HDAC Inhibitors for which Cancer/Autism?

Most types of autism can be viewed as the miss-expression of a few hundred genes, in some cases this has been caused by an initial defect in just one gene.  These single gene autisms are the ones that are usually studied.

Epigenetics has been covered previously in this blog and can either be made to look ultra-complex, which is the reality, or quite simple. The simple view is that in some people genes are miss-expressed because they have been tagged with heritable and removable markers; these can be wiped away. One type of epigenetic marker can be modified by an HDAC inhibitor or HDI.  

Some medical conditions featured genes turned off when they should be on. For example tumor suppressor gene (and autism gene) PTEN is turned off in the prostate of many males with prostate cancer; a neat therapy would be to switch it back on.  Deacetylation of PTEN by SIRT1 deacetylase and, by HDAC1, can stimulate its activity, so probably a good thing for people with this kind of common cancer.

In some types of autism there is a deficiency of a single protein because one of the two copies of the gene that encodes it does not work (Haploinsufficiency) and a neat therapy would be to make the remaining copy of that gene work harder. When I originally looked at epigenetics I thought it would not be possible to epigenetically tag the good copy of the specific gene, to switch it on. However it seems that we do not need to tag a specific gene, just provide the “post-it” notes and let the body do the tagging.

All this leads to the use of HDIs to treat cancer, leaving the body to figure out the hard part of which genes.  In reality an HDI will change the expression of numerous genes, not just the one(s) you wanted.

Different Colours of Tags

Just as those useful Post-It notes come in multiple colours, epigenetic markers come in different varieties.  This has been well studied in the cancer research.

HDAC1 inhibitors only affect part of the epigenome; there are other modifiers that are required to affect other genes.

In autism, as in cancer, you need to know which genes are miss-expressed and then you can see if an epigenetic therapy exists that covers them.  Put more simply if HDAC1 inhibitors affect only yellow post-its, which cancers/autisms would become treatable?

The more complex explanation regarding different colours of post-its:

“Important epigenetic modifications known to regulate gene expression. a DNA methylation of CpG islands in promoter regions by DNA methyltransferases (DNMT) represses gene activity. Posttranslational covalent histone modifications of lysine (K), arginine (R) or serine (S) residues in the “histone tail” also influence gene expression in different ways. b Histone acetylation (Ac) catalysed by histone acetyltransferases (HAT) is usually correlated to increased gene activity, whereas histone deacetylation caused by histone deacetylases (HDAC) is considered to decrease gene expression, even though histone hyperacetylation not always matches regions of increased gene activity. c Histone methylation (Me) and demethylation by histone methyltransferases (HMT) and histone demethylases (HDM) at lysine or arginine residues show different effects on gene activity depending on number and position of methyl groups. d Histone ubiquitinylation (Ub) at lysine residues alters histone structure and allows access of enzymes involved in transcription. e Histone phosphorylation (P) at distinct serine residues is known to be associated with increased gene expression, and it is also involved in DNA damage response and chromatin remodelling. Phosphorylation at linker histone (LH) H1 is considered to be a signal for the release of histone H1 from chromatin. In general, epigenetic regulation depends on the addition of epigenetic marks by writer enzymes (e.g. DNMT, HMT, HAT) and the removal of these marks by epigenetic eraser enzymes (e.g. HDAC and HDM) as well as epigenetic reader enzymes (not shown in this figure)”

https://clinicalepigeneticsjournal.biomedcentral.com/articles/10.1186/s13148-015-0095-z

Treating cancer is always going to be more difficult than treating autism because by the time it has been identified a whole cascade of changes is already underway and whereas autism is not degenerative, cancer by definition is. So even a very partially effective cancer drug might be potent enough for autism, or just a tiny dose of an effective cancer drug.

Source: https://www.sciencedirect.com/science/article/pii/S1044579X17300536

This post is about HDAC1&2 / yellow Post-its 

1.  The Grant Application 

Discovery of Novel Drugs for Autism

The goal of this study is to discover novel, mechanism-based pharmacological intervention for autism, a devastating neurodevelopmental disorder with no treatment currently. Genetic sequencing has revealed extensive overlap in risk genes for autism and for cancer, many of which are chromatin remodeling factors important for transcriptional regulation, suggesting the possibility of repurposing the anti-cancer drugs targeting epigenetic enzymes for autism treatment. ASDDR LLC and Yan Lab at SUNY-Buffalo propose to jointly investigate the hypothesis that histone deacetylase (HDAC) inhibitors are able to restore the expression of key autism risk factors and induce long-lasting rescue of autism-like behavioral and synaptic deficits. Combined behavioral, biochemical and electrophysiological approaches will be used to address two specific aims. 

Aim 1. To discover HDAC inhibitors that can alleviate autism-like behavioral deficits in autism mouse models. Yan lab screened a number of drugs and found that a brief treatment with the highly potent and class I-specific HDAC inhibitor, romidepsin (Istodax, an FDA-approved anti-cancer agent) at the very low dose, led to dramatic and prolonged rescue of the social deficits in the Shank3-deficient mouse model of autism. To determine whether this pharmacological agent can serve as a tool compound for autism drug development, its therapeutic efficacy and safety will be examined in two different models of autism, Shank3-deficient mice and BTBR mice.

Aim 2. To identify the molecular targets of HDAC inhibitors as benchmarks for the treatment of autism. For the discovery of effective drugs to treat autism, the molecular pathways on which HDAC inhibitors act to alleviate the autism-like behavioral deficits in Shank3-deficient mice need to be understood. We will reveal the potential benchmark, such as actin regulators and NMDARs, as molecular targets of romidepsin. This phase I preclinical study will provide great promise for the discovery of new and effective pharmacological agents to treat the social interaction deficits, a core symptom of autism.

Public Health Relevance

This project is to discover novel, mechanism-based therapeutic strategies for autism. The corporate and academic partners propose to jointly investigate the hypothesis that histone deacetylase (HDAC) inhibitors are able to restore the expression of key autism risk factors and induce long-lasting rescue of autism-like behavioral and synaptic deficits.

2. Study Press Release 

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 model of autism 

 “The advantage of being able to adjust a set of genes identified as key autism risk factors may explain the strong and long-lasting efficacy of this therapeutic agent for autism.”

BUFFALO, N.Y. — Of all the challenges that come with a diagnosis of autism spectrum disorder (ASD), the social difficulties are among the most devastating. Currently, there is no treatment for this primary symptom of ASD. New research at the University at Buffalo reveals the first evidence that it may be possible to use a single compound to alleviate the behavioral symptoms by targeting sets of genes involved in the disease.

The research, published today in Nature Neuroscience, demonstrated that brief treatment with a very low dose of romidepsin, a Food and Drug Administration-approved anti-cancer drug, restored social deficits in animal models of autism in a sustained fashion.

The three-day treatment reversed social deficits in mice deficient in a gene called Shank 3, an important risk factor for ASD. This effect lasted for three weeks, spanning the juvenile to late adolescent period, a critical developmental stage for social and communication skills. That is equivalent to several years in humans, suggesting the effects of a similar treatment could potentially be long-lasting, the researchers say.

Profound, prolonged effect

“We have discovered a small molecule compound that shows a profound and prolonged effect on autism-like social deficits without obvious side effects, while many currently used compounds for treating a variety of psychiatric diseases have failed to exhibit the therapeutic efficacy for this core symptom of autism,” said Zhen Yan, PhD, professor in the Department of Physiology and Biophysics in the Jacobs School of Medicine and Biomedical Sciences at UB, and senior author on the paper.

The study builds on her previous research from 2015. That work revealed how the loss of Shank 3 disrupts neuronal communications by affecting the function of the NMDA (n-methyl-D-aspartate) receptor, a critical player in regulating cognition and emotion, leading to deficits in social preference that are common in ASD.

In the new research, the UB scientists found they could reverse those social deficits with a very low dose of romidepsin, which, they found, restores gene expression and function using an epigenetic mechanism, where gene changes are caused by influences other than DNA sequences. Yan noted that human genetics studies have suggested that epigenetic abnormalities likely play a major role in ASD.

To pursue these promising findings, Yan has founded a startup company called ASDDR, which was awarded a Small Business Technology Transfer grant from the National Institutes of Health last summer for more than $770,000.

Epigenetics in ASD

Many of the mutations in ASD, Yan explained, result from chromatin remodeling factors, which are involved in dynamically changing the structure of chromatin, the complex of genetic material in the cell nucleus that condenses into chromosomes.

“The extensive overlap in risk genes for autism and cancer, many of which are chromatin remodeling factors, supports the idea of repurposing epigenetic drugs used in cancer treatment as targeted treatments for autism,” said Yan.

She and her colleagues knew that chromatin regulators — which control how genetic material gains access to a cell’s transcriptional machinery — were key to treating the social deficits in ASD, but the challenge was to know how to affect key risk factors at once.

“Autism involves the loss of so many genes,” Yan explained. “To rescue the social deficits, a compound has to affect a number of genes that are involved in neuronal communication.”

To do so, the team turned to a type of chromatin remodeler called histone modifiers. They modify proteins called histones that help organize genetic material in the nucleus so gene expression can be regulated. Since many genes are altered in autism, the UB scientists knew a histone modifier might be effective.

Loosening up chromatin

In particular, they were interested in histone deacetylase (HDAC), a family of histone modifiers that are critically involved in the remodeling of chromatin structure and the transcriptional regulation of targeted genes.

“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 HDAC inhibitor loosens up the densely packed chromatin so that the transcriptional machinery gains access to the promoter area of the genes; thus they can be expressed,” Yan said.

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.

“The advantage of being able to adjust a set of genes identified as key autism risk factors may explain the strong and long-lasting efficacy of this therapeutic agent for autism,” Yan explained. She and her colleagues will continue their focus on discovering and developing better therapeutic agents for autism.  

Full study:-  

Social deficits in Shank3-deficientmouse models of autism are rescued by histone deacetylase (HDAC) inhibition

HDAC Inhibitors

HDIs have a long history of use in psychiatry and neurology as mood stabilizers and anti-epileptics. More recently they are being investigated as possible treatments for cancers, parasitic and inflammatory diseases. 

HDAC inhibitors have effects on non-histone proteins that are related to acetylation. HDIs can alter the degree of acetylation of these molecules and, therefore, increase or repress their activity.

“To carry out gene expression, a cell must control the coiling and uncoiling of DNA around histones. This is accomplished with the assistance of histone acetyl transferases (HAT), which acetylate the lysine residues in core histones leading to a less compact and more transcriptionally active chromatin, and, on the converse, the actions of histone deacetylases (HDAC), which remove the acetyl groups from the lysine residues leading to the formation of a condensed and transcriptionally silenced chromatin. Reversible modification of the terminal tails of core histones constitutes the major epigenetic mechanism for remodeling higher-order chromatin structure and controlling gene expression. HDAC inhibitors (HDI) block this action and can result in hyperacetylation of histones, thereby affecting gene expression.^[5][6][7] The open chromatin resulting from inhibition of histone deacetylases can result in either the up-regulation or the repression of genes.”

Pitt Hopkins Research

We saw that transcription factor TCF4 (the Pitt Hopkins gene) is also lacking in some MR/ID and schizophrenia. We saw in an earlier post that TCF4 can be upregulated by PKA (protein kinase A) and that this can be achieved using a PDE4 inhibitor as used to treat asthma and COPD. So in theory Daxas should help.

The lack of the TCF4 protein in Pitt Hopkins causes a cascade of other genes to be miss-expressed. The logical thing to do is to correct that miss-expression. 

The Shank3 research is not the first to suggest that HDAC inhibition as a potentially viable therapy. In 2016 the same idea was suggested for Pitt Hopkins and while this is a rare condition, milder dysfunctions of the same TCF4 gene are seen as common in MR/ID and indeed in schizophrenia. So HDAC inhibition may be a viable therapy for many people.

HDACi meds may reverse effects of Pitt Hopkins

In a paper published this week by the journal Cell Reports, Sweatt and his colleagues at the University of Alabama at Birmingham (UAB) report that mice deficient in Tcf4 exhibit impairments in social interaction, vocalization, learning and memory characteristic of PTHS.

The impairments were “normalized” when the mice were given small-molecule drugs called HDAC inhibitors, which alter Tcf4-associated gene expression in the brain. The finding suggests that “broadly acting, epigenetically targeted therapeutics … might be particularly beneficial in PTHS patients,” the researchers concluded.

“We are quite excited by these findings, said Sweatt, a Vanderbilt University-trained pharmacologist who formerly chaired the Department of Neurobiology and directed the McKnight Brain Institute, both at UAB.

“Pitt-Hopkins Syndrome is an orphan disease that has not been extensively studied,” he said. “Having identified one potential avenue for possible therapeutics is an important step forward.”

http://www.cell.com/cell-reports/fulltext/S2211-1247(16)31036-1

“Nearly one-quarter of the genes dysregulated in the Tcf4(+/−) mice are also regulated by HDAC inhibition. The strong negative correlation between Tcf4(+/−) and CI-994 DEGs (R² = 0.72) suggests HDAC inhibition is a viable avenue for correcting a large percentage of transcriptional dysregulation associated with Tcf4 haploinsufficiency.”

Which HDAC Inhibitor?

It should be noted that Romidepsin inhibits both HDAC1 and HDAC2.

There are HDACs numbered 1 through 10.

HDAC inhibitors vary in potency. Below is a chart comparing different HDI drugs in the activation of HIV expression.

In vitro activation of HIV expression by HDAC inhibitors in an in vitro latency model.

  

The role of diet

I know that many readers of this blog like dietary interventions and do not like drugs.

In cancer I think diet can be preventative rather than therapeutic or curative. Once cancer takes hold you need very potent therapies.

In dementia it looks like diet can be preventative and therapeutic.

In mild ADHD and mild autism it looks like dietary intervention can be sufficient.  

Many flavonoids have mild epigenetic properties. They are unlikely to be potent enough to halt the cascade of changes seen in a runaway cancer, but they may well be chemoprotective, i.e. they prevent cancer developing in the first place.

Since in some autism we only need a relatively mild  effect perhaps flavonoids do have some potential, depending on which genes are miss expressed.

Epigenetic activities of flavonoids in the prevention and treatment of cancer

Food containing high amounts of epigenetically active flavonoids

Description	Class	Flavonoid	Ǿ mg/100 g	Sources of data
Grapefruit, raw (not specified as to colour) (Citrus paradisi)	Flavanones	Hesperetin	1.50	aUSDA Database for the Flavonoid Content of Selected Foods: e.g. [193]
		Naringenin	53.00
	Flavonols	Kaempferol	0.40
		Quercetin	0.50
Onions, red, raw	Flavones	Apigenin	0.24	aUSDA Database for the Flavonoid Content of Selected Foods: e.g. [193, 194, 195, 196]
		Luteolin	0.16
	Flavonols	Kaempferol	0.70
		Myricetin	2.16
		Quercetin	39.21
Soybeans, mature seeds, raw (all sources)	Isoflavones	Daidzein	62.07	bUSDA Database for the Isoflavone Content of Selected Foods: e.g. [197, 198, 199, 200, 201, 202]
		Genistein	80.99
Spices, parsley, dried (Petroselinum crispum)	Flavones	Apigenin	4503.50	aUSDA Database for the Flavonoid Content of Selected Foods: e.g. [196]
		Luteolin	19.75
Strawberries (including frozen unsweetened strawberries)	Flavonols	Fisetin	16	[203]
		Kaempferol	0.49	aUSDA Database for the Flavonoid Content of Selected Foods: e.g. [204, 205]
		Myricetin	0.35
		Quercetin	0.46
Cacao beans	Flavan-3-ols	(+)-Catechin	88.45	aUSDA Database for the aFlavonoid Content of Selected Foods: e.g. [206]
		(−)-Epicatechin	99.18
Tea, black, brewed, prepared with tap water	Flavan-3-ols	(+)-Catechin	1.51	aUSDA Database for the Flavonoid Content of Selected Foods: e.g. [196, 207, 208, 209]
		(−)-Epigallocatechin 3-gallate	9.36
	Flavonols	Kaempferol	1.41
		Myricetin	0.45
		Quercetin	2.19
Tea, green, brewed, decaffeinated	Flavan-3-ols	(−)-Epigallocatechin 3-gallate	26.05	aUSDA Database for the Flavonoid Content of Selected Foods:
	Flavonols	Kaempferol	1.00
		Myricetin	1.00
		Quercetin	2.77

A good example is EGCG 

In earlier posts on EGCG, being trialed in Spain on Down Syndrome and Fragile X; I was intrigued by the its long-lasting effects: 

Green tea extract 'boosts mental ability' in people with Down's

For most of the tests (21 of 24) there were no differences between the groups. 

However, in three tests people who'd taken EGCG did better. This improvement lasted for six months after the study ended. 

Another example is Sulforaphane (sometimes)

It appears that some people taking sulforaphane experience disease changing results, which are likely caused by the epigenetic effects of inhibiting HDAC. 

Sulforaphane from Broccoli Reduces Symptoms of Autism: A Follow-up Case Series from a Randomized Double-blind Study

Summarized Case Reports

A.    Three participants who took SF did not appear to improve during the study. Their parents reported lack of a noticeable effect and were not aware whether their young adults had been taking SF or placebo.

B.     One participant no longer uses SF. However, he improved dramatically while taking it during the study and remained “improved” after the study, suggesting to the study team a possible “epigenetic switch” might have been triggered.

“W is doing fantastic. He really turned into the most relaxed and fantastic child (on sulforaphane). Definitely something great. Helped him a lot. His friends, family, and members at his home all noticed a wonderful change. He is off the sulforaphane and has been since the end of his study in 2012.”

  

Perhaps Butyrate?  

Butyrate, Neuroepigenetics and the Gut Microbiome: Cana High Fiber Diet Improve Brain Health?

As interest in the gut microbiome has grown in recent years, attention has turned to the impact of our diet on our brain. The benefits of a high fiber diet in the colon have been well documented in epidemiological studies, but its potential impact on the brain has largely been understudied. Here, we will review evidence that butyrate, a short-chain fatty acid (SCFA) produced by bacterial fermentation of fiber in the colon, can improve brain health. Butyrate has been extensively studied as a histone deacetylase (HDAC) inhibitor but also functions as a ligand for a subset of G protein-coupled receptors and as an energy metabolite. These diverse modes of action make it well suited for solving the wide array of imbalances frequently encountered in neurological disorders. In this review, we will integrate evidence from the disparate fields of gastroenterology and neuroscience to hypothesize that the metabolism of a high fiber diet in the gut can alter gene expression in the brain to prevent neurodegeneration and promote regeneration.

  

Butyrate enhances mitochondrial function during oxidative stress in cell lines from boys with autism

In general, these data suggest that BT can enhance mitochondrial function in the context of physiological stress and/or mitochondrial dysfunction, and may be an important metabolite that can help rescue energy metabolism during disease states. Thus, insight into this metabolic modulator may have wide applications for both health and disease since BT has been implicated in a wide variety of conditions including ASD. However, future clinical studies in humans are needed to help define the practical implications of these physiological findings.

Conclusion

Clearly HDAC inhibitors are beneficial in some cancer and some autism.

In cancer the dose required is so high there almost inevitably will be some side effects, particularly in people already in poor health.

Hopefully when Dr Yan moves on to trial Romidepsin in her second mouse model, the BTBR model, she will be as successful as with the Shank3 model.

Ultimately, I assume she will trial her low dose Romidepsin as a single dose in humans. I am sure plenty of people will be interested in that, including all the Pitt Hopkins families. Hopefully someone will trial Daxas in Pitt Hopkins (upregulate PKA which then upregulates TCF4).

Dietary HDAC inhibitors include butyrate and sulforaphane. They are much weaker than Romidepsin. Would a very large dose of sulforaphane/butyrate have the potency of a small dose of Romidepsin?

To be effective in autism the HDAC inhibitor would have to freely cross the blood barrier, clearly drugs used to treat brain cancer tick this box.

Vorinostat/Zolinza also looks interesting.

We should not overlook Valproic acid, another HDAC inhibitor. This epilepsy drug can cause autism when taken during pregnancy, but is taken by some children with autism. Unlike Romidepsin and Vorinostat, which are hugely expensive, Valproic acid is cheap.

Continued use of Valproic acid can cause side effects, as seen in the comments section of this blog. A short sharp shock with valproic acid might be different.

I am sure Dr Yan chose Romidepsin for its potency. A small dose of Romidepsin is likely much more effective than a bucket load of broccoli sprouts (sulforophane).  

Just how low a dose is Dr Yan talking about? Recall that Professor Catterall’s  low dose of clonazepam (to modulate alpha3 subunits of GABAa receptors) was so low in humans it has none of the well-known drawbacks of benzodiazepine use (addiction, tolerance etc).

Dr Naviaux’s use of Suramin was long thought to be impractical in humans due to side effects, but now this appears not to be the case.

Back to Dr Yan:- 

Social deficits in Shank3-deficient mouse models of autism are rescued by histone deacetylase (HDAC) inhibition

Treatment with the HDAC inhibitor romidepsin lastingly relieves autism-like social deficits in Shank3-deficient mice. The level of global H3 acetylation (Fig. 1a) in the frontal cortex of Shank3+/ΔC mice was significantly lower than that from wild-type (WT) mice. 

 A systemic administration of low-dose romidepsin (0.25 mg/kg, intraperitoneally (i.p.), once daily for 3 d), a highly potent and brainpermeable class I-specific HDAC inhibitor (with nanomolar in vitro potency25) approved by the US Food and Drug Administration (FDA) for cancer treatment26–28, significantly elevated the level of acetylated H3 in Shank3+/ΔC mice, while it had little effect in WT mice. These data suggest that Shank3-deficient mice have an abnormally low level of histone acetylation, which can be restored by romidepsin treatment. 

This dose looks like about one tenth of the used in mice in cancer trials.

In humans, Romidepsin is for intravenous infusion only. Each 10 mg single-use vial of Romidepsin/Istodax costs about $2,800.

Vorinostat/Zolinza costs about $3,800 for 30 capsules.

If the autism effects of a potent HDAC1/2 inhibitor can last for several years in humans, as suggested by Dr Yan, and if the dose is a tenth of the cancer dose, the cost would not seem to be such a barrier.

The open question is the safety profile of Romidepsin at a single low dose in otherwise physically healthy children.

Risk vs Reward

While nobody wants side effects, one has to consider the risk versus the reward. In some single gene types of severe autism it is clear what the outcome with no intervention will be; perhaps that looming outcome warrants taking a bigger risk than someone with mild autism struggling with social difficulties? But then again, perhaps an HDAC1/2 inhibitor might improve social functioning so someone with Asperger’s, or indeed schizophrenia, does not commit suicide?