Problems with PARKIN in PARIS

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PARKIN is a protein that is associated with a young-onset form of Parkinson’s. Individuals carrying tiny genetic variants in the region of DNA producing this protein have a higher risk of developing Parkinson’s before the age of 40 than non-carriers.

The PARKIN protein is believed to play an important role in the disposal of old/damaged mitochondria (the power stations of cells). But recent research points towards another protein – that interacts with PARKIN – which may also be implicated in the health and well being of mitochondria.

That other protein is called PARIS.

In today’s post, we will discuss what PARKIN does, explore how PARIS could be involved, and reflect on what this could mean for future therapies targeting PARKIN-associated Parkinson’s.

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paris

No label required. A magnificent city. Source: HathawaysofHaworth

Paris is not my favourite city (Hanoi takes that spot), but it is probably in the top 10.

Like London and New York, La Ville Lumière is an incredible place to be fortunate enough to visit.

If you ever find yourself in Paris, bored of all the art, culture, food, etc, and you feel like something more scientific, make your way up the Seine river to the 5th arrondissement, and try to find the Muséum national d’histoire naturelle. Once you get there, ask for the “Galerie de Paléontologie et d’Anatomie comparée” (Paleontology and comparative Anatomy Gallery):

This is the realm of Georges Cuvier – the French paleontologist who researched fossils and in 1796 laid out the first ideas for extinction theory. It is a hall of scientific wonder.

As I say, it is worth a visit if ever you are bored in Paris. But be warned that parking is an issue at the Jardin des plantes where the gallery is located.

In fact, parking is an issue everywhere in Paris.

It seems like Parking and Paris do not mix.

I’m sorry, but what does this have to do with Parkinson’s?

Well, recently Parkinson’s research has also demonstrated that a different kind of PARKIN and PARIS also do not mix.

Quoi? You’ve completely lost me. What are you talking about?

Recently this report was published:

Title: Defects in Mitochondrial Biogenesis Drive Mitochondrial Alterations in PARKIN-Deficient Human Dopamine Neurons
Authors: Kumar M, Acevedo-Cintrón J, Jhaldiyal A, Wang H, Andrabi SA, Eacker S, Karuppagounder SS, Brahmachari S, Chen R, Kim H, Ko HS, Dawson VL, Dawson TM
Journal: Stem Cell Reports Published online: August 13, 2020
PMID:  32795422              (This report is OPEN ACCESS if you would like to read more)

In this study, the researchers were interested in a Parkinson’s associated protein called PARKIN.

What is PARKIN?

Sometimes referred to as PARK2 (as errors in the region of DNA that encodes PARKIN was the second genetic risk factor to be associated with Parkinson’s).

The structure of ubiquitin. Source: Wikipedia

Genetic variations in PARKIN are associated with early onset Parkinson’s.

Biologically speaking, what does PARKIN do?

PARKIN is an enzyme. It functions as an E3 ubiquitin ligase.

What is an E3 ubiquitin ligase?

A ligase is an enzyme that initiates the joining of two molecules. It forms a new chemical bond between them.

Ubiquitin is a marvellous little protein that – as the name suggests – is ‘ubiquitous’ in all cells, and it affects all aspects of cell biology. It works its magic by being bound to proteins through a process known as ubiquitination.

Think of PARKIN as an enzyme that connects ubiquitin with other proteins. The E3 part refers to the third and final step in the ubiquitination process. So PARKIN is involved in that final stage of ubiquitination.

In the interior of cells, PARKIN appears to have many different cellular functions involving ubiquitination, but it has been most thoroughly studied in the context of mitophagy.

And what is mitophagy?

Mitophagy involves the disposal of old or dysfunctional mitochondria.

And before you ask, mitochondria are the power stations of each cell. They help to keep the lights on. Without them, the party is over and the cell dies.

Mitochondria

Mitochondria and their location in the cell. Source: NCBI

You may remember from high school biology class that mitochondria are tiny bean-shaped objects within the cell. They convert nutrients from food into Adenosine Triphosphate (or ATP). ATP is the fuel which cells run on. Given their critical role in energy supply, mitochondria are plentiful (some cells have thousands) and highly organised within the cell, being moved around to wherever they are needed.

Like you, me and all other things in life, mitochondria have a use-by date. And as mitochondria get old and worn out (or damaged) with time, the cell will dispose of them via the process of mitophagy.

How is PARKIN involved in mitophagy?

In mitophagy, PARKIN interacts with another Parkinson’s associated protein called PINK1. Genetic variations in the PINK1 gene are also associated with early onset Parkinson’s.

In the process of mitophagy, these two protein play important functions.

PINK1 acts like a kind of handle on the surface of mitochondria. In normal, healthy cells, the PINK1 protein attaches to the surface of mitochondria and it is slowly absorbed until it completely disappears from the surface and is degraded. In unhealthy cells, however, this process is inhibited and PINK1 starts to accumulate on the outer surface of the mitochondria. Lots of handles poking out of the surface of the mitochondria.

Now, if PINK1 is a handle, then PARKIN is a flag that likes to hold onto the PINK1 handle. While exposed on the surface of mitochondria PINK1 starts grabbing the PARKIN protein. This pairing is a signal to the cell that this particular mitochondrion (singular) is not healthy and needs to be removed. The pairing start the process that leads to the development of the phagophore (a sack-like structure that surrounds the damaged/old mitochondria and degrades it) and eventually mitophagy.

601587-fig-003

Pink1 and Parkin in normal (right) and unhealthy (left) situations. Source: Hindawi

In the absence of normal PINK1 or PARKIN proteins, there is no handle-flag system and old/damaged mitochondria start to pile up. They are not disposed of appropriately and as a result the cell gets sick and ultimately dies.

Mitophagy. Source: Frontiersin

As I said above, people with particular mutations in the PINK1 or PARKIN genes are vulnerable to developing an early onset form of Parkinson’s. It has been proposed that the dysfunctional disposal of (and accumulation of) old mitochondria is part of the reason why these individuals develop the condition at such an early age.

Disrupted mitophagy has long been considered to be part of the problem in these cases.

But recently, there has been some evidence questioning this idea.

And this is where PARIS comes into the story.

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RECAP #1:  PARKIN is a Parkinson’s-associated protein that has many functions within cells. The most well studied of those is mitophagy (the removal of old or damaged mitochondria).

Mitochondria are the power stations of cells, providing them with all the energy they need to conduct all of their functions. Accumulation of damaged/old mitochondria can be dangerous for cells as they can cause cellular stress. Thus, correct disposal of them (mitophagy) is important.

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What is PARIS?

Parkin Interacting Substrate (or PARIS; also known as Zinc Finger Protein 746 – ZNF746) is a KRAB and zinc finger protein. In cells, it suppresses a protein called peroxisome proliferator-activated receptor γ coactivator-1α (PGC-1α).

Sorry, but that does that mean?

PARIS is a protein that blocks the activity of PGC-1α.

And PGC-1α is a protein that activates neuroprotective pathways. Mice with no PGC-1α are more prone to develop Parkinson’s like features following exposure to high levels of human α-synuclein (Click here to read more about this).

Ok. What do we know about PARIS in Parkinson’s?

A few years ago, a group of researchers led by Prof Ted Dawson at John Hopkins School of Medicine published this study:

cell

Title: PARIS (ZNF746) repression of PGC-1α contributes to neurodegeneration in Parkinson’s disease.
Authors: Shin JH, Ko HS, Kang H, Lee Y, Lee YI, Pletinkova O, Troconso JC, Dawson VL, Dawson TM.
Journal: Cell. 2011 Mar 4;144(5):689-702.
PMID: 21376232        (This article is OPEN ACCESS if you would like to read it)

In this study, the researchers noticed that the protein PARIS was accumulating in cells that did not have PARKIN. They discovered that PARKIN was important for labelling old PARIS protein for disposal. Thus, in the absence of PARKIN, PARIS protein would not be disposed of and simply piled up.

This build up of PARIS resulted in the loss of dopamine neurons (a set of cells in the brain that are particularly vulnerable and severely affected in Parkinson’s) in mice that did not produce PARKIN. When the researchers re-introduced normal PARKIN protein, the researchers were able to rescue the cell loss. Interestingly, the researchers also found that over-production of PARIS in normal mice resulted in cell loss which could be rescued by a similar over-production of PARKIN.

When they looked in postmortem human brains, the researchers found that levels of PARIS protein were more than two times higher in regions affected by Parkinson’s (the striatum and the substantia nigra) of people with sporadic Parkinson’s when compared to healthy controls. Interestingly, this increase was only seen with PARIS protein, and not PARIS RNA (where the scientists saw no different with control samples), suggesting a potential problem in the disposal of PARIS protein in the Parkinsonian brain.

The investigators concluded that this meant PARIS was could be playing a role in the cell loss associated with Parkinson’s.

They followed up this research a few years later with this publication:

parkins

Title: Parkin loss leads to PARIS-dependent declines in mitochondrial mass and respiration.
Authors: Stevens DA, Lee Y, Kang HC, Lee BD, Lee YI, Bower A, Jiang H, Kang SU, Andrabi SA, Dawson VL, Shin JH, Dawson TM.
Journal: Proc Natl Acad Sci U S A. 2015 Sep 15;112(37):11696-701.
PMID: 26324925     (This article is OPEN ACCESS if you would like to read it)

In this study, the same researchers found that when they genetically remove PARKIN protein from the brains of adult mice there would be a decrease in the size and number of mitochondria. The researchers also demonstrated that this phenomenon could reversed by removing PARIS protein from these no-PARKIN mice. And this last trick would prevent any associated loss of dopamine neurons.

Interestingly, they also demonstrated that the decrease in the size and number of mitochondria (and subsequent loss of dopamine neurons) could be caused by over production of PARIS in normal mice.

All of these results pointed towards an important role for both PARKIN and PARIS in the maintenance of healthy mitochondria.

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RECAP #2:  PARIS is a protein that blocks another protein called PGC-1α. PGC-1α activates different neuroprotective pathways.

PARKIN is involved with the disposal of PARIS, and in the absence of PARKIN, PARIS begins to accumulate and block PGC-1α – making cells more vulnerable to damage or stress.

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So what new research has been published about PARIS?

In the recently published study, the researchers wanted to better characterise the relationship between PARKIN and PARIS. Here is their report:

Title: Defects in Mitochondrial Biogenesis Drive Mitochondrial Alterations in PARKIN-Deficient Human Dopamine Neurons
Authors: Kumar M, Acevedo-Cintrón J, Jhaldiyal A, Wang H, Andrabi SA, Eacker S, Karuppagounder SS, Brahmachari S, Chen R, Kim H, Ko HS, Dawson VL, Dawson TM
Journal: Stem Cell Reports Published online: August 13, 2020
PMID:  32795422              (This report is OPEN ACCESS if you would like to read more)

In this study, the scientists took embryonic stem cells with the PARKIN gene mutated and they generated dopamine neurons in cell culture from them. These were compared to dopamine neurons grown from embryonic stem cells with no PARKIN variants.

The researchers found that there was a 40% reduction in the number of dopamine neurons from the cells lacking PARKIN (compared to the normal cells). This was not due to a similar reduction in the number of neurons (the cells lacking PARKIN produced only 20% less neurons than the control cells). Further investigations indicated that this reduction in dopamine neurons was the results of cell death.

To determine why there was an increase in cell death in the dopamine neurons from cells lacking PARKIN, the researchers shifted their attention to the health of the mitochondria in those cells. They found that the loss of PARKIN leads to issues in mitochondrial respiration (energy production). A 24% reduction in basal levels to be exact. The investigators also found a significant reduction in levels of mitophagy and production of new mitochondria (“biogenesis”) in the dopamine neurons from cells lacking PARKIN.

Given their previous interest in PARIS, the researchers also looked that the levels of this protein and they found that PARIS levels were elevated 3x higher in the dopamine neurons from cells lacking PARKIN (compared to the control cells). This rise in PARIS was associated with a 55% reduction in PGC-1α levels.

By adding extra PARKIN to the cells, the researchers found that they could rescue the mitophagy issues and PGC-1α levels…. but not the reduction in production of new mitochondria.

Subsequent experiments demonstrated that reducing PARIS in the cells lacking PARKIN rescued the production of new mitochondria, but not mitophagy levels.

In their conclusions, the researchers wrote that their results highlight “the importance mitochondrial biogenesis versus mitophagy in the pathogenesis of PD due to inactivation or loss of PARKIN in human dopamine neurons“.

Interesting. Has this ever been observed before?

Sort of.

Several years ago, this paper was published by the same researchers:

dawson

Title: PINK1 Primes Parkin-Mediated Ubiquitination of PARIS in Dopaminergic Neuronal Survival.
Authors: Lee Y, Stevens DA, Kang SU, Jiang H, Lee YI, Ko HS, Scarffe LA, Umanah GE, Kang H, Ham S, Kam TI, Allen K, Brahmachari S, Kim JW, Neifert S, Yun SP, Fiesel FC, Springer W, Dawson VL, Shin JH, Dawson TM.
Journal: Cell Rep. 2017 Jan 24;18(4):918-932.
PMID: 28122242       (This article is OPEN ACCESS if you would like to read it)

In their study, the researchers found that PARKIN is not the only Parkinson’s associated protein in the PARIS story.

We mentioned PINK1 further above and have previously talked about it on the SoPD (click here to read a previous SoPD post on this protein) – and yes, you would be forgiven if you start to think that all Parkinson’s related proteins start with the latter ‘P’.

As we discussed above, PINK1 grabs PARKIN and causes it to bind to dysfunctional mitochondria. PARKIN then signals to the rest of the cell for that particular mitochondria to be disposed of. In this study, the researchers found that PINK1 also grabs PARIS and signals for PARKIN to dispose of it. In the absence of PINK1, normal PARKIN protein does not label old PARIS protein for disposal and PARIS starts to pile up.

The researchers then began manipulating the levels of PINK1 in the brains of mice and they observed PARIS-dependent cell loss – that is to say, in the absence of PINK1, cells died only when PARIS was present.

These findings suggest that therapies targeting PARIS could be useful in people with Parkinson’s who are carrying either a PARKIN or a PINK1 mutation (both very common in early onset Parkinson’s).

Source: Biolegend

So what does it all mean?

PARKIN is recognised by many researchers as a protein that plays a role in Parkinson’s, and we have previously discussed efforts to replace this protein in the cells of people with PARKIN-associated Parkinson’s (Click here to read a previous SoPD post on this topic). But new research suggests that simply replacing PARKIN might not be enough. It would appear that the build up of a protein called PARIS (in the absence of PARKIN) is also playing a role in some of the issues observed in PARKIN-associated Parkinson’s.

Perhaps treatments elevating levels of PARKIN will be enough to slow the progression of Parkinson’s. But one could envisage a future dual therapy approach which not only raises PARKIN activity, but also inhibits PARIS – thus allowing for a healthier situation with regards to mitochondria biogenesis and mitophagy. The assumption now is that the researchers behind the studies discussed in today’s post will be trying to identify molecules that can inhibit or reduce PARIS. And hopefully some of those agents could be clinically tested – not only on individuals with PARKIN-associated Parkinson’s, but also perhaps idiopathic PD.

Here at the SoPD, we will be keeping an eye out for that kind of follow-up research.

 

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The banner for today’s post was sourced from ParisJourney.

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