Prenatal epigenetic age acceleration in Down syndrome

That’s a result of Xu et al 2022, “Accelerated epigenetic aging in newborns with Down syndrome”.

This study furthers our understanding of a syndrome of accelerated aging. The authors show a significant acceleration of an epigenetic aging marker in the blood of people with Down syndrome. Furthermore, they show that this effect is present at birth and is significantly stronger in newborns who have Down syndrome plus GATA1 mutations. This association with GATA1 mutations is intriguing as GATA1 mutations are associated with transient abnormal myelopoiesis. One thing that this study does not do is investigate the mechanism by which this age acceleration occurs.

One hypothesis based on this finding is that it might help explain why people with Down syndrome have an increased susceptibility to Alzheimer’s disease. Lore has long been that this is due to the triplication of amyloid precursor protein, however, this study suggests that age acceleration may also play at least a part in the increased susceptibility of people with Down syndrome to aging-associated cognitive impairment and Alzheimer-type neuropathology.

from https://onlinelibrary.wiley.com/doi/10.1111/acel.13652

Advertisement

A neural pacemaker of aging?

Here is an interesting grant from Karl Deisseroth and Anne Brunet that I saw on NIH Reporter. It will be very interesting to see the results from these experiments in a few years.

Aging is a gradual process that results in the loss of cellular function across the body, leading to numerous chronic diseases that promote mortality. Elucidating the precise mechanisms of aging is critical for reducing illness and extending healthy lifespan. However, almost every tissue in the body is modified by aging, making it difficult to pinpoint the principal controller of aging. The goal of this proposal is to determine whether the brain modulates aging through coordinated activity patterns within discrete neuronal networks. We will use one of the shortest-living vertebrates, the African turquoise killifish, as a rapid, high-throughput model of aging to uncover genetically- defined neurons that regulate cellular metabolism and lifespan. Employing large-scale light-sheet imaging in killifish, we will visualize brain-wide calcium activity dynamics to unbiasedly identify neurons that respond to longevity interventions. We will characterize the genetic profiles of the identified neurons via a combination of immunohistochemical, single cell, and phosphorylated ribosome capture approaches. To examine whether these neurons play a causal role to control overall cellular function in the brain and other tissues, we will optogenetically activate these neurons and measure molecular signatures of youth and in vivo metabolic activity in the brain and peripheral tissues. We will monitor and manipulate neural activity throughout the short lifespan of killifish using fiber photometry to determine if this ‘neural pacemaker’ dictates the tempo of aging and youthful behavior. These approaches will then be extended to longer-lived species – zebrafish and mice. Knowledge resulting from these studies should be transformative to understand the fundamental mechanisms that regulate and synchronize aging and longevity. As age is the prime risk factor for many diseases, including neurodegenerative diseases, this proposal should provide new, circuit-based approaches to treat these diseases.

https://reporter.nih.gov/search/hKEP095-sESXSOTnzu5o7Q/project-details/10207466

Everest regression and the effect of age in Alzheimer’s disease

A new-to-me concept is the idea of an Everest regression — “controlling for altitude, Everest is room temperature” — wherein you use a regression model to remove a critical property of an entity, and then go on to make inappropriate/confusing/misleading inferences about that entity.

My immediate thought is that this is an excellent analogy for one of my concerns regarding regressing out the effect of age in studies of Alzheimer’s disease (AD). It’s such a tricky topic.

On the one hand, not everyone who reaches advanced age develops the amyloid beta plaques and other features that defines the cluster of AD pathology. Whereas there are potentially other changes in brain biology that you will see in advanced aging but not AD, such loss of dendritic spines, epigenetic changes, and accumulation of senescent cells.

On the other hand, advanced age is the most important risk factor for AD and explains most of the variance in disease status on a population basis. Arguably, a key part of why some “oldest old” folks do not have AD are protective factors. There have also been suggestions that accelerating aging is part of AD pathophysiology; although, as far as I can tell, the evidence for this remains preliminary. From this perspective, advanced age in AD is like the high altitude of Everest — it’s one of the key associated features.

So if you are trying to find the effects of AD pathophysiology, for example in a study of postmortem human brain samples, should you adjust for the effect of age or not? This is a practical and tricky question without a clear answer. It probably depends on your underlying model of how AD develops in the first place.

So I think it’s worthwhile to be cognizant of the potential hazards of adjusting for age — namely, that you risk inadvertently performing an Everest regression and removing an important chunk of the pathophysiology that you actually want to understand.

Single cell histone modifications seem to accumulate randomly during aging

One of the most remarkable findings in aging over the past decade is that it’s possible to track the rate of aging based on stereotyped DNA methylation changes across a diverse set of tissues. These are known as epigenetic clocks.

But as anyone in the gene expression field knows, changes in the levels of epigenetic markers between groups (like young vs older) is confounded by cell type proportion differences between those groups.

This cell type proportion confound makes it harder to tell whether the changes in DNA methylation are truly a marker of aging or whether they are due to cell type proportion variations that may be already known to occur during aging, like naive T cell depletion due to thymus atrophy.

Single cell epigenetics has the potential to address this problem. By measuring DNA methylation patterns within individual cells, you can compare the epigenetic patterns within the same cell type between groups, and don’t have to worry (as much) about overall changes in cell type proportion [1].

I was interested to see whether anyone has used single cell epigenetic profiling, which was just come out within the past couple of years, to measure whether changes in epigenetic marks can be seen within single cells during aging.

First, let’s back up a second and talk about epigenetics. Two of the major factors that defines a cell’s epigenome are its DNA methylation patterns and its histone post-translational modifications.

DNA methylation has been studied a bit in single cells. One study looked at DNA methylation in hepatocytes and didn’t find many differences between old and young cells.

However, as a recent review points out, single cell DNA methylation data are currently limited because of sample quantity within each cell, and can’t easily compare methylation patterns between different cells in the same region of the genome.

On the histone modification front, I found a nice article by Cheung et al 2018, who measured histone post-translational modifications (PTMs) in single cells derived from blood samples. They found that in aging, there was increased variability histone PTMs both between individuals and between cells.

So, in summary, here are some future directions for this research field that it would be prudent to keep an eye one:

1. How much of the changes in DNA methylation seen in aging are due to changes in relative cell type proportions as opposed to changes within single cells? If we assume that age-related changes in DNA methylation will be similar to age-related changes in histone PTMs, then Cheung et al.’s results suggest that the changes in DNA methylation are probably due to true changes within single cells during aging.
2. Is there a way to slow or reverse age-related changes in DNA methylation or histone PTMs, perhaps targeted to stem cell populations? It’s not clear that this can be done in a practical way, especially if age-related changes are driven primarily by an increase in variability/entropy.
3. If it is possible to slow or reverse DNA methylation or histone PTMs, would that help to slow aging and thus “square the curve” of age-related disease? Aging might be too multifactorial for a single intervention like this to make a major difference, though.

---

[1]: I add “as much” here because differential expression analysis in single cell data is far from straightforward, and e.g. has the potential to be biased by subtle differences in the distribution of sub-cell type spectrum between groups.

Microglia can last a lifetime

An important paper from Füger et al last month, in which they labelled individual microglia in mouse brains and tracked their locations over 1.5 years. Here were some of their major findings:

• The median lifespan of microglia was estimated to be approximately 2.5 years, which is close to the mean lifespan of the mice that they were studying. So, it is fair to think of microglia as long-lived tissue macrophages. It is also clear how changes in microglia epigenetics in earlier life could affect late-life cognitive outcomes.
• Microglia died at a higher rate in older mice, suggesting that aging may lead to alterations in microglia function that could affect neurodegenerative disease.
• In APPPS1 mice, microglia proliferate 3x more than usual in areas of the cortex without amyloid plaque, but only proliferate a normal amount in areas of the cortex with amyloid plaque. This suggests that any increase in microglia near plaque is likely due to migration, not local proliferation.

Problems with the diagnosis of idiopathic normal pressure hydrocephalus

Idiopathic normal pressure hydrocephaus (NPH) is a diagnosis of occult hydrocephalus with normal CSF pressure on LP that was first described in 1965 and is often considered one of the treatable causes of dementia.

The original paper used the now uncommon brain imaging technique of pneumoencephalography, which involved draining the CSF, injecting air as a contrast medium, and performing a brain xray:

Figure 2 from Adams et al 1965 showing uniformly enlarged ventricles; doi: 10.1056/NEJM196507152730301

At my med school we learned NPH by the triad of “wet, wobbly, and wacky”, referring to its classic triad of symptoms: urinary incontinence, gait disturbance, and cognitive impairment.

Like many symptom triads, these symptoms are non-sensitive, with the full triad seen in <60% of patients. It is also non-specific, as urinary incontinence is seen in ~20-40% of those over 60, gait impairment is seen in ~20% over those over 75, and mild cognitive impairment is seen in ~35% of those over 70.

Espay et al explain all of this in the introduction of their critical literature review of idiopathic NPH. One of their major points is that ventricle enlargement is also non-specific, as it is common in other neurodegenerative diseases such as AD, DLB, and PSP.

Here are some of their other points:

• There are no specific clinical, imaging, or neuropathologic findings in NPH.
• The determination of ventricle enlargement on MRI is subjective and not standardized.
• A “true” diagnosis is dependent upon a treatment response to CSF diversion via a ventriculoperitoneal shunt (VPS), which is circular and problematic.
•  There has never been a well-defined RCT to evaluate the use of VPS in NPH.
• Because many patients diagnosed with NPH may in fact have NPH that is secondary rather than a precursor to other neurodegenerative diseases, the fact that VPS may lead to short-term cognitive amelioration even in these patients suggests that VPS should still be considered as a way to improve cognition even in patients that are diagnosed with these neurodegenerative diseases.

Overall, this paper is well worth a read for people interested in treatments for dementia.

Transplanting dopaminergic neurons into MPTP-treated monkeys improves their symptoms

Over the last few years researchers have figured out how to transform iPS cells into dopamine-producing neurons, raising the possibility of transplanting dopaminergic cells into the brains of patients with Parkinson’s disease (PD).

Kikuchi et al. looked at the effect of dopaminergic cell transplantation into the putamen on PD symptoms in monkeys treated with MPTP, which is a model of PD.

Compared to placebo injections, the stem cell transplantation improved symptoms. Notably, it did so somewhat less well than L-DOPA, but it seems plausible that this therapy could be eventually used once L-DOPA has failed, as L-DOPA tends to do over time in PD.

Extended Data Fig 2K/I; doi:10.1038/nature23664

Perhaps the best news from this study is that they identified no markers of cancer formation in the transplanted brains after more than a year post-transplant. It’s always good news when your proposed therapy turns out to be less likely to cause brain cancer as a side effect.

Clinical trials will apparently start soon — from which we will have much to learn, and hopefully some good news.

Cerebral blood flow regulation systematically decreases after a stroke

In everyday life, your muscles, metabolism, and nervous system work together to ensure that your cerebral blood flow meets the metabolic needs of your various brain regions. So if you are trying to scrutinize an impressionist painting, your body will likely relocate more blood flow to your visual cortex.

Following a stroke, this cerebral blood flow regulation is impaired. But, the degree and spread of the impairment is unknown. To investigate this, Hu et al. measured systemic blood pressure (BP) and used a transcranial doppler to measure cerebral blood flow velocity (BFV) at the same time.

In their model, better regulation of cerebral blood flow corresponds to a sharper phase shift between blood pressure (BP) and cerebral blood flow velocity (BFV). Individuals with the highest score of a 9 on their autoregulation index (ARI) have more regulation than those with the lowest score of 0, which corresponds to no phase shift.

When they compared patients who had experienced MCA infarcts (a common type of stroke) and healthy controls, they found that stroke patients had significantly less phase coupling between blood pressure and cerebral blood flow. This effect was pronounced over a wide range of blood pressure oscillation frequencies.

Given enough time and the right conditions, can the body repair its ability to regulate cerebral blood flow following a stroke? When the researchers examined this, they found no statistically significant difference between the BFV-BP phase difference and time since stroke.

But, that doesn’t mean that there’s a statistically significant lack of difference. So, further longitudinal studies will be needed to help clarify whether, in certain people in certain environments, the brain improves its cerebral regulation following stroke.

Reference

Hu K, Lo M-T, Peng C-K, Liu Y, Novak V (2012) A Nonlinear Dynamic Approach Reveals a Long-Term Stroke Effect on Cerebral Blood Flow Regulation at Multiple Time Scales. PLoS Comput Biol 8(7): e1002601. doi:10.1371/journal.pcbi.1002601

Denervation of neuromuscular junctions in the extensor digitorum longus of aging mice

How does the connection morphology of motor neuron axons and muscle fiber endplates change with age? Chai et al recently published some results addressing, in part, this question.

Their study compared young 3 month and geriatric 29 month old mice, which, as the authors note, correspond to roughly 20 and 80 years in humans, respectively. However, it’s always important to keep in mind that mice differ from humans in many important ways.

The researchers cut out muscle tissue, sectioned it in 20 um segments, and double stained with antibodies for both synaptophysin (to detect pre-synaptic nerve terminals) and α-bungarotoxin (to detect postsynaptic muscle endplates).

They then classified neuromuscular junctions that stained positive for both synaptophysin and α-bungarotoxin as innervated, and classified junctions positive for α-bungarotoxin only as denervated. Below is an example of a confocal image of a double stained tissue slice.

EDL = extensor digitorum longus; synaptophysin = red; α-bungarotoxin = green; overlay = yellow; white circle = example of endplate positive for only α-bungarotoxin; scale bars = 75 um; doi:10.1371/journal.pone.0028090.g002 part d-f

Across all samples analyzed, ~7 +/- 2% of neuromuscular junctions were fully denervated in 3 month old mice and ~20 +/- 3% of neuromuscular junctions were fully denervated in 29 month old mice. Such denervation could help account for any age-related decrease in muscle function.

Interestingly and importantly, the researchers did not find a similar trend in the soleus. The lack of concordance underscores some of the variability across tissues of the same type in aging.

Reference

Chai RJ, Vukovic J, Dunlop S, Grounds MD, Shavlakadze T (2011) Striking Denervation of Neuromuscular Junctions without Lumbar Motoneuron Loss in Geriatric Mouse Muscle. PLoS ONE 6(12): e28090. doi:10.1371/journal.pone.0028090

Proteins differentially expressed in the aging hippocampus

In their review of the “neuroproteome” associated with aging and cognitive decline, VanGuilder and Freeman discuss some of the technical approaches and findings in the field.

This illustrative figure shows some of the major cellular players involved and lists some example proteins involved in four important pathways:

"numerous cell types (microglia (green), astrocytes (orange), oligodendrocytes (blue), and neurons (violet)) and subcellular components (mitochondria (brown), endoplasmic reticulum (green), cytoskeleton (orange/red), and synaptic machinery) are affected by brain aging"; doi: 10.3389/fnagi.2011.00008

As you can see, many proteins have been implicated, although the degree of up-/down-regulation of these proteins is not fully elucidated.

The authors mention the value of standardizing efforts to profile the proteome in important brain regions across the lifespan of rodent models. This step would make these results more robustly quantitative and help iterate towards a consensus.

Reference

VanGuilder H. D. and Freeman W. M (2011) The hippocampal neuroproteome with aging and cognitive decline: past progress and future directions. Front. Ag. Neurosci. 3:8. doi: 10.3389/fnagi.2011.00008