Showing posts with label Rapamycin. Show all posts
Showing posts with label Rapamycin. Show all posts

Tuesday, 14 March 2023

Differentially expressed immune-related genes (dIRGs) in Changsha and Rapamycin/mTOR


I did write about an interesting paper last year concerning calcium channels and intellectual disability; it was from a city in China called Changsha.

Epiphany: Calcium channelopathies and intellectual disability

Changsha is on the old train line and the new high speed line from Beijing to Hong Kong. So like many other people, I must have passed by this city of 10 million on the old line, as a backpacking student many years ago.

After three years of closure, China announced that it is reopening to foreign visitors. China is well worth a visit and their high speed trains make travel much easier than it used to be.

Before moving on to today’s paper, I will mention the case study below from one of China’s top hospitals, the PLA hospital in Beijing.  They used the well known mTOR inhibitor Rapamycin to successfully treat an 8 year old boy with idiopathic (of unknown cause) autism.  This drug has been used in models of autism. The mTOR inhibitor Everolimus is approved as adjunctive therapy for a single gene autism called TSC to treat seizures. Click on the link below to read the one page case report.

Rapamycin/Sirolimus Improves the Behavior of an 8-Year-Old Boy With Nonsyndromic Autism Spectrum Disorder

Some readers have mentioned this case study and at least one has made a trial.  In that case the drug was well tolerated but did not moderate autism symptoms.

Mammalian target of rapamycin (mTOR) regulates cell proliferation, autophagy, and apoptosis by participating in multiple signaling pathways in the body. Studies have shown that the mTOR signaling pathway is also associated with cancer, arthritis, insulin resistance, osteoporosis, and other diseases including some autism.

Today we return to Changsha for another interesting paper about the altered immune system in autism and other neurological conditions.  It is an interesting study because it is based on samples from 2,500 brains of controls and patients with six major brain disorders - schizophrenia, bipolar disorder, autism spectrum disorder, major depressive disorder, Alzheimer’s disease, and Parkinson’s disease.

One of the reasons so little progress has been made in treating any neurological condition is the inability to take physical samples to experiment with.  All the 2,500 brain samples are taken from brain banks, not live people.

When it comes to autism that means the sample likely reflects severe autism (DSM3 autism).  No self-identified autism in today’s samples, their brains are unlikely to be donated to medical science. 

Immunity-linked genes expressed differently in brains of autistic people 

Genes involved in immune system function have atypical expression patterns in the brains of people with some neurological and psychiatric conditions, including autism, according to a new study of thousands of postmortem brain samples.

Of the 1,275 immune genes studied, 765 — 60 percent — showed elevated or reduced expression in the brains of adults with one of six conditions: autism, schizophrenia, bipolar disorder, depression, Alzheimer’s disease or Parkinson’s disease. The expression patterns varied by condition, suggesting that there are distinct “signatures” for each one, says lead researcher Chunyu Liu, professor of psychiatry and behavioral sciences at Upstate Medical University in Syracuse, New York.

The expression of immune genes could potentially serve as a marker for inflammation, Liu says. Such immune activation — particularly while in utero — has been associated with autism, though the mechanisms are far from clear.

“My impression is the immune system is not really a very minor player in brain disorders,” Liu says. “It is a major player.”

It’s impossible to discern from this study whether immune activation played a role in contributing to any condition or whether the condition itself led to altered immune activation, says Christopher Coe, professor emeritus of biopsychology at the University of Wisconsin-Madison, who was not involved in the work.

“A study of the postmortem brain is informative,” Coe says. “But not definitive.”

Liu and his team analyzed the expression levels of 1,275 immune genes in 2,467 postmortem brain samples, including 103 from autistic people and 1,178 from controls. The data came from two transcriptomics databases — ArrayExpress and the Gene Expression Omnibus — and other previously published studies.

Brains from autistic people had, on average, 275 genes with expression levels that differed from those of controls; brains from people with Alzheimer’s disease had 638 differentially expressed genes, followed by those with schizophrenia (220), Parkinson’s (97), bipolar disorder (58) and depression (27).

Autistic men’s expression levels varied more than those of autistic women, whereas the brains of women with depression showed more variation than those of men with depression. The other four conditions showed no sex differences.

The autism-related expression pattern more closely resembled those of the neurological conditions — Alzheimer’s and Parkinson’s — than the other psychiatric ones. Neurological conditions, by definition, must have a known physical signature in the brain, such as Parkinson’s characteristic loss of dopaminergic neurons. Researchers have not found such a signature for autism.

“This [similarity] just provides some kind of additional direction we should look into,” Liu says. “Maybe one day we will understand the pathology better.”

The findings were published in Molecular Psychiatry in November.

Two genes, CRH and TAC1, are the most commonly altered among the conditions: CRH is downregulated in all of the conditions but Parkinson’s, and TAC1 is downregulated in all but depression. Both genes affect the activation of microglia, the brain’s immune cells.

Atypical microglial activation may be “derailing normal neurogenesis and synaptogenesis,” Coe says, disrupting neuronal activity similarly across the conditions.

Genes involved in astrocyte and synapse function are similarly expressed in people with autism, schizophrenia or bipolar disorder, a 2018 study of postmortem brain tissue found. But microglial genes are overexpressed in autism alone, that study found.

People with more intensely upregulated immune genes could have a “neuroinflammatory condition,” says Michael Benros, professor and head of research on biological and precision psychiatry at the University of Copenhagen in Denmark, who was not involved in the work.

“It could be interesting to try to identify these potential subgroups and of course provide them more specific treatment,” Benros says.

Most of the expression changes observed in the brain tissue samples did not appear in datasets of gene expression patterns in blood samples from people with the same conditions, the study shows. This “somewhat surprising” finding indicates the importance of studying brain tissue, says Cynthia Schumann, professor of psychiatry and behavioral sciences at the University of California Davis MIND Institute, who was not involved in the study.

“If you want to know about the brain, you have to look at the brain itself,” Schumann says.


I am always reminding people not to think that blood samples are going to tell them how to treat autism.  The above commentary also highlights this fact.  If you want to know what is going on in the brain, you have to look there or in spinal fluid.  Looking just at blood samples may send an investigation in completely the wrong direction. Spinal fluid flows around the brain and spinal cord to help cushion them from injury and provide nutrients. Testing spinal fluid requires an invasive procedure, parents do not like it and so it is very rarely carried out until adulthood.  Time has then been lost.


Here is the link to the full paper and some highlights I noted.


Neuroimmune transcriptome changes in patient brains of psychiatric and neurological disorders 

Neuroinflammation has been implicated in multiple brain disorders but the extent and the magnitude of change in immune-related genes (IRGs) across distinct brain disorders has not been directly compared. In this study, 1275 IRGs were curated and their expression changes investigated in 2467 postmortem brains of controls and patients with six major brain disorders, including schizophrenia (SCZ), bipolar disorder (BD), autism spectrum disorder (ASD), major depressive disorder (MDD), Alzheimer’s disease (AD), and Parkinson’s disease (PD). There were 865 IRGs present across all microarray and RNA-seq datasets. More than 60% of the IRGs had significantly altered expression in at least one of the six disorders. The differentially expressed immune-related genes (dIRGs) shared across disorders were mainly related to innate immunity. Moreover, sex, tissue, and putative cell type were systematically evaluated for immune alterations in different neuropsychiatric disorders. Co-expression networks revealed that transcripts of the neuroimmune systems interacted with neuronal-systems, both of which contribute to the pathology of brain disorders. However, only a few genes with expression changes were also identified as containing risk variants in genome-wide association studies. The transcriptome alterations at gene and network levels may clarify the immune-related pathophysiology and help to better define neuropsychiatric and neurological disorders. 


Multiple lines of evidence support the notion that the immune system is involved in major “brain disorders,” including psychiatric disorders such as schizophrenia (SCZ), bipolar disorder (BD), and major depressive disorder (MDD), brain development disorders such as autism spectrum disorder (ASD), and neurodegenerative diseases such as Alzheimer's disease (AD), and Parkinson's disease (PD). Patients with these brain diseases share deficits in cognition, blunted mood, restricted sociability and abnormal behavior to various degrees. Transcriptome studies have identified expression alterations of immune-related genes (IRGs) in 49 postmortem brains of AD, PD, ASD, SCZ and BD separately. Cross disorder transcriptomic studies further highlighted changes in IRGs. At the protein level, several peripheral cytokines showed reproducible disease-specific changes in a meta-analysis. Since brain dysfunction is considered the major cause of these disorders, studying immune gene expression changes in patient brains may reveal mechanistic connections between immune system genes and brain dysfunction. Most previous studies were limited to the analysis of  individual disorders. There is no comprehensive comparison of the pattern and extent of inflammation-related changes in terms of immune constructs (subnetworks), neuro-immune interaction, genetic contribution, and relationship between diseases.  Neuroinflammation, an immune response taking place within the central nervous system,  can be activated by psychological stress, aging, infection, trauma, ischemia, and toxins. It is regulated by sex, tissue type and genetics, many of which are known disease risk factors for both psychiatric and neurological diseases. The primary function of neuroinflammation is to maintain brain homeostasis through protection and repair. Abnormal neuroinflammation activation could lead to dysregulation of mood, social behaviors, and cognitive abilities. Offspring who were fetuses when their mothers’ immune system was activated (MIA) showed dopaminergic hyperfunction, cognitive impairment, and behavioral abnormalities as adults. Alternatively, acute and chronic neuroinflammation in adulthood can also alter cognition and behavior. In animal models, both adult and developmental maternal immune activation in the periphery can lead to increases in pro-inflammatory cytokines in the brain , similar to what is found in humans with major mental illness.  Previous studies identified immune gene dysregulations in brains of patients with several major brain disorders. For example, Gandal et al. found that up-regulated genes and isoforms in SCZ, BD, and ASD were enriched in pathways such as inflammatory response and response to cytokines. One brain co-expression module up-regulated specifically in MDD was enriched for genes of cytokine-cytokine interactions, and hormone activity pathways. The association of neurological diseases such as AD and PD with IRGs has also been reported. These studies examined the changes of immune system as a whole without going into details of specific subnetworks, the disease signature, or genetic versus environmental contribution. We hypothesize that expression changes of specific subsets of IRGs constitute part of the transcriptome signatures that distinguishes diseases. Since tissue specificity, sex and genetics all could influence such transcriptome signatures, we analyzed their effects. Furthermore, we expect that neurological diseases and psychiatric disorders bear transcriptomic changes that may help to address how similar immunological mechanisms lead to distinct brain disorders. The current boundary between neurological diseases and psychiatric disorders is primarily the presence of known pathology. Neurological diseases have more robust histological changes while psychiatric disorders have more subtle subcellular changes. Nonetheless, pathology evidence is always a subject to be revised with new research.  To investigate immune-related signatures of transcriptome dysregulation in brains of six neurological and psychiatric disorders, we studied a selected list of 1,275 genes known to be associated with neuroinflammation and interrogated their expression across disorders. We collected and analyzed existing transcriptome data of 2,467 postmortem brain samples from donors with AD, ASD, BD, MDD, PD, SCZ and healthy controls (CTL). We identified the differentially expressed IRGs shared across disorders or specific to each disorder, and their related coexpression modules (Fig. S1). These genes and their networks and pathways provided important insight into how immunity may contribute to the risk of these neurological and psychiatric disorders, with a potential to refine disease classification.


The two most shared dIRGs are Corticotropin-releasing hormone (CRH) and Tachykinin Precursor 1 (TAC1), which were differentially expressed in five of the six diseases (Fig. 2D). They both involve innate immunity according to the databases we used and literature. CRH was downregulated in five of the six disorders; the exception was PD. CRH can regulate innate immune activation with neurotensin (NT), stimulating mast cells, endothelia, and microglia. TAC1 was down-regulated in five of the six disorders, the exception being MDD.  TAC1 encodes four products of substance P, which can alter the immune functions of activated microglia and astrocytes. Independent RNA-seq data confirmed both CRH and TAC1 findings. These transcripts are also neuromodulators and have action on neurons so they have roles in addition to immune functions. 

This indicated that even though immune dysfunction is widespread in the six disorders, signature patterns of the subset innate immune genes are sufficient to differentiate neurological from psychiatric disorders. 

Disease-specific IRMs in AD, ASD, and PD imply distinct biological processes.

We also searched for disease-specific IRMs for each disorder. We used rWGCNA to construct brain co-expression networks in the brains of each disorder and of controls, then compared them against each other to identify disease-specific IRMs (Fig.5A). Based on preservation results of one disease versus controls and against all other diseases (Fig. 5B, z-summary < 10), as well as immune gene enrichment results (Table S9; enrichment q.value < 0.05), we identified six disease-specific IRMs, including one for AD, three for ASD, and two for PD. We did not detect disease-specific IRMs for SCZ, BD, or MDD, which are considered psychiatric disorders. The disease-specific IRMs were enriched for various functions (Fig. 5C, Table S9). The AD specific IRM was enriched for neuron part (GO:0097458, q.value= 4.57E-4) and presynapse (GO:0098793, q.value = 4.57E-4). The PD-specific IRM was enriched for positive regulation of  angiogenesis (GO:0045766, q.value = 9.65E-06) and secretory granule (GO:0030141, q.value= 220 6.31E-06). The ASD-specific IRMs were enriched for developmental biological processes such as negative regulation of cell proliferation and growth factor receptor binding. 

Our reader Eszter will be pleased to see that the research links the differentially expressed genes more with Alzheimer’s than with Bipolar or Schizophrenia.  She has noted the overlap in effective therapies between Alzheimer’s and autism. 

We came up with four major findings of the neuroimmune system in brains of different neuropsychiatric disorders: 1) the innate immune system carries more alterations than the adaptive immune systems in the six disorders; 2) the altered immune systems interact with other biological pathways and networks contributing to the risk of disorders; 3) common SNPs have a limited contribution to immune-related disease risks, suggesting the environmental contribution may be substantial; and 4) the expression profiles of dIRGs, particularly that of innate immune genes, group neurodevelopment disorder ASD with neurological diseases (AD and PD) instead of with psychiatric disorders (BD, MDD, and SCZ) Dysregulation of the innate immune system is a common denominator for all six brain disorders. We found that more than half of the shared dIRGs and dIRG-enriched pathways were related to the innate immune system. The two most shared dIRGs, TAC1 and CRH, have known effects on innate immune activation(66, 67). Both genes were downregulated in patient brains. Additionally, TLR1/2 mediates microglial activity, which could contribute to neuronal death through the release of inflammatory mediators. Furthermore, innate immunity is critical in maintaining homeostasis in the brain. For example, the innate immune system has been reported to function in the CNS's resilience and in synaptic pruning throughout brain growth. When homeostasis is disrupted, the abnormal innate immunity may impact a wide range of brain functions.


Microglia are affected specifically in autism and Alzheimer’s.

Microglia are highlighted in the immune changes in brains of AD and ASD in this study. Microglia is the major cell type participating in the brain’s immune system. Our analyses showed that the IRM12 coexpression module was enriched for microglia genes and associated with inflammatory transcriptional change in AD and ASD but not the other four diseases. Does this suggest that microglial dysfunction contributes more to AD and ASD than to the other disorders? The PsychENCODE study showed the microglial module upregulated in ASD and downregulated in SCZ and BD(16), but the fold changes in SCZ and BD were much smaller than that in ASD (Fig 7.B in original paper(16)). Larger sample size may be needed to detect microglia contribution to other disorders such as SCZ and BD. 

Sex contributes to the disease-related immune changes too. Our results revealed sex-bias dysregulation of IRGs in brains of ASD and MDD but not in other disorders. These two  disorders are known to have sex differences in prevalence. Previous studies also have suggested that sex differences in stress-related neuroinflammation might account for the overall sex bias in stress-linked psychiatric disorders, including female bias in MDD and male bias in ASD. We did not observe sex-biased IRGs in other diseases with known sex-biased prevalence, such as SCZ and AD suggesting that sex differences in SCZ and AD may not involve IRG changes. 

Our results showed how immune system dysregulation may influence gene expression of the networked other non-immune genes and contribute to the pathology of these diseases specifically. Six disease-specific IRMs were detected in AD, ASD, and PD, showing that several functions of the immune-related networks also involved in corresponding disorders such as presynaptic related AD-IRM and Growth factor receptors-related ASD-IRMs. Presynaptic proteins are essential for synaptic function and are related to cognitive impairments in AD(85). Growth factor receptors and N-acetylcysteine are involved in the etiology of ASD. Secretogranin may be a pivotal component of the neuroendocrine pathway and play an essential role in neuronal communication and neurotransmitter release in PD (88). Furthermore, the immune system has been found to regulate presynaptic proteins(89), EGFR(90), and secretogranin(88). Our results indicate that alterations of the immune network can be disease-specific, affecting specific coexpression networks and driving distinct risk of each disorder. 

To our surprise, neurodevelopment disorder ASD was grouped with neurological diseases (AD  and PD) instead of with psychiatric disorders (BD, MDD, and SCZ) according to the changes of IRGs, particularly innate immune genes. Hierarchical clustering analysis based on the effect size of IRGs placed the presumed psychiatric disorder ASD with other neurological diseases. Previous studies have reported that ASD patients exhibited more neurological and immunological problems(99-102) compared to healthy people and to other brain disorders. As more etiologies are uncovered, the traditional classification of these diseases is increasingly challenged(93). Furthermore, we found that dIRGs change more in neurological diseases (AD, PD, and ASD) than in the psychiatric disorders (BD, SCZ, and MDD). It suggested that neuroimmunity dysregulation is more severe in neurological diseases than in psychiatric disorders, led by AD. Neuroimmunity may help to redefine disease classification in the future.



It is good to see there is excellent research coming from China. Our reader Stephen has noted some interesting research underway in Russia. Look both East and West.

Intranasal Inhalations of M2 Macrophage Soluble Factors in Children With Developmental Speech Disorders

In today’s paper the focus was just on immune related genes.  That in itself is a big step forward, since in this blog we are well aware of the key role of the immune system in autism.

In this study all of autism was grouped together, when we know there will be many subgroups with totally different profiles.  In terms of treatment, you would need to know which subgroup you are part of.

But it does tell you that part of your autism therapy is going to have to account for an altered immune status. 

I would have to say that it does follow Western research in getting a bit lost in the detail.  We know that they found 275 of the immune genes mis-expressed in autism.

How about presenting a simple list of the 275 with whether the genes were over or under expressed ?

There are vast spreadsheets in the supplemental data, but nothing as down to earth and common sense as that.

Instead the researchers were preoccupied with overlaps between different conditions and churning out statistics.

It is notable from the first paper I mentioned today that one of the very top Chinese hospitals is actually trying to apply personalized medicine using Rapamycin for autism and publishing a case history. Bravo !!

A logical next step after trying to modify mTOR would be to try epigenetic modification therapy using HDAC inhibition.

One issue here is the age at which therapy begins, not surprisingly some therapies need to commence at birth (or ideally before) and do not give much effect later in life.

Romidepsin is one HDAC inhibitor used in the research.

In the studies below Chinese researchers in the US are making progress. 

In 2018:

Autism's social deficits are reversed by an anti-cancer drug

Using an epigenetic mechanism, romidepsin restored gene expression and alleviated social deficits in animal models of autism.

"In the autism model, HDAC2 is abnormally high, which makes the chromatin in the nucleus very tight, preventing genetic material from accessing the transcriptional machinery it needs to be expressed," said Yan. "Once HDAC2 is upregulated, it diminishes genes that should not be suppressed, and leads to behavioral changes, such as the autism-like social deficits."

But the anti-cancer drug romidepsin, a highly potent HDAC inhibitor, turned down the effects of HDAC2, allowing genes involved in neuronal signaling to be expressed normally.

The rescue effect on gene expression was widespread. When Yan and her co-authors conducted genome-wide screening at the Genomics and Bioinformatics Core at UB's New York State Center of Excellence in Bioinformatics and Life Sciences, they found that romidepsin restored the majority of the more than 200 genes that were suppressed in the autism animal model they used.

In 2021:

Synergistic inhibition of histone modifiers produces therapeutic effects in adult Shank3-deficient mice

 We found that combined administration of the class I histone deacetylase inhibitor Romidepsin and the histone demethylase LSD1 inhibitor GSK-LSD1 persistently ameliorated the autism-like social preference deficits, while each individual drug alone was largely ineffective.


We now need some leading researchers/clinicians in China to actually translate this approach to humans and see if it works.  Hopefully the PLA hospital in Beijing are keeping an eye out on what Zhen Yan is up to at the University of Buffalo, NY.  With luck they will not wait 20 years to try it!

Thursday, 29 November 2018

What, When and Where of Autism – Critical Periods and Sensitive Periods

When time is of the essence

All kinds of dysfunctions may appear in autistic brains, which in itself make it a highly complex condition. There is also the when and where aspects of these dysfunctions, which often gets overlooked, or lost in oversimplification.
This then has to fit into the concept of critical periods, that I introduced in an earlier post. 

Critical periods are times during the brain’s development when it is particularly vulnerable to any disturbance, for example an excitatory/inhibitory imbalance.
This then leads to another related concept which is that of sensitive periods; these are periods when the person should be responsive to particular therapy.
Sensitive periods are very important to be understood by those planning clinical trials, because a therapy may indeed be effective only when given within a specific time window. During this time the person is sensitive to the therapy, but they will not be a responder after the time window has passed.
I am pleased to say that more research is beginning to consider the when aspect and not just the what aspect of biological dysfunction in autism.
The where aspect reflects the fact that in one part of the brain there might be, say, NMDA hypofunction, while in another part the opposite is present, NMDA hyperfunction.  Since most therapies come as pills you swallow, you cannot treat one part of the brain for one problem and another part of the brain for the opposite problem. There is currently no way around this issue, you just have to do what is best for the brain overall. In practical terms it means you may make one problem better, but create a new one. 

New research in a mouse model suggests that the drug rapamycin can reverse autism-like social deficits -- but only if given early. The study is the first to shed light on the crucial timing of therapy to improve social impairments in a condition associated with autism spectrum disorder. Its findings could help inform future clinical trials in children with tuberous sclerosis complex. 

Full Paper:


Mefenamic Acid
I have mentioned mefenamic acid (Ponstan) in several posts. It is the only human autism therapy currently in development that has a treatment window.  It is suggested that the sensitive period to take this drug is the second year of life, to avoid severe non-verbal autism. 

The good news is that we have seen time and again that it is never too late to treat autism. Clearly the earlier you do start, the more extensive the long term benefit should be. So once you realize that intervention is possible, best not to delay.
When autism  is of a single gene origin, there really should eventually be scope to make some kind of permanent fix, if you can intervene very early and so still during that intervention’s sensitive period.  This might involve something very clever like gene editing, which you cannot do at home, or it might be just some drug therapy, like Rapamycin in TSC1 as in the above study.

Monday, 30 May 2016

Sense, Missense or Nonsense - Interpreting Genetic Research in Autism (TCF4, TSC2 , Shank3 and Wnt)

Some clever autism researchers pin their hopes on genetics, while some equally clever ones are not convinced.

One big problem is that genetic testing is still not very rigorous, it is fine if you know what you are looking for, like a specific single gene defect, but if it is a case of find any possible defect in any of the 700+ autism genes it can be hopeless.

Most of the single gene types of autism can be diagnosed based on known physical differences and then that specific gene can be analyzed to confirm the diagnosis.

Today’s post includes some recent examples from the research, and they highlight what is often lacking - some common sense.

There are numerous known single gene conditions that lead to a cascade of dysfunctions that can result in behaviors people associate with autism.  However in most of these single gene conditions, like Fragile X or Pitt-Hopkins, there is a wide spectrum, from mildly affected to severely affected.

There are various different ways in which a gene can be disturbed and so within a single gene condition there can be a variety of sub-dysfunctions.  A perfect example was recently forwarded to me, a study showing how a partial deletion of the Pitt Hopkins gene (TCF4) produced no physical features of the syndrome, but did unfortunately produce intellectual disability.

The study goes on to suggest that “screening for mutations in TCF4 could be considered in the investigation of NSID (non-syndromic intellectual disability)”

Partial deletion of TCF4 in three generation family with non-syndromic intellectual disability, without features of Pitt-Hopkins syndrome

This all matters because one day when therapies for Pitt Hopkins are available, they would very likely be effective on the cognitive impairment of those with undiagnosed partial-Pitt Hopkins.

Another reader sent me links to the studies showing:-

Rapamycin reverses impaired social interaction in mouse models of tuberous sclerosis complex.

Reversal of learning deficits in a Tsc2+/- mouse model of tuberous sclerosis.

But isn’t that Tuberous sclerosis (TSC) extremely rare? like Pitt Hopkins.  Is it really relevant?

Tuberous sclerosis (TSC)  is indeed a rare multisystem genetic disease that causes benign tumors to grow in the brain and on other vital organs such as the kidneys, heart, eyes, lungs, and skin. A combination of symptoms may include seizures, intellectual disability, developmental delay, behavioral problems, skin abnormalities, and lung and kidney disease. TSC is caused by a mutation of either of two genes, TSC1 and TSC2, 

About 60% of people with TSC have autism (biased to TSC2 mutations) and many have epilepsy.

How rare is TSC?  According to research between seven and 12 cases per 100,000, with more than half of these cases undetected.  

Call it 0.01%, rare indeed.

How rare is partial TSC?  What is partial TSC?  That is just my name for what happens when you have just a minor missense mutation, you have a mutation in TSC2 but have none of the characteristic traits of tuberous sclerosis, except autism.
In a recent study of children with autism 20% has a missense mutation of TSC2. 

Not so rare after all.

Mutations in tuberous sclerosis gene may be rife in autism

Mutations in TSC2, a gene typically associated with a syndrome called tuberous sclerosis, are found in many children with autism, suggests a genetic analysis presented yesterday at the 2016 International Meeting for Autism Research in Baltimore.
The findings support the theory that autism results from multiple ‘hits’ to the genome.
Tuberous sclerosis is characterized by benign tumors and skin growths called macules. Autism symptoms show up in about half of all people with tuberous sclerosis, perhaps due to abnormal wiring of neurons in the brain. Tuberous sclerosis is thought to result from mutations in either of two genes: TSC1 or TSC2.
The new analysis finds that mutations in TSC2 can also be silent, as far as symptoms of the syndrome go: Researchers found the missense mutations in 18 of 87 people with autism, none of whom have any of the characteristic traits of tuberous sclerosis.
“They had no macules, no seizure history,” says senior researcher Louisa Kalsner, assistant professor of pediatrics and neurology at the University of Connecticut School of Medicine in Farmington, who presented the results. “We were surprised.”
The researchers stumbled across the finding while searching for genetic variants that could account for signs of autism in children with no known cause of the condition. They performed genetic testing on blood samples from 87 children with autism.

Combined risk:

To see whether silent TSC2 mutations are equally prevalent in the general population, the researchers scanned data from 53,599 people in the Exome Aggregation Consortium database. They found the mutation in 10 percent of the individuals.
The researchers looked more closely at the children with autism, comparing the 18 children who have the mutation with the 69 who do not.
Children with TSC2 mutations were diagnosed about 10 months earlier than those without a mutation, suggesting the TSC2 mutations increase the severity of autism features. But in her small sample, Kalsner says, the groups show no differences in autism severity or cognitive skills. The researchers also found that 6 of the 18 children with TSC2 mutations are girls, compared with 12 of 69 children who don’t have the mutation.
TSC2 variants may combine with other genetic variants to increase the risk of autism. “We don’t think TSC is the sole cause of autism in these kids, but there’s a significant chance that it increases their risk,” Kalsner says.

"hyperactivation of the mechanistic target of rapamycin complex 1 (mTORC1) is a consequence of tuberous sclerosis complex (TSC) 1/2 inactivation."

"the combination of rapamycin and resveratrol may be an effective clinical strategy for treatment of diseases with mTORC1 hyperactivation."

So for the 20% of autism with partial TSC, so-called Rapalogs and other mTOR inhibitors could be helpful, but Rapalogs all have side effects.

One interesting option that arose in my earlier post on Type 3 diabetes and intranasal insulin is Metformin. The common drug used for type 2 diabetes.


Metformin regulates mTORC1 signaling (but so does insulin).

'Metformin activates AMPK by inhibiting oxidative phosphorylation, which in turn negatively regulates mTORC1 signaling via activation of TSC2 and inhibitory phosphorylation of raptor. In parallel, metformin inhibits mTORC1 signaling by suppressing the activity of the Rag GTPases and upregulating REDD1."

Source:  Rapalogs and mTOR inhibitors as anti-aging therapeutics

Clearly you could also just use intranasal insulin.  It might be less potent but should have less side effects because it acting only within the CNS (Metfornin would be given orally).

The Shank protein and the Wnt protein family

Mutations in a gene called Shank3 occur in about 0.5 percent of people with autism.  
But what about partial Shank3 dysfunction?

Shank proteins also play a role in synapse formation and dendritic spine maturation.

Mutations in this gene are associated with autism spectrum disorder. This gene is often missing in patients with 22q13.3 deletion syndrome

Researchers at MIT have just shown, for the first time, that loss of Shank3 affects a well-known set of proteins that comprise the Wnt signaling pathway.  Without Shank3, Wnt signaling is impaired and the synapses do not fully mature.

“The finding raises the possibility of treating autism with drugs that promote Wnt signaling, if the same connection is found in humans”

I have news for MIT, people already do use drugs that promote Wnt signaling, FRAX486 and Ivermectin for example.  All without any genetic testing, most likely.

Reactivating Shank3, or just promote Wnt signaling

The study below showed that in mice, aspects of autism were reversible by reactivating the Shank3 gene.  You might expect that in humans with a partial Shank3 dysfunction you might jump forward to the Wnt signaling pathway and intervene there.

Mouse study offers promise of reversing autism symptoms

One reader of this blog finds FRAX486 very helpful and to be without harmful side effects.  FRAX 486 was recently acquired by Roche and is sitting over there on a shelf gathering dust.

Where from here?

I think we should continue to look at the single gene syndromes but realize that very many more people may be partially affected by them.

Today’s genetic testing gives many false negatives, unless people know what they are looking for; so many dysfunctions go unnoticed.

This area of science is far from mature and there may be many things undetected in the 97% of the genome that is usually ignored that affect expression of the 3% that is the exome.

So best not to expect all the answers, just yet, from genetic testing; maybe in another 50 years.

Understanding and treating multiple-hit-autism, which is the majority of all autism, will require more detailed consideration of which signaling pathways have been disturbed by these hits.  There are 700 autism genes but there a far fewer signaling pathways, so it is not a gargantuan task.  For now a few people are figuring this out at home.   Good for them.

I hope someone does trials of metformin and intranasal insulin in autism.  Intranasal insulin looks very interesting and I was surprised to see in those earlier posts is apparently without side effects.

The odd thing is that metformin is indeed being trialed in autism, but not for its effect on autism, but its possible effect in countering the obesity caused by the usual psychiatric drugs widely prescribed in the US to people with autism.

My suggestion would be to ban the use of drugs like Risperdal, Abilify, Seroquel, Zyprexa etc.

Vanderbilt enrolling children with autism in medication-related weight gain study

Here are details of the trial.

Metformin will be dispensed in a liquid suspension of 100 mg/mL. For children 6-9 years of age, metformin will be started at 250 mg at their evening meal for 1 week, followed by the addition of a 250 mg dose at breakfast for 1 week. At the Week 2 visit, if metformin is well-tolerated, the dose will be increased to 500 mg twice daily. For children from 10-17 years of age, metformin will be started at 250 mg at their evening meal for 1 week, followed by the addition of a 250 mg dose at breakfast for 1 week. At the Week 2 visit, if metformin is well-tolerated, the dose will be increased to 500 mg twice daily. At the Week 4 visit, if metformin is well-tolerated, the dose will be increased to 850 mg twice daily.

Wednesday, 2 December 2015

“Autism treatments proposed by clinical studies and human genetics are complementary” & the NSAID Ponstan as a Novel Autism Therapy

Today’s post was not my idea at all, it was the author of one of the papers who has drawn my attention to the subject.

Genetic studies are complicated and are not the sort of thing I would have chosen to read, let alone write about, before starting this blog. 

The optimal time to initiate pharmacological 
intervention in Autism?

However, much of the complex subject matter has now already been covered, step by step, in earlier posts. Regular readers should not feel put off.

It is perhaps easier to think about ion channel dysfunctions, or channelopathies.  Some of the key genetic dysfunctions produce these channelopathies.  There are many posts in this blog about channelopathies, partly because many therapies already exist to treat them.

Then we have the complex signaling pathways which are often the subject of cancer research, but we have seen that certain ones like RAS and PTEN are key to conditions like some autism and some MR/ID.

So it is not a big leap therefore to consider the findings of a statistical reassessment of the existing genome-wide association studies (GWAS).  As is often the case in medical science, it is the acronyms/abbreviations, like GWAS, that make it look more complex than it really is.

If you only ever read one paper about the genetics of autism, I suggest you make it this one.

Fortunately, the conclusion from the genetic study really fits nicely with the clinical studies reviewed on this blog and even my own first-hand experience of investigating and treating my n=1 case of autism.

Knut, the Biometrician

It was Knut who left a brief comment on this blog and, after a little digging, I was very surprised how much a statistician/biometrician could figure out about autism, from re-analyzing the existing genome-wide association studies (GWAS).

I think the Simons Foundation could save themselves a decade or two by giving him a call.

The Research

For those wanting the science-lite version, there is a short article reviewing the research in lay terms:-

Biostatistics provides clues to understanding autism: an interview with Dr Knut M. Wittkowski

“Hence, modulation of ion channels in children at the age of about 12 months, when the first symptoms of autism can be detected, may prevent progression to the more severe end of the spectrum.” .

The actual research paper is here:-

You may find it heavy going and I have highlighted some key parts.

A novel computational biostatistics approach implies impaired dephosphorylationof growth factor receptors as associated with severity of autism

“Despite evidence for a likely involvement of de novo and environmental or epigenetic risk factors, including maternal antibodies or stress during pregnancy  and paternal age, we contend that coding variations contribute substantially to the heritability of ASD and can be successfully detected and assembled into connected pathways with GWAS—if the experimental design, the primary outcome, the statistical methods used, and the decision rules applied were better targeted toward the particulars of non-randomized studies of common diseases.”

The data comes from the Autism Genome Project (AGP), and there are two sets of data AGPI and AGPPII.

The third data set is for Childhood Absence Epilepsy (CAE)

What I would call Classic Autism, others call severe autism or autistic disorder; Knut calls it Strict Definition Autism (SDA).  HFA is high functioning autism, much of which is Asperger’s Syndrome.

“Study design We aimed at risk factors specific to strict definition autism (SDA) by comparing case subpopulations meeting the definition of SDA and milder cases with ASD (excluding SDA), for which we here use the term ‘highfunctioning autism’ (HFA). To reduce variance, we included only subjects of European ancestry genotyped on the more frequently used platform in either stage. In AGP II, we also excluded female cases because of confounding between chip platform and disease severity. The total number of subjects included (m: male/f: female) was 547/98 (SDA) and 358/68 (HFA) in AGP I and 375 (SDA) and 201 (HFA) in AGP II.

Overall, the results (see Supplementary Figure 1 for a Manhattan plot) are highly consistent with previously proposed aspects of the etiology of ASD. The clusters of genes implicated in both of the independent stages (Figure 2a/b) consistently overlap with our published CAE results (Figure 2c), confirming the involvement of ion channels (top right) and signaling downstream of RAS (bottom left), with two noticeable additional gene clusters in ASD. Both stages implicate several genes involved in deactivation of growth factor (GF) receptors (Figure 2a/b, top left) as ASD-specific risk factors and chloride (Cl − ) signaling, either through Ca2+ activated Cl− channels

Click to enlarge the figure 

A new term is PTPR (protein tyrosine phosphatases receptor), just to confuse us it is also called RPTP.

Receptor Protein Tyrosine Phosphatases in Nervous System Development


For example, the receptor protein tyrosine phosphatases gamma (PTPRG) and zeta (PTPRZ) are expressed primarily in the nervous system and mediate cell adhesion and signaling events during development.

In an earlier post I highlighted the numerous dysfunctions in growth factors (GF) in autism.  Knut is highlighting here the effect of PTPR on growth factors.  Later it is suggested that this cascade of GF dysfunctions could be halted, pharmacologically if it was identified very early.  But, as Courchesne from UC San Diego noted, by the time people have been identified as having autism, around three years old, the accelerated brain growth has already run its course.

You would need to intervene around one year old.

Broad evidence for involvement of PTPRs One of the most striking observations is the involvement of at least five PTPRs in ASD (Figure 2, 10 o’clock position). PTPRs (Table 1e) regulate GF signaling through reversible protein tyrosine dephosphorylation.72 PTPRT (90th/20th, 8.57) was implicated in ASD by a deletion73 (Table S2 AU018704) and a somatic mutation

It was my post pondering the reasons for the positive effect of potassium supplementation that drew Knut’s attention to this blog.  Now we move on to Knut’s ideas on potassium and chloride channels.

K+ and Cl− ion channels as drug targets

Aside from PTPRs (Figure 2, 10 o’clock) as a risk factor for protracted GF signaling, our results suggest a second functional cluster of genes, involved in Cl− transport and signaling, as specific to ASD (Table 1f). In AGP I, the CaCCs ANO4 and ANO7 scored 1st and 70th, respectively. In AGP II, the lysosome membrane H+ /Cl- exchange transporter CLCN7 scored 21st, followed by CAMK2A, which regulates ion channels, including anoctamins82 (55th), and LRRC7 (densin-180), which regulates CAMK2A83 (Figure 2a/b, 2 o’clock). The role of the anoctamins in pathophysiology is not well understood, except that CaCC activity in some neurons is predicted to be excitatory84 and to have a role in neuropathic pain or nerve regeneration. More recently, CaCCs have also been suggested as involved in ‘neurite (re)growth’. Finally, we compared the HFA and SDA cases as separate groups against all parental controls in the larger AGP I population. Overall, the level of significance is lower and the enrichment is less pronounced, especially for the SDA cases (Supplementary Figure 9), as expected when cases and some controls are related. For the HFA cases (Figure 4, and Supplementary Figure 8), however, a second anoctamin, ANO2, located on the other arm of chromosome 12, competes with ANO4 (Figure 1, left), for the most significant gene among the result. Hence, drugs targeting anoctamins might have broader benefits for the treatment of ASD than in preventing progression to more severe forms of autism. ANO2 and ANO6 are associated with panic disorder and major depressive disorder, respectively. ANO3, ANO4, ANO8 and ANO10, but not ANO1, are also expressed in neuronal tissue.86 As ‘druggable channels’, anoctamins ‘may be ideal pharmacological targets to control physiological function or to correct defects in diseases’.  Few drugs, however, target individual anoctamins or even exclusively CaCCs. Cl− channel blockers such as fenamates, for instance, may decrease neuronal excitability primarily by activating Ca2+-dependent outward rectifying K+ channels.

Here is a follow-up paper with consideration of the possible next steps.

Gene gene environment behavior development interaction at the core of autism:

Here, we combine a recent wide-locus approach with novel decision strategies fine-tuned to GWAS. With these methodological advances, mechanistically related clusters of genes and novel treatment options, including prevention of more severe forms of ASD, can now be suggested from studies of a few hundred narrowly defined cases only.
(Nonsyndromic) autism starts with largely unknown prenatal events (: age, : virus/stress ...)
• Mutations in growth factor regulators (PTPRs) lead to neuronal overgrowth (brain sizes).
• Mutations in K+/Cl− channels cause Ca2+ mediated over excitation of neurons (“intense world”).
• Stressful environments (urbanization) contribute to epistatic interaction (increasing prevalence).
• This GGE interaction causes “migraine-like” experiences during the “stranger anxiety” period where children learn verbal/social skills, leading to behavioral maladaptation (“tune-out”).
The lack of verbal/social stimuli causes “patches of disorganization” (Stoner 2014, NEJM) as a form of developmental maladaptation when underutilized brain areas are permanently “pruned”. The PTPRs point to a short window of opportunity (WoO) for pharmacological intervention:
• Treatment has to begin as early as possible, while neurons are still growing (12 months of age. Broad support for the proposed unifying etiology and the 2nd year of life as the WoO:
• Regression (“loss of language”) seen in some children >12 mos of age.
• “Patches of disorganization” in >2 yr old brains.
• Romanian orphans developed “quasi-autism” when placed into foster care at >24 mos of age. 
• Hearing impairment leading to intellectual disability when diagnosed >24 mos of age.

 A rational drug target: treating either of two epistatic risk factors suffices:
• Blocking growth factors (Gleevac, ...) is unacceptable in children merely at risk of ASD.
• Ion channel modulators have been used in small children for arthritis and seizures.

Here is a response to Knut’s first paper from a professor at the UCLA medical school who suggests the combination of the specific NSAID and bumetanide. 
The professor would better understand the mechanism of action of bumetanide in autism if he read Ben Ari’s research more thoroughly, or even this blog.
The article by Wittkowski et al.1 reports results of human genetic studies that suggest that a nonsteroidal anti-inflammatory drug (NSAID) given for a few months from the time of the first symptoms might help some children who are at risk of developing more severe forms of atrial septal defect.
While the authors mention the recent article by Lemonnier et al.,2 which reported that a clinical study of the diuretic Bumetanide was partially effective in children with milder forms of autism, they seem to have overlooked that these two treatments may well be complementary, leading to sequential interventions, each targeting specific risks related to well-defined stages in the development of brain and social interactions.
Since abnormal brain development in autistic disorder goes through different stages from infancy to childhood, targeting different developmental stages with different treatment interventions may well be necessary to foster continued normalization of brain growth.
Bumetanide is known to block inward chloride transporters, yet the relation of this mechanism to the etiology of autism is unknown. Wittkowski et al. identified mutations in calcium-activated (outward) chloride channels as associated with autistic disorder, suggesting loss-of-function mutations in anoctamins as one of the risk factors for autism. This provides a testable hypothesis for the mechanism by which Bumetanide alleviates symptoms of autism. For example, mouse models could test whether Bumetanide ameliorates a stress-induced phenotype caused by a knockout/down in ANO2 and/or ANO4.
A second cluster of genes identified receptor protein tyrosine phosphatases, which downregulate growth factors. These findings support the notion that successful treatment should start as early as possible,3 while neuronal development still takes place.
The rationale for combining these two treatments rests on the fact that Bumetanide is contraindicated in infancy because it is known to interfere with neuronal development when used long term. In contrast, the NSAID proposed in the second study has been given for decades to children with juvenile idiopathic arthritis from 6 months of age on, with no adverse effects on brain development. It is known to modulate chloride channels (see above) as well as potassium channels.4
In conclusion, I wish to extend their hypothesis based on the synergy of the two treatment approaches: (1) early treatment with NSAID can reduce early maladaptive behaviors that cause abnormal pruning of neurons in the cortical areas; (2) these children could subsequently benefit from Bumetanide, which would compensate for the primary ion channel defect, but could not reverse the secondary effect of abnormal pruning.
This hypothesis allows for a novel two-way interaction between behavior and molecular events. Traditionally, one assumes that molecular events determine behavior. The new hypothesis, based on human genetics, also allows for symptoms (such as the absence of social interactions, delayed speech onset and language development) during certain sensitive periods to change molecular events (pruning of neurons in areas required for normal development).

Therapeutic implications from the genetic analysis

Some of the therapies that Knut is proposing, based on the genetic analysis, have already been reviewed in this blog.  Some have not.  A few therapeutic ideas in this blog actually target genes Knut has identified, but not highlighted a therapy.

I will just review the drugs and genes that the above study highlights.


Low dose clonazepam fits in this category.  We have the work of Professor Catterall to support its use.  At higher doses, benzodiazepines have different effects but use is associated with various troubling side effects.


Bumetanide is at the core of my suggested therapy for classic autism or what Knut calls SDA (strict definition autism).  We have Ben-Ari to thank for this

Fenamates (ANO 2/4/7 & KCNMA1)

Here Knut is trying to target the ion channels expressed by the genes ANO 2/4/7 & KCNMA1. 

·        ANO 2/4/7 are calcium activated chloride channels. (CACCs)

·        KCNMA1 is a calcium activated potassium channel.  KCNMA1 encodes the ion channel KCa1.1, otherwise known as BK (big potassium).  This was the subject of post that I never got round to publishing.
Fenamates are an important group of clinically used non-steroidal anti-inflammatory drugs (NSAIDs), but they have other effects beyond being anti-inflammatory.  They act as CaCC inhibitors and also stimulate BKCa channel activity.

Fenamates stimulate BKCachannel osteoblast-like MG-63 cells activity in the human.

 The fenamates can stimulate BKCa channel activity in a manner that seems to be independent of the action of these drugs on the prostaglandin pathway”

Molecular and functional significance of Ca2+-activated Cl− channels in pulmonary arterial smooth muscle

Of this “first generation” of CaCC inhibitors, NFA (a fenamate called niflumic acid)  is the most potent blocker of these channels and the compound most frequently used to investigate the physiological role of CaCCs”

Choice of Fenamate
There are several fenamate-type NSAIDs, but one is a very well used generic drug, Mefenamic acid known as Ponstan, Ponalar, Ponstyl, Ponstel and other generic names.  It is even available as a syrup for children.
 It is not available in all countries.


Gabapentin is used primarily to treat seizures and neuropathic pain. It is also commonly prescribed for many off-label uses, such as treatment of anxiety disorders, insomnia, and bipolar disorder.

Some people with autism are prescribed Gabapentin.  Some people suffer side effects and others do not.

If you have a dysfunction of voltage operated calcium channels, Gabapentin should help.


This is all about modifying NMDA receptors.  Memantine is but one method.


Minocycline is an antibiotic with several little known extra properties.  In autism, we looked at its ability to reduce microglial activation and so improve autism.  A clinical trial showed that it did not help autism.

Minocycline also affects MMP-9.  MMP-9 is an enzyme found to be associated with numerous pathological processes, including cancer, immunologic and cardiovascular diseases.

High MMP-9 activity levels in fragile X syndrome are lowered by minocycline.

 “ The results of this study suggest that, in humans, activity levels of MMP-9 are lowered by minocycline and that, in some cases, changes in MMP-9 activity are positively associated with improvement based on clinical measures.

So if you are treating a case of Fragile-X, or partial "Fragile-X-like" autism, better take note.


Rapamycin and mTOR was the subject of the following post:

mTOR – Indirect inhibition, the Holy Grail for Life Extension and Perhaps Some Autism

Both too much and too little mTOR can occur in autism.


My conclusion is probably different to yours.

For me, it seems that all the pieces really are fitting together and so this blog on the cause and treatment of classic autism will eventually cover the current scientific knowledge, in its entirety.  No complex areas are off limits, because in the end they are not as complex as they seem, when you lift the veil of jargon and acronyms.

From the all-important therapeutic perspective, new insights from today’s post are:-

·        Those with a dysfunction of voltage operated calcium channels might want to give Gabapentin (Neurontin) a try.

·        The fenamate-type NSAID mefenamic acid,  widely known as Ponstan, really should be tested, either at home, or in a clinical trial.

This statistical analysis is based on “all autism”, so any one person would be highly unlikely to have all the mentioned dysfunctions.  These are the most common genetic dysfunctions and many can both hypo and hyper, as in the case of NMDA dysfunctions and indeed mTOR. 

In Knut’s chart, I would add a green line pointing to RAS and PTEN with the word Atorvastatin.  Baclofen would point to the growth factors.  Verapamil would point in multiple places.

The motto of University of Tübingen, where Knut originally comes from, is Attempto !  The Latin for "I dare".

This might be a useful motto for readers of this blog, and also a good tittle for a book on treating autism.