to study the role of neurotrophic factors in Rett syndrome, specifically whether Rett syndrome has abnormal levels of specific neurotrophic factors in serum and cerebrospinal fluid and whether the changes differ from other neuropediatric patients, for example, those with infantile autism. Four neurotrophic factors were measured: nerve growth factor, brain-derived neurotrophic factor, glial cell line—derived neurotrophic factor, and insulin-like growth factor 1 from the frozen cerebrospinal fluid and from serum (except glial cell line—derived neurotrophic factor) by enzyme-linked immunosorbent assay and cerebrospinal fluid glutamate and aspartate by high-performance liquid chromatography (HPLC) method in patients with Rett syndrome. Insulin-like growth factor 1 was measured from the cerebrospinal fluid of patients with infantile autism. We found low concentrations of cerebrospinal fluid nerve growth factor in patients with Rett syndrome compared with control patients. The serum levels and other cerebrospinal fluid neurotrophic factor levels of the patients did not differ from the controls. Patients with Rett syndrome had high cerebrospinal fluid glutamate levels. Patients with infantile autism had low cerebrospinal fluid insulin-like growth factor 1 levels. Nerve growth factor acts especially on cholinergic neurons of the basal forebrain, whereas insulin-like growth factor 1 acts on cerebellar neurons. In Rett syndrome, the forebrain is more severely affected than the other cortical areas. In autism, many studies show hippocampal or cerebellar pathology. Our findings are in agreement with the different morphologic and neurochemical findings (brain growth, affected brain areas, neurotransmitter metabolism) in the two syndromes. Impairment in dendritic development in Rett syndrome could be the consequence of cholinergic deficiency and of neurotrophic factor/glutamate imbalance. Cholinergic gene expression might be influenced by the Rett syndrome gene directly or via the neurotrophic factor system.

 Then we have research showing GH/IGF-1 has secondary functions beyond those in the text books.  Lots of nice words like neuroprotective, regenerative etc.

Role of the Growth Hormone/Insulin-Like GrowthFactor 1 Axis in Neurogenesis

Abstract

The growth hormone/insulin-like growth factor 1 (GH/IGF-1) axis is not only involved in brain growth, development and myelination, but also in brain plasticity as indexed by neurogenesis. This may have links to various cognitive effects of GH and IGF-1. GH and IGF-1 affect the genesis of neurons, astrocytes, endothelial cells and oligodendrocytes. Specifically, IGF-1 increases progenitor cell proliferation and numbers of new neurons, oligodendrocytes, and blood vessels in the dentate gyrus of the hippocampus. In the adult cerebral cortex IGF-1 only affects oligodendrogenesis. Recently, GH therapy has also been shown to induce cell genesis in the adult brain. The profile of effects by GH therapy may be somewhat different than that of IGF-1. In addition, GH secretagogues (GHS) also have neuroprotective and cell regenerative effects per se in the brain. Finally, transgenic disruptions in GH signaling pathways affect neuron and astrocyte cell numbers during development and during adulthood. Altogether, data suggest that both exogenous and endogenous GH and/or IGF-1 may be used as agents to enhance cell genesis and neurogenesis in the adult brain. Theoretically these substances could be used to enhance recovery after brain injuries. However, further experiments with specific animal models for brain injuries are needed before clinical trials can be started. 

For those of you that like mice studies:

Growth factor improves autism symptoms in mice

Now back down under to let the Aussies make their case:

The Case for IGF-1 and IGF-1 (1-3) Glypromate in Autism

Courtesy of our friends “down under” you can read a presentation explaining the likely merits of both IGF-1 and its “terminal tripeptide” IGF-1 (1-3) as therapeutic agents in autism.  The clever Aussies have gone one better and produced NNZ-2566.  It is an analog of and IGF-1 (1-3).  This means it has that the molecule has been very slightly modified.  In this case this has been done to allow it to be orally available (i.e. not by injection) and to better cross the blood brain barrier (BBB). 

NNZ-2566 rationale for use in Autism Spectrum Disorders

Mount Sinai Hospital Clinical trial of IGF-1

Mount Sinai Hospital is a leading US teaching hospital in New York; they are carrying out a trial of IGF-1 in autism.  They are starting with a sub type with a genetic deficiency called SHANK3, but they will then look at the benefit in other types of ASD. 

http://clinicaltrials.gov/ct2/show/NCT01525901 

"In an important test of one of the first drugs to target core symptoms of autism, researchers at Mount Sinai School of Medicine are undertaking a pilot clinical trial to evaluate insulin-like growth factor (IGF-1) in children who have SHANK3 deficiency (also known as 22q13 Deletion Syndrome or Phelan-McDermid Syndrome), a known cause of autism spectrum disorder (ASD).

The seven-month study, which begins this month, will be conducted under the leadership of the Seaver Autism Center Clinical Director Alex Kolevzon, MD, and will utilize a double-blind, placebo-controlled crossover design in children ages 5 to 17 years old with SHANK3 deletions or mutations. Patients will receive three months of treatment with active medication or placebo, separated by a four-week washout period. Future trials are planned to explore the utility of IGF-1 in ASD without SHANK3 deficiency."

 

Conclusion

For a change, my conclusion is that further study is needed (by me).  Probably all the hormonal disruptions in autism need to be looked at together (serotonin, T3 etc) before any wild conclusions are drawn.